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License: BSD 3-Clause "New" or "Revised" License
A conda-smithy repository for ctng-compilers.
License: BSD 3-Clause "New" or "Revised" License
I'm trying to include CXX compilers and NVCC compilers in my environment file to build C extensions for Python.
Steps to reproduce the issue:
nvcc
with g++
11.2.0 (ref https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html#system-requirements):CMakeLists.txt
:
cmake_minimum_required(VERSION 3.4)
project(nvcc-gxx-test LANGUAGES CXX CUDA)
find_package(CUDA REQUIRED)
environment.yaml
:
name: nvcc-gxx11-test
channels:
- defaults
- nvidia/label/cuda-11.5.0
- nvidia
- conda-forge
dependencies:
- cmake >= 3.4
- make
- cxx-compiler
- gxx = 11
- nvidia/label/cuda-11.5.0::cuda-nvcc
- nvidia/label/cuda-11.5.0::cuda-cudart-dev
Result:
$ mamba env create --file environment.yaml --no-default-packages
anaconda/pkgs/r/linux-64 No change
anaconda/pkgs/r/noarch No change
anaconda/pkgs/msys2/linux-64 No change
conda-forge/noarch No change
anaconda/pkgs/main/linux-64 No change
anaconda/pkgs/main/noarch No change
anaconda/pkgs/msys2/noarch No change
conda-forge/linux-64 No change
pytorch/linux-64 No change
pytorch/noarch No change
nvidia/label/cuda-11.5.0/linux-64 No change
nvidia/linux-64 No change
nvidia/label/cuda-11.5.0/noarch No change
nvidia/noarch No change
Looking for: ["cmake[version='>=3.4']", 'make', 'cxx-compiler', 'gxx=11', 'nvidia/label/cuda-11.5.0::cuda-nvcc', 'nvidia/label/cuda-11.5.0::cuda-cudart-dev']
Transaction
Prefix: /home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test
Updating specs:
- cmake[version='>=3.4']
- make
- cxx-compiler
- gxx=11
- nvidia/label/cuda-11.5.0::cuda-nvcc
- nvidia/label/cuda-11.5.0::cuda-cudart-dev
Package Version Build Channel Size
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+ _libgcc_mutex 0.1 main mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ _openmp_mutex 5.1 1_gnu mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ _sysroot_linux-64_curr_repodata_hack 3 haa98f57_10 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/noarch Cached
+ binutils_impl_linux-64 2.38 h2a08ee3_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ binutils_linux-64 2.38.0 hc2dff05_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ bzip2 1.0.8 h7b6447c_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ c-ares 1.18.1 h7f8727e_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ ca-certificates 2022.4.26 h06a4308_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ cmake 3.22.1 h1fce559_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ cuda-cccl 11.7.58 hc415cf5_0 nvidia/linux-64 Cached
+ cuda-cudart 11.5.50 h79feb7f_0 nvidia/label/cuda-11.5.0/linux-64 Cached
+ cuda-cudart-dev 11.5.50 h2215e51_0 nvidia/label/cuda-11.5.0/linux-64 Cached
+ cuda-nvcc 11.5.50 h8f81028_0 nvidia/label/cuda-11.5.0/linux-64 Cached
+ cxx-compiler 1.0.0 hf484d3e_0 mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64 Cached
+ expat 2.4.4 h295c915_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ gcc 11.2.0 h702ea55_10 mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64 Cached
+ gcc_impl_linux-64 11.2.0 h1234567_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ gcc_linux-64 11.2.0 h5c386dc_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ gxx 11.2.0 h702ea55_10 mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64 Cached
+ gxx_impl_linux-64 11.2.0 h1234567_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ gxx_linux-64 11.2.0 hc2dff05_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ kernel-headers_linux-64 3.10.0 h57e8cba_10 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/noarch Cached
+ krb5 1.19.2 hac12032_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ ld_impl_linux-64 2.38 h1181459_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ libcurl 7.82.0 h0b77cf5_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ libedit 3.1.20210910 h7f8727e_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ libev 4.33 h7f8727e_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ libgcc-devel_linux-64 11.2.0 h1234567_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ libgcc-ng 11.2.0 h1234567_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ libgomp 11.2.0 h1234567_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ libnghttp2 1.46.0 hce63b2e_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ libssh2 1.10.0 h8f2d780_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ libstdcxx-devel_linux-64 11.2.0 h1234567_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ libstdcxx-ng 11.2.0 h1234567_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ libuv 1.40.0 h7b6447c_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ lz4-c 1.9.3 h295c915_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ make 4.2.1 h1bed415_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ ncurses 6.3 h5eee18b_3 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ openssl 1.1.1p h5eee18b_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ rhash 1.4.1 h3c74f83_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ sysroot_linux-64 2.17 h57e8cba_10 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/noarch Cached
+ xz 5.2.5 h7f8727e_1 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ zlib 1.2.12 h7f8727e_2 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
+ zstd 1.5.2 ha4553b6_0 mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64 Cached
Summary:
Install: 44 packages
Total download: 0 B
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Downloading and Extracting Packages
cxx-compiler-1.0.0 | 4 KB | #################################################################################################################################################### | 100%
gcc-11.2.0 | 24 KB | #################################################################################################################################################### | 100%
gxx-11.2.0 | 24 KB | #################################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate nvcc-gxx11-test
#
# To deactivate an active environment, use
#
# $ conda deactivate
$ mkdir build
$ cd build
$ conda activate nvcc-gxx11-test
$ cmake ..
-- The CXX compiler identification is GNU 11.2.0
-- The CUDA compiler identification is unknown
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/bin/x86_64-conda-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting CUDA compiler ABI info
-- Detecting CUDA compiler ABI info - failed
-- Check for working CUDA compiler: /home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/bin/nvcc
-- Check for working CUDA compiler: /home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/bin/nvcc - broken
CMake Error at /home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/share/cmake-3.22/Modules/CMakeTestCUDACompiler.cmake:56 (message):
The CUDA compiler
"/home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/bin/nvcc"
is not able to compile a simple test program.
It fails with the following output:
Change Dir: /home/PanXuehai/test/build-gxx11/CMakeFiles/CMakeTmp
Run Build Command(s):/home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/bin/make -f Makefile cmTC_45341/fast && /home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/bin/make -f CMakeFiles/cmTC_45341.dir/build.make CMakeFiles/cmTC_45341.dir/build
make[1]: Entering directory '/home/PanXuehai/test/build-gxx11/CMakeFiles/CMakeTmp'
Building CUDA object CMakeFiles/cmTC_45341.dir/main.cu.o
/home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/bin/nvcc -c /home/PanXuehai/test/build-gxx11/CMakeFiles/CMakeTmp/main.cu -o CMakeFiles/cmTC_45341.dir/main.cu.o
Linking CUDA executable cmTC_45341
/home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/bin/cmake -E cmake_link_script CMakeFiles/cmTC_45341.dir/link.txt --verbose=1
"" -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/lib -Wl,-rpath-link,/home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/lib -L/home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test/lib CMakeFiles/cmTC_45341.dir/main.cu.o -o cmTC_45341
Error running link command: No such file or directory
make[1]: *** [CMakeFiles/cmTC_45341.dir/build.make:99: cmTC_45341] Error 2
make[1]: Leaving directory '/home/PanXuehai/test/build-gxx11/CMakeFiles/CMakeTmp'
make: *** [Makefile:127: cmTC_45341/fast] Error 2
CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:2 (project)
-- Configuring incomplete, errors occurred!
See also "/home/PanXuehai/test/build-gxx11/CMakeFiles/CMakeOutput.log".
See also "/home/PanXuehai/test/build-gxx11/CMakeFiles/CMakeError.log".
Everything works fine if I change spec gxx = 11
to gxx = 10
.
# packages in environment at /home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
_sysroot_linux-64_curr_repodata_hack 3 haa98f57_10
binutils_impl_linux-64 2.38 h2a08ee3_1
binutils_linux-64 2.38.0 hc2dff05_0
bzip2 1.0.8 h7b6447c_0
c-ares 1.18.1 h7f8727e_0
ca-certificates 2022.4.26 h06a4308_0
cmake 3.22.1 h1fce559_0
cuda-cccl 11.7.58 hc415cf5_0
cuda-cudart 11.5.50 h79feb7f_0
cuda-cudart-dev 11.5.50 h2215e51_0
cuda-nvcc 11.5.50 h8f81028_0
cxx-compiler 1.0.0 hf484d3e_0
expat 2.4.4 h295c915_0
gcc 11.2.0 h702ea55_10
gcc_impl_linux-64 11.2.0 h1234567_1
gcc_linux-64 11.2.0 h5c386dc_0
gxx 11.2.0 h702ea55_10
gxx_impl_linux-64 11.2.0 h1234567_1
gxx_linux-64 11.2.0 hc2dff05_0
kernel-headers_linux-64 3.10.0 h57e8cba_10
krb5 1.19.2 hac12032_0
ld_impl_linux-64 2.38 h1181459_1
libcurl 7.82.0 h0b77cf5_0
libedit 3.1.20210910 h7f8727e_0
libev 4.33 h7f8727e_1
libgcc-devel_linux-64 11.2.0 h1234567_1
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libnghttp2 1.46.0 hce63b2e_0
libssh2 1.10.0 h8f2d780_0
libstdcxx-devel_linux-64 11.2.0 h1234567_1
libstdcxx-ng 11.2.0 h1234567_1
libuv 1.40.0 h7b6447c_0
lz4-c 1.9.3 h295c915_1
make 4.2.1 h1bed415_1
ncurses 6.3 h5eee18b_3
openssl 1.1.1p h5eee18b_0
rhash 1.4.1 h3c74f83_1
sysroot_linux-64 2.17 h57e8cba_10
xz 5.2.5 h7f8727e_1
zlib 1.2.12 h7f8727e_2
zstd 1.5.2 ha4553b6_0
active environment : nvcc-gxx11-test
active env location : /home/PanXuehai/Miniconda3/envs/nvcc-gxx11-test
shell level : 1
user config file : /home/PanXuehai/.condarc
populated config files : /home/PanXuehai/.condarc
conda version : 4.13.0
conda-build version : not installed
python version : 3.9.12.final.0
virtual packages : __linux=5.10.102.1=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/PanXuehai/Miniconda3 (writable)
conda av data dir : /home/PanXuehai/Miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/linux-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/noarch
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/noarch
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r/linux-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r/noarch
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2/linux-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2/noarch
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
package cache : /home/PanXuehai/Miniconda3/pkgs
/home/PanXuehai/.conda/pkgs
envs directories : /home/PanXuehai/Miniconda3/envs
/home/PanXuehai/.conda/envs
platform : linux-64
user-agent : conda/4.13.0 requests/2.28.0 CPython/3.9.12 Linux/5.10.102.1-microsoft-standard-WSL2 ubuntu/20.04.3 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False
Issue:
g++ fails with internal compiler error.
Consider a C++ program:
/* File test.cpp */
int rand();
template<typename T>
struct s
{
int count() { return rand(); }
};
template<typename v>
int f(s<v> a)
{
int const x = a.count();
int r = 0;
auto l = [&](int& r)
{
for(int y = 0, yend = (x); y < yend; ++y)
{
r += y;
}
};
l(r);
}
template int f(s<float>);
int main()
{
}
Which triggers the gcc bug:
$ g++ -c test.cpp
test.cpp: In instantiation of 'f(s<v>)::<lambda(int&)> [with v = float]':
test.cpp:14:16: required from 'struct f(s<v>) [with v = float]::<lambda(int&)>'
test.cpp:14:10: required from 'int f(s<v>) [with v = float]'
test.cpp:24:24: required from here
test.cpp:16:24: internal compiler error: in maybe_undo_parenthesized_ref, at cp/semantics.c:1705
for(int y = 0, yend = (x); y < yend; ++y)
^~~~
Please submit a full bug report,
with preprocessed source if appropriate.
See <https://gcc.gnu.org/bugs/> for instructions.
Notice that the same compilation error happens with the following commands
g++ -c -std=c++14 test.cpp
g++ -c -std=c++17 test.cpp
but not with
g++ -c -std=c++11 test.cpp
Also note that g++ from Debian has a fix to the above bug, see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=882855 .
conda list
):
$ conda list
# packages in environment at /home/pearu/miniconda3/envs/test-gcc-bug:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main conda-forge
binutils-meta 1.0.4 0 conda-forge
binutils_impl_linux-64 2.33.1 he1b5a44_7 conda-forge
binutils_linux-64 2.33.1 h9595d00_15 conda-forge
c-compiler 1.0.4 h516909a_0 conda-forge
compilers 1.0.4 0 conda-forge
cxx-compiler 1.0.4 hc9558a2_0 conda-forge
fortran-compiler 1.0.4 he991be0_0 conda-forge
gcc_impl_linux-64 7.3.0 habb00fd_2 conda-forge
gcc_linux-64 7.3.0 h553295d_15 conda-forge
gfortran_impl_linux-64 7.3.0 hdf63c60_2 conda-forge
gfortran_linux-64 7.3.0 h553295d_15 conda-forge
gxx_impl_linux-64 7.3.0 hdf63c60_2 conda-forge
gxx_linux-64 7.3.0 h553295d_15 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_7 conda-forge
libgcc-ng 9.2.0 hdf63c60_0 conda-forge
libgfortran-ng 7.3.0 hdf63c60_2 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_0 conda-forge
conda
and system ( conda info
):
$ conda info
active environment : test-gcc-bug
active env location : /home/pearu/miniconda3/envs/test-gcc-bug
shell level : 2
user config file : /home/pearu/.condarc
populated config files : /home/pearu/.condarc
conda version : 4.7.12
conda-build version : 3.18.11
python version : 3.7.3.final.0
virtual packages : __cuda=10.1
base environment : /home/pearu/miniconda3 (writable)
channel URLs : file:///home/pearu/miniconda3/conda-bld/linux-64
file:///home/pearu/miniconda3/conda-bld/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/pearu/miniconda3/pkgs
/home/pearu/.conda/pkgs
envs directories : /home/pearu/miniconda3/envs
/home/pearu/.conda/envs
platform : linux-64
user-agent : conda/4.7.12 requests/2.22.0 CPython/3.7.3 Linux/4.15.0-70-generic ubuntu/18.04.3 glibc/2.27
UID:GID : 1000:1000
netrc file : None
offline mode : False
As I mentioned in #18 , we're running into a bug in gcc 7.3
Would a PR that bumped 7.3 to 7.5 be able to be accepted?
https://anaconda.org/conda-forge/libstdcxx-ng needs to be updated to v6.0.29
The problem is that the current version 6.0.28 is breaking all AppImages we are building for FreeCAD.
FreeCAD/FreeCAD-Bundle#73 (comment)
First off, congratulations for getting the mingw compilers off the ground, @isuruf!
In the notes for today's core call, you note:
MinGW UCRT compilers are ready to test
- gcc and VC are compatible (C only), but gxx is not (different C++ libraries)
- R and Python use different C++ libraries, so we need to be careful about directly linking across this ecosystem boundary.
I was wondering if there's a fundamental blocker for aligning this with our platform defaults, and thus avoid this boundary in the first place? After all, for clangxx_win-64
, we manage to use the windows C++ libraries as well.
We might even be able to reuse msvc-headers-libs
/ winsdk
directly? I'm assuming that R doesn't actually depend on a specific flavour of C++ stdlib (I'd be surprised if it did...).
On most system package managers, libstdc++ provides an automatic integration into gdb
by placing a file into share/gdb/auto-load
that loads the pretty-printers that are present in share/gcc-x.x.x/python/libstdcxx
. This integration seems to be missing from conda, which makes debugging binaries that were compiled with conda's C++ compiler unnecessarily tedious.
Two possible solutions to this would be 1. creating a custom gdbinit
file that sets the auto-load safe-path and loads the file or 2. creating the file in the expected location for libstdc++.so
in the first place, which can be seen by running gdb on a simple C++ test program:
> gdb ./test
> set debug auto-load on
> run
...
auto-load: Attempted file "/usr/share/gdb/auto-load/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28-gdb.py" exists.
auto-load: Loading python script "/usr/share/gdb/auto-load/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28-gdb.py" by extension for objfile "/lib/x86_64-linux-gnu/libstdc++.so.6".
auto-load: Matching file "/usr/share/gdb/auto-load/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28-gdb.py" to pattern "/usr/lib/debug"
auto-load: Not matched - pattern "/usr/lib/debug".
auto-load: Matching file "/usr/share/gdb/auto-load/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28-gdb.py" to pattern "/usr/share/gdb/auto-load"
auto-load: Matched - file "/usr/share/gdb/auto-load" to pattern "/usr/share/gdb/auto-load"
...
# packages in environment at /root/miniconda3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 4.5 1_gnu
binutils 2.35.1 hdd6e379_2 conda-forge
binutils_impl_linux-64 2.35.1 h27ae35d_9
binutils_linux-64 2.35 h67ddf6f_30 conda-forge
brotlipy 0.7.0 py39h27cfd23_1003
c-compiler 1.2.0 h7f98852_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
certifi 2022.6.15 py39hf3d152e_0 conda-forge
cffi 1.15.0 py39hd667e15_1
charset-normalizer 2.0.4 pyhd3eb1b0_0
colorama 0.4.4 pyhd3eb1b0_0
conda 4.13.0 py39hf3d152e_1 conda-forge
conda-content-trust 0.1.1 pyhd3eb1b0_0
conda-package-handling 1.8.1 py39h7f8727e_0
cryptography 36.0.0 py39h9ce1e76_0
cxx-compiler 1.2.0 h4bd325d_0 conda-forge
gcc_impl_linux-64 9.3.0 h70c0ae5_19 conda-forge
gcc_linux-64 9.3.0 hf25ea35_30 conda-forge
gdb 11.2 py39he3c4487_2
gxx_impl_linux-64 9.3.0 hd87eabc_19 conda-forge
gxx_linux-64 9.3.0 h3fbe746_30 conda-forge
idna 3.3 pyhd3eb1b0_0
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
ld_impl_linux-64 2.35.1 h7274673_9
libffi 3.3 he6710b0_2
libgcc-devel_linux-64 9.3.0 h7864c58_19 conda-forge
libgcc-ng 9.3.0 h5101ec6_17
libgomp 9.3.0 h5101ec6_17
libstdcxx-devel_linux-64 9.3.0 hb016644_19 conda-forge
libstdcxx-ng 11.2.0 h1234567_1
ncurses 6.3 h7f8727e_2
openssl 1.1.1q h7f8727e_0
pip 21.2.4 py39h06a4308_0
pycosat 0.6.3 py39h27cfd23_0
pycparser 2.21 pyhd3eb1b0_0
pygments 2.11.2 pyhd3eb1b0_0
pyopenssl 22.0.0 pyhd3eb1b0_0
pysocks 1.7.1 py39h06a4308_0
python 3.9.12 h12debd9_0
python_abi 3.9 2_cp39 conda-forge
readline 8.1.2 h7f8727e_1
requests 2.27.1 pyhd3eb1b0_0
ruamel_yaml 0.15.100 py39h27cfd23_0
setuptools 61.2.0 py39h06a4308_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.38.2 hc218d9a_0
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tk 8.6.11 h1ccaba5_0
tqdm 4.63.0 pyhd3eb1b0_0
tzdata 2022a hda174b7_0
urllib3 1.26.8 pyhd3eb1b0_0
wheel 0.37.1 pyhd3eb1b0_0
xz 5.2.5 h7b6447c_0
yaml 0.2.5 h7b6447c_0
zlib 1.2.12 h7f8727e_1
active environment : base
active env location : /root/miniconda3
shell level : 1
user config file : /root/.condarc
populated config files :
conda version : 4.13.0
conda-build version : not installed
python version : 3.9.12.final.0
virtual packages : __linux=5.4.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /root/miniconda3 (writable)
conda av data dir : /root/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /root/miniconda3/pkgs
/root/.conda/pkgs
envs directories : /root/miniconda3/envs
/root/.conda/envs
platform : linux-64
user-agent : conda/4.13.0 requests/2.27.1 CPython/3.9.12 Linux/5.4.0-110-generic ubuntu/20.04.4 glibc/2.31
UID:GID : 0:0
netrc file : None
offline mode : False
Would it be appropriate to provide our own custom commands for ldd?
When cross compiling, had trouble getting the ldd command to work.
conda-forge/libvips-feedstock#72
My solution was to copy it from CONDA_BUILD_SYSROOT
and update the location the shared libraries defined in RTLDLIST
within the ldd
bash script.
Issue:
conda list
):
$ conda list
conda
and system ( conda info
):
$ conda info
ctng-compilers-feedstock/recipe/build.sh
Line 122 in 1e2c3c8
I see where it was defined higher in build.sh when originally added in #56. Any objections to taking it back out @isuruf ? I was getting confused trying to figure out where it was coming from.
Hi,
I'm using clang as a compiler (from the clangxx
conda package) and also include gxx_impl_linux-64
in my environment to link against libstdc++. Unfortunately, I cannot see proper pretty printers for stdlib types when debugging the binary with gdb.
Usually distros will provide a *-dbgsym
package for these, but I'm not sure how to get them from conda-forge.
Note that there's also #105 so I'm not sure if my issue is the same, or only related (since clang and gcc may have different behavior here).
Appreciate all the help!
Are there any plans to bump the glibc version this package compiles against to 2.17? Or possibly adding the compile flag: --enable-libstdcxx-time
When libstdc++ is compiled against a glibc older than 2.17 there is a compatibility defines set (_GLIBCXX_USE_CLOCK_GETTIME_SYSCALL
) in the header so that the built libstdc++ library forces std::chrono::system_clock::now()
to use the syscall version of clock_gettime instead of one that can be accelerated by vdso. (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=59177)
The effect of this any code built in an environment using this package has a fairly large performance penalty when running querying the system clock this way.
From https://gcc.gnu.org/onlinedocs/libstdc++/manual/configure.html
For Linux targets, if clock_gettime is not used then the [time.clock] implementation
will use a system call to access the realtime and monotonic clocks, which is
significantly slower than the C library's clock_gettime function.
To see if it is set:
$ grep _GLIBCXX_USE_CLOCK_GETTIME_SYSCALL pkgs/libstdcxx-devel_linux-64-12.2.0-h3b97bd3_19/x86_64-conda-linux-gnu/include/c++/12.2.0/x86_64-conda-linux-gnu/bits/c++config.h
#define _GLIBCXX_USE_CLOCK_GETTIME_SYSCALL 1
Thank you
gcc -o t t.c -mcpu=native
cc1: error: unrecognized argument in option '-mcpu=native'
cc1: note: valid arguments to '-mcpu=' are: 401 403 405 405fp 440 440fp 464 464fp 476 476fp 505 601 602 603 603e 604 604e 620 630 740 7400 7450 750 801 821 823 8540 8548 860 970 G3 G4 G5 a2 cell e300c2 e300c3 e500mc e500mc64 e5500 e6500 ec603e power10 power3 power4 power5 power5+ power6 power6x power7 power8 power9 powerpc powerpc64 powerpc64le rs64 titan
# packages in environment at /home/raji/anaconda3/envs/gccissue1:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_sysroot_linux-ppc64le_curr_repodata_hack 4 h43410cf_14 conda-forge
binutils_impl_linux-ppc64le 2.40 hba8546e_0 conda-forge
bzip2 1.0.8 ha17a0cc_5 conda-forge
ca-certificates 2024.2.2 h0f6029e_0 conda-forge
gcc 13.2.0 hb8c6617_3 conda-forge
gcc_impl_linux-ppc64le 13.2.0 h7908001_5 conda-forge
kernel-headers_linux-ppc64le 3.10.0 h23d7e6c_14 conda-forge
ld_impl_linux-ppc64le 2.40 hfa29eb9_0 conda-forge
libffi 3.4.2 h4e0d66e_5 conda-forge
libgcc-devel_linux-ppc64le 13.2.0 hf1adbf4_105 conda-forge
libgcc-ng 13.2.0 h31ea8bd_5 conda-forge
libgomp 13.2.0 h31ea8bd_5 conda-forge
libnsl 2.0.1 ha17a0cc_0 conda-forge
libsanitizer 13.2.0 h0849fd4_5 conda-forge
libsqlite 3.45.3 hd4bbf49_0 conda-forge
libstdcxx-ng 13.2.0 h0849fd4_5 conda-forge
libuuid 2.38.1 h4194056_0 conda-forge
libxcrypt 4.4.36 ha17a0cc_1 conda-forge
libzlib 1.2.13 ha17a0cc_5 conda-forge
ncurses 6.4.20240210 h8800142_0 conda-forge
openssl 3.2.1 ha17a0cc_1 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
python 3.10.14 h4005451_0_cpython conda-forge
readline 8.2 h0b9b154_1 conda-forge
setuptools 69.5.1 pyhd8ed1ab_0 conda-forge
sqlite 3.45.3 h63c7444_0 conda-forge
sysroot_linux-ppc64le 2.17 h23d7e6c_14 conda-forge
tk 8.6.13 hd4bbf49_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
xz 5.2.6 hb283c62_0 conda-forge
zlib 1.2.13 ha17a0cc_5 conda-forge
active environment : gccissue1
active env location : /home/raji/anaconda3/envs/gccissue1
shell level : 2
user config file : /home/raji/.condarc
populated config files : /home/raji/.condarc
conda version : 22.9.0
conda-build version : 3.22.0
python version : 3.9.13.final.0
virtual packages : __linux=4.18.0=0
__glibc=2.28=0
__unix=0=0
__archspec=1=ppc64le
base environment : /home/raji/anaconda3 (writable)
conda av data dir : /home/raji/anaconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-ppc64le
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-ppc64le
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-ppc64le
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/raji/anaconda3/pkgs
/home/raji/.conda/pkgs
envs directories : /home/raji/anaconda3/envs
/home/raji/.conda/envs
platform : linux-ppc64le
user-agent : conda/22.9.0 requests/2.28.1 CPython/3.9.13 Linux/4.18.0-513.24.1.el8_9.ppc64le rhel/8.9 glibc/2.28
UID:GID : 1011:1011
netrc file : None
offline mode : False
How hard would it be to add the libgccjit library to this package? It is needed for emacs native compilation. conda-forge/emacs-feedstock#83
On the conda-forge site https://anaconda.org/conda-forge/_openmp_mutex/files
The latest version is 4.5.1, but it's suffixed with llvm. There's an older version 4.5.0 but only for gnu. I have been installing the latest one with llvm, but wondering if I should be using the older one.
I am compiling a C++ program with gcc and openmp (libgomp) which makes me feel like I should be using 4.5.0_gnu. Is there a reason why gnu does not have a 4.5.1 like llvm? Are you required to compile with clang to use 4.5.1_llvm?
/t/nwani_1597448808 ❯❯❯ ldd $CONDA_PREFIX/lib/libstdc++.so
linux-vdso.so.1 (0x00007ffe5b797000)
libm.so.6 => /lib64/libm.so.6 (0x00007f0881491000)
libc.so.6 => /lib64/libc.so.6 (0x00007f08812c7000)
/lib64/ld-linux-x86-64.so.2 (0x00007f0881791000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f08812ac000) <-----------This should have been from $CONDA_PREFIX
/t/nwani_1597448808 ❯❯❯ readelf -a $CONDA_PREFIX/lib/libstdc++.so | grep RPATH
0x000000000000000f (RPATH) Library rpath: [/home/conda/feedstock_root/build_artifacts/ctng-compilers_1596393189889/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib]
No response
Issue: all the lib*.so files installed by libgcc-ng, and libgomp, have an unpatched RPATH
which means (for example), linking against libasan.so
can yield linker errors (e.g. unable to find the libstdc++.so.6
that libasan
requires, as it doesn't look in $ORIGIN
etc).
$ for f in *.so; echo $f; readelf -d $f | grep 'rpath'; end
libasan.so
0x000000000000000f (RPATH) Library rpath: [/home/conda/feedstock_root/build_artifacts/gcc_compilers_1632803321475/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/../lib]
libatomic.so
0x000000000000000f (RPATH) Library rpath: [/home/conda/feedstock_root/build_artifacts/gcc_compilers_1632803324264/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib]
libcc1.so
0x000000000000000f (RPATH) Library rpath: [$ORIGIN/.]
libgcc_s.so
readelf: Error: Not an ELF file - it has the wrong magic bytes at the start
libgomp.so
0x000000000000000f (RPATH) Library rpath: [/home/conda/feedstock_root/build_artifacts/gcc_compilers_1632803324264/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib]
libitm.so
0x000000000000000f (RPATH) Library rpath: [/home/conda/feedstock_root/build_artifacts/gcc_compilers_1632803324264/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib]
liblsan.so
0x000000000000000f (RPATH) Library rpath: [/home/conda/feedstock_root/build_artifacts/gcc_compilers_1632803321475/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/../lib]
libquadmath.so
0x000000000000000f (RPATH) Library rpath: [/home/conda/feedstock_root/build_artifacts/gcc_compilers_1632803324264/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib]
libstdc++.so
libtsan.so
0x000000000000000f (RPATH) Library rpath: [/home/conda/feedstock_root/build_artifacts/gcc_compilers_1632803321475/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/../lib]
libubsan.so
0x000000000000000f (RPATH) Library rpath: [/home/conda/feedstock_root/build_artifacts/gcc_compilers_1632803321475/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/../lib]
conda list
):
$ conda list
# packages in environment at /tmp/moo:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_1 conda-forge
gcc_impl_linux-64 9.4.0 h03d3576_9 conda-forge
gcc_linux-64 9.4.0 h391b98a_1 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_14 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libgcc-devel_linux-64 9.4.0 hd854feb_9 conda-forge
libgcc-ng 11.2.0 h1d223b6_9 conda-forge
libgomp 11.2.0 h1d223b6_9 conda-forge
libsanitizer 9.4.0 h79bfe98_9 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_9 conda-forge
sysroot_linux-64 2.12 he073ed8_14 conda-forge
conda
and system ( conda info
):
$ conda info
active environment : None
user config file : /home/mgodbolt/.condarc
populated config files :
conda version : 4.10.3
conda-build version : 3.21.4
python version : 3.7.7.final.0
virtual packages : __linux=4.15.0=0
__glibc=2.27=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/mgodbolt/.cache/ozy/conda/4.8.3 (writable)
conda av data dir : /home/mgodbolt/.cache/ozy/conda/4.8.3/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/mgodbolt/.cache/ozy/conda/4.8.3/pkgs
/home/mgodbolt/.conda/pkgs
envs directories : /home/mgodbolt/.cache/ozy/conda/4.8.3/envs
/home/mgodbolt/.conda/envs
platform : linux-64
user-agent : conda/4.10.3 requests/2.23.0 CPython/3.7.7 Linux/4.15.0-159-generic ubuntu/18.04.6 glibc/2.27
UID:GID : 5011:5011
netrc file : None
offline mode : False
@conda-forge-admin, please add user @xhochy
Issue:
When using the compilers
package to compile code, I get linking errors against libquadmath.so.0 on linux seemingly with 9.3.0 build 11 which I did not get a week ago with a slightly different environment.
Below is a snippet from our logs:
[2020-07-31T08:01:07.989183Z] /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/bin/x86_64-conda_cos6-linux-gnu-c++ -o tests/decoratedImage -Wl,-rpath-link -Wl,/j/ws/stack-os-matrix/d318ecacbb/lsstsw/build/afw/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/astshim/20.0.0+1/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/geom/20.0.0-2-gec03fae+6/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/sphgeom/20.0.0-3-gd2e950e/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/pex_config/20.0.0+4/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/daf_persistence/20.0.0+5/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/pex_policy/20.0.0+4/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/log/20.0.0-1-gd1c87d7+2/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/daf_base/20.0.0-1-g8a53f90+2/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/utils/20.0.0+3/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/pex_exceptions/20.0.0+3/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/base/20.0.0-4-g4a2362f/lib -fno-lto -Wl,-rpath=/j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib tests/decoratedImage.o -Llib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/astshim/20.0.0+1/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/geom/20.0.0-2-gec03fae+6/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/sphgeom/20.0.0-3-gd2e950e/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/daf_persistence/20.0.0+5/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/pex_policy/20.0.0+4/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/log/20.0.0-1-gd1c87d7+2/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/daf_base/20.0.0-1-g8a53f90+2/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/utils/20.0.0+3/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/pex_exceptions/20.0.0+3/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/base/20.0.0-4-g4a2362f/lib -L/j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib -L/j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib/python3.7/config-3.7m-x86_64-linux-gnu -lafw -lastshim -last -last_pal -last_grf_2.0 -last_grf_3.2 -last_grf_5.6 -last_grf3d -last_pass2 -last_err -lm -lboost_serialization -lcfitsio -lgsl -lgslcblas -lMinuit2 -lgeom -lsphgeom -lfftw3f -lfftw3 -lboost_math_c99 -ldaf_persistence -lpex_policy -lboost_filesystem -lboost_system -llog -llog4cxx -ldaf_base -lboost_regex -lutils -lpex_exceptions -lbase -lpthread -lboost_unit_test_framework
[2020-07-31T08:01:08.613851Z] /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libquadmath.so.0, needed by /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib/./libgfortran.so.4, not found (try using -rpath or -rpath-link)
[2020-07-31T08:01:08.614308Z] /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib/./libgfortran.so.4: undefined reference to `fmodq@QUADMATH_1.0'
[2020-07-31T08:01:08.614804Z] /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib/./libgfortran.so.4: undefined reference to `quadmath_snprintf@QUADMATH_1.0'
[additional symbol errors here]
Here is a diff of my environment export between versions which work and don't work:
diff --git a/etc/conda3_packages-linux-64.yml b/etc/conda3_packages-linux-64.yml
index 06870cb..35c8ab5 100644
--- a/etc/conda3_packages-linux-64.yml
+++ b/etc/conda3_packages-linux-64.yml
@@ -38,7 +38,7 @@ dependencies:
- bzip2=1.0.8=h516909a_2
- c-ares=1.16.1=h516909a_0
- c-compiler=1.1.1=h516909a_0
- - ca-certificates=2020.6.20=hecda079_0
+ - ca-certificates=2020.6.24=0
- certifi=2020.6.20=py37hc8dfbb8_0
- cffi=1.14.1=py37h2b28604_0
- cfitsio=3.470=hce51eda_6
@@ -137,10 +137,10 @@ dependencies:
- libev=4.33=h516909a_0
- libevent=2.1.10=hcdb4288_1
- libffi=3.2.1=he1b5a44_1007
- - libgcc-ng=9.3.0=h24d8f2e_11
+ - libgcc-ng=9.2.0=h24d8f2e_2
- libgfortran=3.0.0=1
- - libgfortran-ng=7.5.0=hdf63c60_11
- - libgomp=9.3.0=h24d8f2e_11
+ - libgfortran-ng=7.5.0=hdf63c60_6
+ - libgomp=9.2.0=h24d8f2e_2
- libiconv=1.15=h516909a_1006
- liblapack=3.8.0=17_openblas
- libnghttp2=1.41.0=hab1572f_1
@@ -149,7 +149,7 @@ dependencies:
- libpq=12.3=h5513abc_0
- libprotobuf=3.11.0=h8b12597_0
- libssh2=1.9.0=hab1572f_5
- - libstdcxx-ng=9.3.0=hdf63c60_11
+ - libstdcxx-ng=9.2.0=hdf63c60_2
- libtiff=4.1.0=hc7e4089_6
- libuuid=2.32.1=h14c3975_1000
- libuv=1.38.0=h516909a_0
conda list
):
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/git-lfs-2.11.0-0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2020.6.20-hecda079_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.34-h53a641e_7.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-7.5.0-hdf63c60_11.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-9.3.0-hdf63c60_11.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/mpi-1.0-mpich.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.34-h53a641e_7.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgomp-9.3.0-h24d8f2e_11.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-0_gnu.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/binutils-2.34-h2122c62_9.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.34-hc952b39_20.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-9.3.0-h24d8f2e_11.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/blosc-1.20.0-he1b5a44_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/brotli-1.0.7-he1b5a44_1004.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h516909a_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.16.1-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/eigen-3.3.7-hc9558a2_1001.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/expat-2.2.9-he1b5a44_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.8-nompi_h7f3a6c3_1111.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-7.5.0-hd420e75_6.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gflags-2.2.2-he1b5a44_1004.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/icu-58.2-hf484d3e_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/jpeg-9d-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lapack-3.6.1-ha44fe06_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libapr-1.6.5-h516909a_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libapriconv-1.2.2-h516909a_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libffi-3.2.1-he1b5a44_1007.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.15-h516909a_1006.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.10-pthreads_hb3c22a3_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h14c3975_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libuv-1.38.0-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.1.0-h516909a_3.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.8.3-he1b5a44_1001.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lzo-2.10-h14c3975_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/make-4.3-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/minuit2_standalone-6.18.00-he1b5a44_101.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/mpich-3.2.1-hc99cbb1_1014.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.2-he1b5a44_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1g-h516909a_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pcre-8.44-he1b5a44_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/perl-5.26.2-h516909a_1006.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h14c3975_1001.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/re2-2020.04.01-he1b5a44_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/rhash-1.3.6-h14c3975_1001.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/snappy-1.1.8-he1b5a44_3.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/starlink-ast-9.1.0-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h14c3975_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.9-h14c3975_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h14c3975_1007.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xpa-2.1.20-he1b5a44_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.5-h516909a_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.11-h516909a_1006.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/boost-cpp-1.70.0-ha2d47e9_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/doxygen-1.8.18-hd1b7508_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gcc_linux-64-7.5.0-h09487f9_20.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gettext-0.19.8.1-hc5be6a0_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-7.5.0-hdf63c60_6.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/glog-0.4.0-h49b9bf7_3.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-7.5.0-hdf63c60_6.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.10.6-nompi_h3c11f04_100.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libaprutil-1.6.1-ha1d75be_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libblas-3.8.0-17_openblas.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-h46ee950_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.10-hcdb4288_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.41.0-hab1572f_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.37-hed695b0_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libprotobuf-3.11.0-h8b12597_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.9.0-hab1572f_5.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.13-h14c3975_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.9.9-h13577e0_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/minuit2-6.18.00-minuit2_standalone.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ndarray-1.5.3-h75f6862_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/readline-8.0-he28a2e2_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.10-hed695b0_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/zstd-1.4.4-h3b9ef0a_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/apr-1.6.5-h516909a_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/c-compiler-1.1.1-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/freetype-2.10.2-he06d7ca_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gfortran_linux-64-7.5.0-h09487f9_20.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/grpc-cpp-1.25.0-h213be95_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gxx_linux-64-7.5.0-h09487f9_20.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.17.1-hfafb76e_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.8.0-17_openblas.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.8.0-17_openblas.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.1.0-hc7e4089_6.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.32.3-hcee41ef_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/thrift-cpp-0.12.0-hf3afdfd_1004.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.6.9-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cxx-compiler-1.1.1-hc9558a2_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.13.1-he4413a7_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/fortran-compiler-1.1.1-he991be0_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gsl-2.6-h294904e_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.11-hbd6801e_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.71.1-hcdd3856_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libpq-12.3-h5513abc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/log4cxx-0.10.0-h66fa5af_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pgplot-5.2.2-hac706ba_1006.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/python-3.7.8-h6f2ec95_0_cpython.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/apipkg-1.5-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.3-py_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/asn1crypto-1.4.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/attrs-19.3.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/backoff-1.8.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/backports-1.0-py_2.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/backports.csv-1.0.7-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/boto-2.49.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cfitsio-3.470-hce51eda_6.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/click-7.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/cloudpickle-1.5.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cmake-3.18.0-h5c55442_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.3-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/compilers-1.1.1-0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/cookies-2.2.1-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/curl-7.71.1-he644dc0_4.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/decorator-4.4.2-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/docutils-0.15.2-py37_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/ecdsa-0.13-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/glib-2.65.0-h6f030ca_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/humanize-2.5.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/idna-2.8-py37_1000.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/itsdangerous-1.1.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/jmespath-0.10.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/jsondiff-1.1.2-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/jsonpointer-2.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/mccabe-0.6.1-py_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/more-itertools-8.4.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/mpi4py-3.0.2-py37hcf07815_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/olefile-0.46-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/py-1.9.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pybind11-2.2.4-py37hc9558a2_1001.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pycodestyle-2.5.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pycparser-2.20-pyh9f0ad1d_2.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pyflakes-2.1.1-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pyparsing-2.4.7-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.7-1_cp37m.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pytz-2020.1-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/sip-4.19.8-py37hf484d3e_1000.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/six-1.15.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/sqlparse-0.3.1-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/tabulate-0.8.7-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/termcolor-1.1.0-py_2.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/threadpoolctl-2.1.0-pyh5ca1d4c_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/toolz-0.10.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/tqdm-4.48.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/werkzeug-1.0.1-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/ws4py-0.5.1-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/xmltodict-0.12.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/zipp-3.1.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.7.164-hc831370_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/backports.weakref-1.0.post1-py37hc8dfbb8_1001.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/certifi-2020.6.20-py37hc8dfbb8_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cffi-1.14.1-py37h2b28604_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/chardet-3.0.4-py37hc8dfbb8_1006.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/conda-package-handling-1.6.0-py37h8f50634_2.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/configobj-5.0.6-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/coverage-5.2.1-py37h8f50634_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/cycler-0.10.0-py_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cython-0.29.21-py37h3340039_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cytoolz-0.10.1-py37h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/dbus-1.13.6-he372182_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/docker-pycreds-0.4.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/entrypoints-0.3-py37hc8dfbb8_1001.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/execnet-1.7.1-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/fastavro-0.23.6-py37h8f50634_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/future-0.18.2-py37hc8dfbb8_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/git-2.28.0-pl526h5e3e691_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gstreamer-1.14.5-h36ae1b5_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/importlib-metadata-1.7.0-py37hc8dfbb8_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/jsonpatch-1.24-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.2.0-py37h99015e2_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/markupsafe-1.1.1-py37h8f50634_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/mock-4.0.2-py37hc8dfbb8_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/numpy-1.19.1-py37h8960a57_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/packaging-20.4-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pillow-7.2.0-py37h718be6c_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/psutil-5.7.2-py37h8f50634_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/psycopg2-2.8.5-py37hb09aad4_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pycosat-0.6.3-py37h8f50634_1004.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pyrsistent-0.16.0-py37h8f50634_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pysocks-1.7.1-py37hc8dfbb8_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.1-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pyyaml-5.3.1-py37h8f50634_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ruamel_yaml-0.15.80-py37h8f50634_1001.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/scons-3.1.2-py37hc8dfbb8_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/setproctitle-1.1.10-py37h8f50634_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/sqlalchemy-1.3.18-py37h8f50634_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/terminaltables-3.1.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/tornado-6.0.4-py37h8f50634_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/wcslib-7.2-h345b226_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/websocket-client-0.57.0-py37hc8dfbb8_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/wrapt-1.12.1-py37h8f50634_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/arrow-cpp-0.16.0-py37hb0edad2_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/astropy-4.0.1.post1-py37h8f50634_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/backports.tempfile-1.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/boost-1.70.0-py37h9de70de_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/bottleneck-1.3.2-py37h03ebfcd_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/brotlipy-0.7.0-py37h8f50634_1000.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/cli_helpers-1.2.1-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cryptography-3.0-py37hb09aad4_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/dask-core-2.21.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/deprecated-1.2.10-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/esutil-0.6.4-py37hb3f55d8_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/fitsio-1.1.2-py37h04524ed_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gst-plugins-base-1.14.5-h0935bb2_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/h5py-2.10.0-nompi_py37h90cd8ad_104.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/imagecodecs-lite-2019.12.3-py37h03ebfcd_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/imageio-2.9.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/importlib_metadata-1.7.0-0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lsstdesc.coord-1.2.1-py37h99015e2_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pandas-1.1.0-py37h3340039_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pgspecial-1.11.10-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pywavelets-1.1.1-py37h03ebfcd_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/scipy-1.5.2-py37hb14ef9d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/setuptools-49.2.0-py37hc8dfbb8_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/uncertainties-3.1.4-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/asteval-0.9.16-pyh5ca1d4c_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/autograd-1.3-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/backports.functools_lru_cache-1.6.1-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/flake8-3.7.9-py37hc8dfbb8_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/galsim-2.2.4-py37hd20b5aa_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/jinja2-2.11.2-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/joblib-0.16.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/jsonpickle-1.4.1-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/jsonschema-3.2.0-py37hc8dfbb8_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.0.3-py37h5f35d83_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/networkx-2.4-py_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/numexpr-2.7.1-py37h0da4684_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/parquet-cpp-1.5.1-2.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/patsy-0.5.1-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pluggy-0.13.1-py37hc8dfbb8_2.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pygments-2.6.1-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pyopenssl-19.1.0-py_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/python-jose-3.1.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/qt-5.9.7-h52cfd70_2.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/sshpubkeys-3.1.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/tifffile-2020.6.3-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/treecorr-3.3.11-py37hf484d3e_1001.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/wheel-0.34.2-py_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/flake8-polyfill-1.0.2-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/flask-1.1.2-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/lmfit-1.0.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pip-20.2-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pyarrow-0.16.0-py37h8b68381_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pyqt-5.9.2-py37hcca6a23_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pytables-3.6.1-py37h56451d4_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/scikit-image-0.17.2-py37h0da4684_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/scikit-learn-0.23.1-py37h8a51577_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/seaborn-base-0.10.1-py_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/statsmodels-0.11.1-py37h8f50634_2.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/urllib3-1.25.10-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.5-pyh9f0ad1d_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/botocore-1.17.32-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.0.3-py37_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pep8-naming-0.11.1-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.5-py_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pytest-5.4.3-py37hc8dfbb8_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/requests-2.24.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/seaborn-0.10.1-1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/aws-xray-sdk-0.95-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/conda-4.8.3-py37hc8dfbb8_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/docker-py-4.2.2-py37hc8dfbb8_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/prompt_toolkit-3.0.5-1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pytest-cov-2.10.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pytest-doctestplus-0.6.1-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pytest-flake8-1.0.6-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pytest-forked-1.2.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pytest-openfiles-0.5.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pytest-runner-5.2-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pytest-session2file-0.1.9-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pytest-subtests-0.3.1-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/responses-0.10.15-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/s3transfer-0.3.3-py37hc8dfbb8_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/boto3-1.14.31-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/healpy-1.14.0-py37h539c4ae_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pgcli-3.0.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pytest-xdist-1.34.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/aws-sam-translator-1.25.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cfn-lint-0.24.8-py37_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/moto-1.3.14-py_0.tar.bz2
conda
and system ( conda info
):
$ conda info
When installing a Fortran compiler (either via the fortran-compiler
package as user or via {{ compiler('fortran') }}
in a recipe), the C-include file include/ISO_Fortran_binding.h
is not installed. Missing this file prevents the compilation of modern Fortran-C interfaces. It also prevents autotools from recognizing the Fortran compiler (gfortran) being F2008-compliant. For example, this seems to be the reason, why MPICH does not build the mpi_f08
module (conda-forge/mpich-feedstock#84) preventing the usage of the modern MPI-interface in Fortran programs.
If I build gcc myself, the include file gets installed. (I use the --enable-languages=c,c++,fortran
option).
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
binutils 2.40 hdd6e379_0 conda-forge
binutils_impl_linux-64 2.40 hf600244_0 conda-forge
binutils_linux-64 2.40 hbdbef99_2 conda-forge
c-compiler 1.6.0 hd590300_0 conda-forge
fortran-compiler 1.6.0 heb67821_0 conda-forge
gcc 12.3.0 h8d2909c_2 conda-forge
gcc_impl_linux-64 12.3.0 he2b93b0_3 conda-forge
gcc_linux-64 12.3.0 h76fc315_2 conda-forge
gfortran 12.3.0 h499e0f7_2 conda-forge
gfortran_impl_linux-64 12.3.0 hfcedea8_3 conda-forge
gfortran_linux-64 12.3.0 h7fe76b4_2 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libgcc-devel_linux-64 12.3.0 h8bca6fd_103 conda-forge
libgcc-ng 13.2.0 h807b86a_3 conda-forge
libgfortran5 13.2.0 ha4646dd_3 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
libsanitizer 12.3.0 h0f45ef3_3 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
sysroot_linux-64 2.12 he073ed8_16 conda-forge
active environment : fortran-compiler
active env location : /home/aradi/opt/miniconda3/envs/fortran-compiler
shell level : 2
user config file : /home/aradi/.condarc
populated config files : /home/aradi/.condarc
conda version : 23.7.4
conda-build version : not installed
python version : 3.9.16.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.35=0
__linux=5.18.19=0
__unix=0=0
base environment : /home/aradi/opt/miniconda3 (writable)
conda av data dir : /home/aradi/opt/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/aradi/opt/miniconda3/pkgs
/home/aradi/.conda/pkgs
envs directories : /home/aradi/opt/miniconda3/envs
/home/aradi/.conda/envs
platform : linux-64
user-agent : conda/23.7.4 requests/2.31.0 CPython/3.9.16 Linux/5.18.19-051819-generic ubuntu/22.04.3 glibc/2.35
UID:GID : 1000:1000
netrc file : None
offline mode : False
Issue:
conda list
):
$ conda list
conda
and system ( conda info
):
$ conda info
Right now we have separate gfortran builds for osx in different feedstocks. If we are moving to a gcc feedstock, we should probably archive those builds and move them to the gcc feedstock. One thing I don't understand is if we need two builds of gfortran, one meant for the clang stack and the other mean for a gcc stack for osx.
It appears the compilers are requiring a newer version of GLIBC. Though I may also be doing something wrong.
Issue:
conda list
):
$ conda list
# packages in environment at /opt/conda/envs/compilers:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
binutils 2.36.1 hdd6e379_2 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_33 conda-forge
c-compiler 1.2.0 h7f98852_0 conda-forge
compilers 1.2.0 ha770c72_0 conda-forge
cxx-compiler 1.2.0 h4bd325d_0 conda-forge
fortran-compiler 1.2.0 h1990efc_0 conda-forge
gcc_impl_linux-64 9.3.0 h6df7d76_17 defaults
gcc_linux-64 9.3.0 hf25ea35_33 conda-forge
gfortran_impl_linux-64 9.3.0 hc4a2995_19 conda-forge
gfortran_linux-64 9.3.0 hdc58fab_33 conda-forge
gxx_impl_linux-64 9.3.0 hbdd7822_17 defaults
gxx_linux-64 9.3.0 h3fbe746_33 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_14 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libgcc-devel_linux-64 9.3.0 hb95220a_17 defaults
libgcc-ng 11.1.0 hc902ee8_4 conda-forge
libgfortran-ng 9.3.0 hff62375_19 conda-forge
libgfortran5 9.3.0 hff62375_19 conda-forge
libgomp 11.1.0 hc902ee8_4 conda-forge
libstdcxx-devel_linux-64 9.3.0 hf0c5c8d_17 defaults
libstdcxx-ng 11.1.0 h56837e0_4 conda-forge
sysroot_linux-64 2.12 he073ed8_14 conda-forge
conda
and system ( conda info
):
$ conda info
active environment : compilers
active env location : /opt/conda/envs/compilers
shell level : 2
user config file : /home/conda/.condarc
populated config files : /home/conda/.condarc
conda version : 4.10.1
conda-build version : 3.21.4
python version : 3.8.10.final.0
virtual packages : __linux=5.10.25=0
__glibc=2.12=0
__unix=0=0
__archspec=1=x86_64
base environment : /opt/conda (writable)
conda av data dir : /opt/conda/etc/conda
conda av metadata url : https://repo.anaconda.com/pkgs/main
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /opt/conda/pkgs
/home/conda/.conda/pkgs
envs directories : /opt/conda/envs
/home/conda/.conda/envs
platform : linux-64
user-agent : conda/4.10.1 requests/2.25.1 CPython/3.8.10 Linux/5.10.25-linuxkit centos/6.10 glibc/2.12
UID:GID : 9001:9001
netrc file : None
offline mode : False
$ docker run --rm -it condaforge/linux-anvil-comp7
[conda@30497e4f296d ~]$ conda activate
(base) [conda@30497e4f296d ~]$ conda create -n compilers compilers
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.10.1
latest version: 4.10.3
Please update conda by running
$ conda update -n base conda
## Package Plan ##
environment location: /opt/conda/envs/compilers
added / updated specs:
- compilers
The following packages will be downloaded:
package | build
---------------------------|-----------------
binutils-2.36.1 | hdd6e379_2 27 KB conda-forge
binutils_impl_linux-64-2.36.1| h193b22a_2 10.4 MB conda-forge
binutils_linux-64-2.36 | hf3e587d_33 22 KB conda-forge
c-compiler-1.2.0 | h7f98852_0 6 KB conda-forge
compilers-1.2.0 | ha770c72_0 5 KB conda-forge
cxx-compiler-1.2.0 | h4bd325d_0 6 KB conda-forge
fortran-compiler-1.2.0 | h1990efc_0 6 KB conda-forge
gcc_impl_linux-64-9.3.0 | h6df7d76_17 44.6 MB defaults
gcc_linux-64-9.3.0 | hf25ea35_33 23 KB conda-forge
gfortran_linux-64-9.3.0 | hdc58fab_33 23 KB conda-forge
gxx_impl_linux-64-9.3.0 | hbdd7822_17 9.0 MB defaults
gxx_linux-64-9.3.0 | h3fbe746_33 23 KB conda-forge
kernel-headers_linux-64-2.6.32| he073ed8_14 708 KB conda-forge
ld_impl_linux-64-2.36.1 | hea4e1c9_2 667 KB conda-forge
libgcc-devel_linux-64-9.3.0| hb95220a_17 2.8 MB defaults
libgcc-ng-11.1.0 | hc902ee8_4 909 KB conda-forge
libgomp-11.1.0 | hc902ee8_4 428 KB conda-forge
libstdcxx-devel_linux-64-9.3.0| hf0c5c8d_17 10.6 MB defaults
libstdcxx-ng-11.1.0 | h56837e0_4 4.2 MB conda-forge
sysroot_linux-64-2.12 | he073ed8_14 31.6 MB conda-forge
------------------------------------------------------------
Total: 115.9 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
binutils conda-forge/linux-64::binutils-2.36.1-hdd6e379_2
binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.36.1-h193b22a_2
binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.36-hf3e587d_33
c-compiler conda-forge/linux-64::c-compiler-1.2.0-h7f98852_0
compilers conda-forge/linux-64::compilers-1.2.0-ha770c72_0
cxx-compiler conda-forge/linux-64::cxx-compiler-1.2.0-h4bd325d_0
fortran-compiler conda-forge/linux-64::fortran-compiler-1.2.0-h1990efc_0
gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-9.3.0-h6df7d76_17
gcc_linux-64 conda-forge/linux-64::gcc_linux-64-9.3.0-hf25ea35_33
gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-9.3.0-hc4a2995_19
gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-9.3.0-hdc58fab_33
gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-9.3.0-hbdd7822_17
gxx_linux-64 conda-forge/linux-64::gxx_linux-64-9.3.0-h3fbe746_33
kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-2.6.32-he073ed8_14
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
libgcc-devel_linu~ pkgs/main/linux-64::libgcc-devel_linux-64-9.3.0-hb95220a_17
libgcc-ng conda-forge/linux-64::libgcc-ng-11.1.0-hc902ee8_4
libgfortran-ng conda-forge/linux-64::libgfortran-ng-9.3.0-hff62375_19
libgfortran5 conda-forge/linux-64::libgfortran5-9.3.0-hff62375_19
libgomp conda-forge/linux-64::libgomp-11.1.0-hc902ee8_4
libstdcxx-devel_l~ pkgs/main/linux-64::libstdcxx-devel_linux-64-9.3.0-hf0c5c8d_17
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-11.1.0-h56837e0_4
sysroot_linux-64 conda-forge/noarch::sysroot_linux-64-2.12-he073ed8_14
Proceed ([y]/n)?
Downloading and Extracting Packages
c-compiler-1.2.0 | 6 KB | ##################################### | 100%
binutils-2.36.1 | 27 KB | ##################################### | 100%
ld_impl_linux-64-2.3 | 667 KB | ##################################### | 100%
libgcc-devel_linux-6 | 2.8 MB | ##################################### | 100%
kernel-headers_linux | 708 KB | ##################################### | 100%
gcc_linux-64-9.3.0 | 23 KB | ##################################### | 100%
gxx_impl_linux-64-9. | 9.0 MB | ##################################### | 100%
cxx-compiler-1.2.0 | 6 KB | ##################################### | 100%
compilers-1.2.0 | 5 KB | ##################################### | 100%
libstdcxx-devel_linu | 10.6 MB | ##################################### | 100%
gfortran_linux-64-9. | 23 KB | ##################################### | 100%
binutils_linux-64-2. | 22 KB | ##################################### | 100%
libstdcxx-ng-11.1.0 | 4.2 MB | ##################################### | 100%
libgcc-ng-11.1.0 | 909 KB | ##################################### | 100%
sysroot_linux-64-2.1 | 31.6 MB | ##################################### | 100%
gxx_linux-64-9.3.0 | 23 KB | ##################################### | 100%
binutils_impl_linux- | 10.4 MB | ##################################### | 100%
fortran-compiler-1.2 | 6 KB | ##################################### | 100%
libgomp-11.1.0 | 428 KB | ##################################### | 100%
gcc_impl_linux-64-9. | 44.6 MB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate compilers
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) [conda@30497e4f296d ~]$ conda activate compilers
(compilers) [conda@30497e4f296d ~]$ ls /usr/lib
lib/ lib64/ libexec/
(compilers) [conda@30497e4f296d ~]$ ls /usr/lib64/
Display all 157 possibilities? (y or n)
coreutils/
cracklib_dict.hwm
cracklib_dict.pwd
cracklib_dict.pwi
games/
gconv/
gio/
krb5/
libbfd-2.20.51.0.2-5.48.el6_10.1.so
libbind9.so.80
libbind9.so.80.0.4
libcrack.so.2
libcrack.so.2.8.1
libcrypto.so.10
libcrypto.so.1.0.1e
.libcrypto.so.1.0.1e.hmac
.libcrypto.so.10.hmac
libcurl.so.4
libcurl.so.4.1.1
libdb-4.7.so
libdns.so.81
libdns.so.81.4.1
libelf-0.164.so
(compilers) [conda@30497e4f296d ~]$ vi main.c
(compilers) [conda@30497e4f296d ~]$ gcc -lcrack main.c
gcc: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by gcc)
(compilers) [conda@30497e4f296d ~]$ exit
(base) jkirkham-mlt:~ jkirkham$ docker run --rm -it condaforge/linux-anvil-comp7
[conda@64cec03fb7fe ~]$ conda activate
(base) [conda@64cec03fb7fe ~]$ conda create -n compilers compilers
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.10.1
latest version: 4.10.3
Please update conda by running
$ conda update -n base conda
## Package Plan ##
environment location: /opt/conda/envs/compilers
added / updated specs:
- compilers
The following packages will be downloaded:
package | build
---------------------------|-----------------
binutils-2.36.1 | hdd6e379_2 27 KB conda-forge
binutils_impl_linux-64-2.36.1| h193b22a_2 10.4 MB conda-forge
binutils_linux-64-2.36 | hf3e587d_33 22 KB conda-forge
c-compiler-1.2.0 | h7f98852_0 6 KB conda-forge
compilers-1.2.0 | ha770c72_0 5 KB conda-forge
cxx-compiler-1.2.0 | h4bd325d_0 6 KB conda-forge
fortran-compiler-1.2.0 | h1990efc_0 6 KB conda-forge
gcc_impl_linux-64-9.3.0 | h6df7d76_17 44.6 MB defaults
gcc_linux-64-9.3.0 | hf25ea35_33 23 KB conda-forge
gfortran_linux-64-9.3.0 | hdc58fab_33 23 KB conda-forge
gxx_impl_linux-64-9.3.0 | hbdd7822_17 9.0 MB defaults
gxx_linux-64-9.3.0 | h3fbe746_33 23 KB conda-forge
kernel-headers_linux-64-2.6.32| he073ed8_14 708 KB conda-forge
ld_impl_linux-64-2.36.1 | hea4e1c9_2 667 KB conda-forge
libgcc-devel_linux-64-9.3.0| hb95220a_17 2.8 MB defaults
libgcc-ng-11.1.0 | hc902ee8_4 909 KB conda-forge
libgomp-11.1.0 | hc902ee8_4 428 KB conda-forge
libstdcxx-devel_linux-64-9.3.0| hf0c5c8d_17 10.6 MB defaults
libstdcxx-ng-11.1.0 | h56837e0_4 4.2 MB conda-forge
sysroot_linux-64-2.12 | he073ed8_14 31.6 MB conda-forge
------------------------------------------------------------
Total: 115.9 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
binutils conda-forge/linux-64::binutils-2.36.1-hdd6e379_2
binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.36.1-h193b22a_2
binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.36-hf3e587d_33
c-compiler conda-forge/linux-64::c-compiler-1.2.0-h7f98852_0
compilers conda-forge/linux-64::compilers-1.2.0-ha770c72_0
cxx-compiler conda-forge/linux-64::cxx-compiler-1.2.0-h4bd325d_0
fortran-compiler conda-forge/linux-64::fortran-compiler-1.2.0-h1990efc_0
gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-9.3.0-h6df7d76_17
gcc_linux-64 conda-forge/linux-64::gcc_linux-64-9.3.0-hf25ea35_33
gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-9.3.0-hc4a2995_19
gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-9.3.0-hdc58fab_33
gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-9.3.0-hbdd7822_17
gxx_linux-64 conda-forge/linux-64::gxx_linux-64-9.3.0-h3fbe746_33
kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-2.6.32-he073ed8_14
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
libgcc-devel_linu~ pkgs/main/linux-64::libgcc-devel_linux-64-9.3.0-hb95220a_17
libgcc-ng conda-forge/linux-64::libgcc-ng-11.1.0-hc902ee8_4
libgfortran-ng conda-forge/linux-64::libgfortran-ng-9.3.0-hff62375_19
libgfortran5 conda-forge/linux-64::libgfortran5-9.3.0-hff62375_19
libgomp conda-forge/linux-64::libgomp-11.1.0-hc902ee8_4
libstdcxx-devel_l~ pkgs/main/linux-64::libstdcxx-devel_linux-64-9.3.0-hf0c5c8d_17
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-11.1.0-h56837e0_4
sysroot_linux-64 conda-forge/noarch::sysroot_linux-64-2.12-he073ed8_14
Proceed ([y]/n)?
Downloading and Extracting Packages
libgcc-ng-11.1.0 | 909 KB | ##################################### | 100%
compilers-1.2.0 | 5 KB | ##################################### | 100%
binutils_linux-64-2. | 22 KB | ##################################### | 100%
kernel-headers_linux | 708 KB | ##################################### | 100%
binutils-2.36.1 | 27 KB | ##################################### | 100%
gfortran_linux-64-9. | 23 KB | ##################################### | 100%
gxx_impl_linux-64-9. | 9.0 MB | ##################################### | 100%
ld_impl_linux-64-2.3 | 667 KB | ##################################### | 100%
gcc_impl_linux-64-9. | 44.6 MB | ##################################### | 100%
sysroot_linux-64-2.1 | 31.6 MB | ##################################### | 100%
libstdcxx-devel_linu | 10.6 MB | ##################################### | 100%
binutils_impl_linux- | 10.4 MB | ##################################### | 100%
libstdcxx-ng-11.1.0 | 4.2 MB | ##################################### | 100%
fortran-compiler-1.2 | 6 KB | ##################################### | 100%
libgomp-11.1.0 | 428 KB | ##################################### | 100%
cxx-compiler-1.2.0 | 6 KB | ##################################### | 100%
c-compiler-1.2.0 | 6 KB | ##################################### | 100%
gcc_linux-64-9.3.0 | 23 KB | ##################################### | 100%
libgcc-devel_linux-6 | 2.8 MB | ##################################### | 100%
gxx_linux-64-9.3.0 | 23 KB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate compilers
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) [conda@64cec03fb7fe ~]$ conda activate compilers
(compilers) [conda@64cec03fb7fe ~]$ vi main.c
(compilers) [conda@64cec03fb7fe ~]$ gcc main.c
gcc: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by gcc)
@conda-forge/ctng-compilers maintainers, I'm debugging a segfault issue in a simple libgomp program. I have a feeling -fsanitize=threads
might help me pinpoint the issue. I'm reading to use TSan, libgomp needs to be recompiled with --disable-linux-futex
(something you would never want to have in a production build).
Since I'm going to muck around with building this locally for myself, if you guys think it would be useful, I can do one of the following:
conda_build_config.yaml
that we only put one value in and then_openmp_mutex
that can be installed with something like conda install openmp_mutex=*=*_gnu_nofutex
and also probably do the same for the llvm openmp implementation because it has to be build explicilty with -DLIBOMP_TSAN_SUPPORT=ON
. It might be better to just name them _gnu_debug
and _llvm_debug
.I'm happy to just do my experiment of rebuilding libgomp for debug but since I'm doing the work, if others would find it useful, I'm willing to share. I don't think I've seen a cfep regarding debug builds of things but maybe I should go look again.
This issue is an xref to AnacondaRecipes/aggregate#172
Looks like the recent gcc 7.5.0 builds somehow got GLIBC_2.14
symbols in them which breaks using them in cos6 environments:
(dev) keith@Keith-PC:~/scratch$ objdump -T bin/x86_64-conda-linux-gnu-c++ | grep GLIBC_2.14
0000000000000000 DF *UND* 0000000000000000 GLIBC_2.14 memcpy
(dev) keith@Keith-PC:~/scratch$ objdump -T bin/x86_64-conda-linux-gnu-cc | grep GLIBC_2.14
0000000000000000 DF *UND* 0000000000000000 GLIBC_2.14 memcpy
This is breaking the PR here: conda-forge/nvcc-feedstock#80
cc @beckermr @xhochy @jakirkham @isuruf to consolidate discussion from gitter / the PR linked
n/a
n/a
Am seeing the following assembly error on CI when building for Linux ARM ( conda-forge/arrow-cpp-feedstock#723 (comment) ):
{standard input}: Assembler messages:
{standard input}:186007: Warning: end of file not at end of a line; newline inserted
{standard input}:186154: Error: unknown pseudo-op: `.alig'
aarch64-conda-linux-gnu-c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
More details in this CI log.
_openmp_mutex 4.5-2_gnu conda-forge
abseil-cpp 20210324.2-h01db608_0 conda-forge
aws-c-cal 0.5.11-h76602a3_0 conda-forge
aws-c-common 0.6.2-hf897c2e_0 conda-forge
aws-c-event-stream 0.2.7-hf314db3_13 conda-forge
aws-c-io 0.10.5-h5a3db43_0 conda-forge
aws-checksums 0.1.11-hafdcbdd_7 conda-forge
aws-sdk-cpp 1.8.186-h3fd84e4_3 conda-forge
boost-cpp 1.79.0-ha1c1135_0 conda-forge
brotli 1.0.9-h4e544f5_7 conda-forge
brotli-bin 1.0.9-h4e544f5_7 conda-forge
bzip2 1.0.8-hf897c2e_4 conda-forge
c-ares 1.18.1-hf897c2e_0 conda-forge
ca-certificates 2021.10.8-h4fd8a4c_0 conda-forge
clang 10.0.1-default_hcf6a1e0_1 conda-forge
clang-tools 10.0.1-default_hcf6a1e0_1 conda-forge
clangdev 10.0.1-default_hcf6a1e0_1 conda-forge
clangxx 10.0.1-default_hde54327_1 conda-forge
gflags 2.2.2-h54f1f3f_1004 conda-forge
glog 0.6.0-h8ab10f1_0 conda-forge
google-cloud-cpp 1.36.0-h82cccae_0 conda-forge
grpc-cpp 1.43.2-h4e595cf_3 conda-forge
icu 70.1-ha18d298_0 conda-forge
keyutils 1.6.1-h4e544f5_0 conda-forge
krb5 1.19.3-h7c456eb_0 conda-forge
ld_impl_linux-aarch64 2.36.1-h02ad14f_2 conda-forge
libblas 3.9.0-14_linuxaarch64_openblas conda-forge
libbrotlicommon 1.0.9-h4e544f5_7 conda-forge
libbrotlidec 1.0.9-h4e544f5_7 conda-forge
libbrotlienc 1.0.9-h4e544f5_7 conda-forge
libcblas 3.9.0-14_linuxaarch64_openblas conda-forge
libclang 10.0.1-default_hcf6a1e0_1 conda-forge
libclang-cpp 10.0.1-default_hcf6a1e0_1 conda-forge
libclang-cpp10 10.0.1-default_hcf6a1e0_1 conda-forge
libcrc32c 1.1.2-h01db608_0 conda-forge
libcurl 7.83.0-h8fd98b7_0 conda-forge
libedit 3.1.20191231-he28a2e2_2 conda-forge
libev 4.33-h516909a_1 conda-forge
libevent 2.1.10-h6aed413_4 conda-forge
libffi 3.4.2-h3557bc0_5 conda-forge
libgcc-ng 11.2.0-hf1cc4e7_16 conda-forge
libgfortran-ng 11.2.0-he9431aa_16 conda-forge
libgfortran5 11.2.0-h440fb59_16 conda-forge
libgomp 11.2.0-hf1cc4e7_16 conda-forge
libgoogle-cloud 1.36.0-h82cccae_0 conda-forge
liblapack 3.9.0-14_linuxaarch64_openblas conda-forge
libllvm10 10.0.1-he513fc3_3 conda-forge
libnghttp2 1.47.0-h75cb1c7_0 conda-forge
libnsl 2.0.0-hf897c2e_0 conda-forge
libopenblas 0.3.20-pthreads_h6cb6f83_0 conda-forge
libprotobuf 3.19.4-h469bdbd_0 conda-forge
libssh2 1.10.0-h1ab2c7b_2 conda-forge
libstdcxx-ng 11.2.0-h0d0a5bb_16 conda-forge
libthrift 0.16.0-h0cb72c4_1 conda-forge
libutf8proc 2.7.0-hf897c2e_0 conda-forge
libuuid 2.32.1-hf897c2e_1000 conda-forge
libzlib 1.2.11-h4e544f5_1014 conda-forge
llvm-tools 10.0.1-he513fc3_3 conda-forge
llvmdev 10.0.1-he513fc3_3 conda-forge
lz4-c 1.9.3-h01db608_1 conda-forge
ncurses 6.3-headf329_1 conda-forge
nlohmann_json 3.10.5-h01db608_0 conda-forge
numpy 1.19.5-py39h53e47e4_3 conda-forge
openssl 1.1.1o-h4e544f5_0 conda-forge
orc 1.7.3-h5c30ecb_0 conda-forge
python 3.9.12-h2eada40_1_cpython conda-forge
python_abi 3.9-2_cp39 conda-forge
rapidjson 1.1.0-h54f1f3f_1002 conda-forge
re2 2022.02.01-h01db608_0 conda-forge
readline 8.1-h1a49cc3_0 conda-forge
s2n 1.0.10-h6aed413_0 conda-forge
snappy 1.1.9-hc7e91e1_0 conda-forge
sqlite 3.38.5-hc74f5b8_0 conda-forge
thrift-compiler 0.16.0-h0cb72c4_1 conda-forge
thrift-cpp 0.16.0-ha072818_1 conda-forge
tk 8.6.12-hd8af866_0 conda-forge
tzdata 2022a-h191b570_0 conda-forge
xz 5.2.5-h6dd45c4_1 conda-forge
zlib 1.2.11-h4e544f5_1014 conda-forge
zstd 1.5.2-h41fb7a4_0 conda-forge
active environment : base
active env location : /opt/conda
shell level : 1
user config file : /home/conda/.condarc
populated config files : /opt/conda/.condarc
/home/conda/.condarc
conda version : 4.12.0
conda-build version : 3.21.8
python version : 3.9.12.final.0
virtual packages : __linux=5.13.0=0
__glibc=2.17=0
__unix=0=0
__archspec=1=aarch64
base environment : /opt/conda (writable)
conda av data dir : /opt/conda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-aarch64
https://conda.anaconda.org/conda-forge/noarch
package cache : /opt/conda/pkgs
/home/conda/.conda/pkgs
envs directories : /opt/conda/envs
/home/conda/.conda/envs
platform : linux-aarch64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/5.13.0-35-generic centos/7.9.2009 glibc/2.17
UID:GID : 1000:1000
netrc file : None
offline mode : False
Issue:
While Switching OpenMP implementation advocates using conda install _openmp_mutex=*=*_gnu
, this leads to
UnsatisfiableError: The following specifications were found to be incompatible with a past
explicit spec that is not an explicit spec in this operation (_openmp_mutex):
- _openmp_mutex[build=*_gnu]
To reproduce, create an environment using pytorch-cuda-dev.yaml file (see below), activate, and run conda install _openmp_mutex=*=*_gnu
.
I also tried inserting _openmp_mutex=*=*_gnu
to the yaml with no success.
What seems to work is a manual reset of the libgomp.so.1->libomp.so
link to libgomp.so.1->libgomp.so
:
$ ln -fs $CONDA_PREFIX/lib/libgomp.so $CONDA_PREFIX/lib/libgomp.so.1
but that is obviously not a sustainable solution.
pytorch-cuda-dev.yaml
:
name: pytorch-cuda-dev
channels:
- conda-forge
- pytorch
- defaults
dependencies:
- python=3
- numpy
- ninja
- pyyaml
- mkl
- mkl-include
- setuptools
- cmake
- cffi
- typing
- pytest
- compilers
- flake8
- psutil
- hypothesis
- nvcc_linux-64=11.0
- magma-cuda110
- mypy
- clang-tools
conda list
):
$ conda list
# packages in environment at /home/pearu/miniconda3/envs/pytorch-cuda-dev:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
_sysroot_linux-64_curr_repodata_hack 3 ha9d2b57_10 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
attrs 20.3.0 pyhd3deb0d_0 conda-forge
binutils 2.35.1 hdd6e379_1 conda-forge
binutils_impl_linux-64 2.35.1 h193b22a_1 conda-forge
binutils_linux-64 2.35 hc3fd857_29 conda-forge
black 20.8b1 py_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.17.1 h36c2ea0_0 conda-forge
c-compiler 1.1.3 h7f98852_0 conda-forge
ca-certificates 2020.12.5 ha878542_0 conda-forge
certifi 2020.12.5 py39hf3d152e_1 conda-forge
cffi 1.14.4 py39he32792d_1 conda-forge
clang 11.0.1 ha770c72_1 conda-forge
clang-11 11.0.1 default_ha53f305_1 conda-forge
clang-tools 11.0.1 default_ha53f305_1 conda-forge
clangxx 11.0.1 default_ha53f305_1 conda-forge
click 7.1.2 pyh9f0ad1d_0 conda-forge
cmake 3.19.3 h4547794_0 conda-forge
compilers 1.1.3 ha770c72_0 conda-forge
cxx-compiler 1.1.3 h4bd325d_0 conda-forge
dataclasses 0.7 pyhb2cacf7_7 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
flake8 3.8.4 py_0 conda-forge
fortran-compiler 1.1.3 h1990efc_0 conda-forge
gcc_impl_linux-64 9.3.0 h70c0ae5_18 conda-forge
gcc_linux-64 9.3.0 h7247604_29 conda-forge
gfortran_impl_linux-64 9.3.0 hc4a2995_18 conda-forge
gfortran_linux-64 9.3.0 ha1c937c_29 conda-forge
gxx_impl_linux-64 9.3.0 hd87eabc_18 conda-forge
gxx_linux-64 9.3.0 h0d07fa4_29 conda-forge
hypothesis 6.0.3 pyhd8ed1ab_0 conda-forge
importlib-metadata 3.4.0 py39hf3d152e_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
kernel-headers_linux-64 3.10.0 h77966d4_10 conda-forge
krb5 1.17.2 h926e7f8_0 conda-forge
ld_impl_linux-64 2.35.1 hea4e1c9_1 conda-forge
libblas 3.9.0 7_openblas conda-forge
libcblas 3.9.0 7_openblas conda-forge
libclang-cpp11 11.0.1 default_ha53f305_1 conda-forge
libcurl 7.71.1 hcdd3856_8 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-devel_linux-64 9.3.0 h7864c58_18 conda-forge
libgcc-ng 9.3.0 h2828fa1_18 conda-forge
libgfortran-ng 9.3.0 hff62375_18 conda-forge
libgfortran5 9.3.0 hff62375_18 conda-forge
libgomp 9.3.0 h2828fa1_18 conda-forge
liblapack 3.9.0 7_openblas conda-forge
libllvm11 11.0.1 hf817b99_0 conda-forge
libnghttp2 1.41.0 h8cfc5f6_2 conda-forge
libopenblas 0.3.12 pthreads_h4812303_1 conda-forge
libssh2 1.9.0 hab1572f_5 conda-forge
libstdcxx-devel_linux-64 9.3.0 hb016644_18 conda-forge
libstdcxx-ng 9.3.0 h6de172a_18 conda-forge
libuv 1.40.0 h7f98852_0 conda-forge
llvm-openmp 11.0.1 h4bd325d_0 conda-forge
magma-cuda110 2.5.2 1 pytorch
mccabe 0.6.1 py_1 conda-forge
mkl 2020.4 h726a3e6_304 conda-forge
mkl-include 2020.4 h726a3e6_304 conda-forge
more-itertools 8.6.0 pyhd8ed1ab_0 conda-forge
mypy 0.800 pyhd8ed1ab_0 conda-forge
mypy_extensions 0.4.3 py39hf3d152e_3 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
ninja 1.10.2 h4bd325d_0 conda-forge
numpy 1.19.5 py39hdbf815f_1 conda-forge
nvcc_linux-64 11.0 h96e36e3_11 conda-forge
openssl 1.1.1i h7f98852_0 conda-forge
packaging 20.8 pyhd3deb0d_0 conda-forge
pathspec 0.8.1 pyhd3deb0d_0 conda-forge
pip 21.0 pyhd8ed1ab_0 conda-forge
pluggy 0.13.1 py39hf3d152e_4 conda-forge
psutil 5.8.0 py39h3811e60_1 conda-forge
py 1.10.0 pyhd3deb0d_0 conda-forge
pycodestyle 2.6.0 pyh9f0ad1d_0 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pyflakes 2.2.0 pyh9f0ad1d_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pytest 6.2.1 py39hf3d152e_1 conda-forge
python 3.9.1 hffdb5ce_3_cpython conda-forge
python_abi 3.9 1_cp39 conda-forge
pyyaml 5.4.1 py39h3811e60_0 conda-forge
readline 8.0 he28a2e2_2 conda-forge
regex 2020.11.13 py39h3811e60_1 conda-forge
rhash 1.4.1 h7f98852_0 conda-forge
sed 4.8 he412f7d_0 conda-forge
setuptools 49.6.0 py39hf3d152e_3 conda-forge
sortedcontainers 2.3.0 pyhd8ed1ab_0 conda-forge
sqlite 3.34.0 h74cdb3f_0 conda-forge
sysroot_linux-64 2.17 h77966d4_10 conda-forge
tk 8.6.10 h21135ba_1 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
torch 1.8.0a0+unknown dev_0 <develop>
typed-ast 1.4.2 py39h3811e60_0 conda-forge
typing 3.7.4.3 pyhd8ed1ab_2 conda-forge
typing_extensions 3.7.4.3 py_0 conda-forge
tzdata 2020f he74cb21_0 conda-forge
wheel 0.36.2 pyhd3deb0d_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h516909a_0 conda-forge
zipp 3.4.0 py_0 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
conda
and system ( conda info
):
$ conda info
active environment : pytorch-cuda-dev
active env location : /home/pearu/miniconda3/envs/pytorch-cuda-dev
shell level : 2
user config file : /home/pearu/.condarc
populated config files : /home/pearu/.condarc
conda version : 4.9.2
conda-build version : not installed
python version : 3.8.5.final.0
virtual packages : __cuda=11.2=0
__glibc=2.27=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/pearu/miniconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/pearu/miniconda3/pkgs
/home/pearu/.conda/pkgs
envs directories : /home/pearu/miniconda3/envs
/home/pearu/.conda/envs
platform : linux-64
user-agent : conda/4.9.2 requests/2.24.0 CPython/3.8.5 Linux/4.15.0-132-generic ubuntu/18.04.4 glibc/2.27
UID:GID : 1000:1000
netrc file : None
offline mode : False
If I try to dlopen with RTLD_DEEPBIND from a Python environment libgomp 13.*, I obtain a segfault. A simple reproducer is just the command python -c "import ctypes; import os; ctypes._dlopen(os.environ['CONDA_PREFIX']+'/lib/libgomp.so.1', os.RTLD_DEEPBIND)"
:
(testsegfault) traversaro@IITICUBLAP257:~$ python -c "import ctypes; import os; ctypes._dlopen(os.environ['CONDA_PREFIX']+'/lib/libgomp.so.1', os.RTLD_DEEPBIND)"
Segmentation fault
The issue does not appear if:
The backtrace is the following:
(gdb) bt
#0 initialize_env () at ../../../libgomp/env.c:2062
#1 0x00007ffff7fc947e in call_init (l=<optimized out>, argc=argc@entry=3, argv=argv@entry=0x7fffffffc1f8, env=env@entry=0x7fffffffc218)
at ./elf/dl-init.c:70
#2 0x00007ffff7fc9568 in call_init (env=0x7fffffffc218, argv=0x7fffffffc1f8, argc=3, l=<optimized out>) at ./elf/dl-init.c:33
#3 _dl_init (main_map=0x555555b8e620, argc=3, argv=0x7fffffffc1f8, env=0x7fffffffc218) at ./elf/dl-init.c:117
#4 0x00007ffff7e09c85 in __GI__dl_catch_exception (exception=<optimized out>, operate=<optimized out>, args=<optimized out>)
at ./elf/dl-error-skeleton.c:182
#5 0x00007ffff7fd0ff6 in dl_open_worker (a=0x7fffffffb910) at ./elf/dl-open.c:808
and seems to indicate that something is going wrong around https://github.com/gcc-mirror/gcc/blob/releases/gcc-13.2.0/libgomp/env.c#L2062 . I have a few ideas to investigate this further, like debugging the value of the environ
global variable, but I am not sure when I will have time for this, so in the meanwhile I opened this issue.
Downstream issue: conda-forge/casadi-feedstock#91 .
(testsegfault) traversaro@IITICUBLAP257:~$ conda list
# packages in environment at /home/traversaro/miniforge3/envs/testsegfault:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_0 conda-forge
libgomp 13.2.0 h807b86a_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libsqlite 3.43.0 h2797004_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
ncurses 6.4 hcb278e6_0 conda-forge
openssl 3.1.2 hd590300_0 conda-forge
pip 23.2.1 pyhd8ed1ab_0 conda-forge
python 3.11.5 hab00c5b_0_cpython conda-forge
readline 8.2 h8228510_1 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
wheel 0.41.2 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
(testsegfault) traversaro@IITICUBLAP257:~$ conda info
active environment : testsegfault
active env location : /home/traversaro/miniforge3/envs/testsegfault
shell level : 1
user config file : /home/traversaro/.condarc
populated config files : /home/traversaro/miniforge3/.condarc
/home/traversaro/.condarc
conda version : 23.3.1
conda-build version : not installed
python version : 3.10.12.final.0
virtual packages : __archspec=1=x86_64
__cuda=12.2=0
__glibc=2.35=0
__linux=5.15.90.1=0
__unix=0=0
base environment : /home/traversaro/miniforge3 (writable)
conda av data dir : /home/traversaro/miniforge3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/traversaro/miniforge3/pkgs
/home/traversaro/.conda/pkgs
envs directories : /home/traversaro/miniforge3/envs
/home/traversaro/.conda/envs
platform : linux-64
user-agent : conda/23.3.1 requests/2.31.0 CPython/3.10.12 Linux/5.15.90.1-microsoft-standard-WSL2 ubuntu/22.04.2 glibc/2.35
UID:GID : 1000:1000
netrc file : None
offline mode : False
Steps to reproduce (on a powerpc box):
# conda create -yp ./dev gxx_linux-ppc64le -c conda-forge
# conda activate ./dev
# cat <<EOF > wth.cpp
#include <iostream>
int main() {
return 0;
}
EOF
# $CXX wth.cpp -g -fno-plt -fuse-ld=gold
./a.out
Illegal instruction
Another pruned example (from mongodb build system):
#include <cstring>
#include <cstdint>
#include <cstdlib>
int main() {
using Native = __vector signed char;
const size_t size = sizeof(Native);
const Native bits = { 120, 112, 104, 96, 88, 80, 72, 64, 56, 48, 40, 32, 24, 16, 8, 0 };
uint8_t inputBuf[size];
std::memset(inputBuf, 0xFF, sizeof(inputBuf));
return 0;
}
This is also reproducible using the cross compilers
+ qemu-static
+ binfmt_misc
+ QEMU_LD_PREFIX
. The error is simply:
qemu: uncaught target signal 4 (Illegal instruction) - core dumped
[1] 641165 illegal hardware instruction (core dumped) ./a.out
Not sure if this has been reported upstream, as I am able to reproduce this only with this combo: -fno-plt
+ -fuse-ld=gold
. If I remove either, the problem goes away.
I saw this problem happen with mongodb and mysql. @hmaarrfk found that downgrading the compiler version to 8 resolves the issue, so I ended up doing that on both these feedstocks.
Issue:
When using a Conda installation of gcc
, system headers are not picked up - only header directories within the Conda environment are searched:
$ gcc -xc -E -v -
Reading specs from /raid/charlesb/miniconda3/envs/ucx/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/specs
COLLECT_GCC=gcc
Target: x86_64-conda-linux-gnu
Configured with: /home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/.build/x86_64-conda-linux-gnu/src/gcc/configure --build=x86_64-build_pc-linux-gnu --host=x86_64-build_pc-linux-gnu --target=x86_64-conda-linux-gnu --prefix=/home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/gcc_built --with-sysroot=/home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/gcc_built/x86_64-conda-linux-gnu/sysroot --enable-languages=c,c++,fortran,objc,obj-c++ --with-pkgversion='crosstool-NG 1.24.0.133_b0863d8_dirty' --enable-__cxa_atexit --disable-libmudflap --enable-libgomp --disable-libssp --enable-libquadmath --enable-libquadmath-support --enable-libsanitizer --enable-libmpx --with-gmp=/home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/.build/x86_64-conda-linux-gnu/buildtools --with-mpfr=/home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/.build/x86_64-conda-linux-gnu/buildtools --with-mpc=/home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/.build/x86_64-conda-linux-gnu/buildtools --with-isl=/home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/.build/x86_64-conda-linux-gnu/buildtools --enable-lto --with-host-libstdcxx='-static-libgcc -Wl,-Bstatic,-lstdc++,-Bdynamic -lm' --enable-threads=posix --enable-target-optspace --enable-plugin --enable-gold --disable-nls --disable-multilib --with-local-prefix=/home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/gcc_built/x86_64-conda-linux-gnu/sysroot --enable-long-long --enable-default-pie
Thread model: posix
gcc version 9.3.0 (crosstool-NG 1.24.0.133_b0863d8_dirty)
COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'
/raid/charlesb/miniconda3/envs/ucx/bin/../libexec/gcc/x86_64-conda-linux-gnu/9.3.0/cc1 -E -quiet -v -iprefix /raid/charlesb/miniconda3/envs/ucx/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/ -isysroot /raid/charlesb/miniconda3/envs/ucx/bin/../x86_64-conda-linux-gnu/sysroot - -mtune=generic -march=x86-64
ignoring nonexistent directory "/raid/charlesb/miniconda3/envs/ucx/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/include"
ignoring duplicate directory "/raid/charlesb/miniconda3/envs/ucx/bin/../lib/gcc/../../lib/gcc/x86_64-conda-linux-gnu/9.3.0/include"
ignoring nonexistent directory "/raid/charlesb/miniconda3/envs/ucx/bin/../x86_64-conda-linux-gnu/sysroot/home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/gcc_built/x86_64-conda-linux-gnu/sysroot/include"
ignoring duplicate directory "/raid/charlesb/miniconda3/envs/ucx/bin/../lib/gcc/../../lib/gcc/x86_64-conda-linux-gnu/9.3.0/include-fixed"
ignoring nonexistent directory "/raid/charlesb/miniconda3/envs/ucx/bin/../lib/gcc/../../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
/raid/charlesb/miniconda3/envs/ucx/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/include
/raid/charlesb/miniconda3/envs/ucx/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/include-fixed
/raid/charlesb/miniconda3/envs/ucx/bin/../x86_64-conda-linux-gnu/sysroot/usr/include
End of search list.
This becomes an issue when compiling libraries that depend on system headers located in /usr/include
, /usr/local/include
, etc. Is there a way to configure the header directories available to Conda gcc
, so that the system header directories could be picked up in addition to or instead of those in the Conda environment?
For context, this issue is coming up for me when trying to compile UCX with InfiniBand/RDMA support (which requires system headers in /usr/include/rdma
) in an environment that has gcc_impl_linux-64
as an implicit dependency.
conda list
):
$ conda list
# packages in environment at /raid/charlesb/miniconda3/envs/ucx:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
autoconf 2.69 pl5320h36c2ea0_10 conda-forge
automake 1.16.2 pl5320ha770c72_3 conda-forge
binutils 2.36.1 hdd6e379_2 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_33 conda-forge
c-compiler 1.2.0 h7f98852_0 conda-forge
ca-certificates 2021.5.30 ha878542_0 conda-forge
certifi 2021.5.30 py37h89c1867_0 conda-forge
cython 0.29.24 py37hcd2ae1e_0 conda-forge
gcc_impl_linux-64 9.3.0 h6df7d76_17
gcc_linux-64 9.3.0 hf25ea35_33 conda-forge
icu 68.1 h58526e2_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_14 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-devel_linux-64 9.3.0 hb95220a_17
libgcc-ng 11.1.0 hc902ee8_4 conda-forge
libgomp 11.1.0 hc902ee8_4 conda-forge
libhwloc 2.5.0 h6746aa3_0 conda-forge
libiconv 1.16 h516909a_0 conda-forge
libstdcxx-ng 11.1.0 h56837e0_4 conda-forge
libtool 2.4.6 h58526e2_1007 conda-forge
libxml2 2.9.12 h72842e0_0 conda-forge
m4 1.4.18 h516909a_1001 conda-forge
make 4.3 hd18ef5c_1 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
openssl 1.1.1k h7f98852_0 conda-forge
perl 5.32.1 0_h7f98852_perl5 conda-forge
pip 21.2.1 pyhd8ed1ab_0 conda-forge
pkg-config 0.29.2 h36c2ea0_1008 conda-forge
psutil 5.8.0 py37h5e8e339_1 conda-forge
python 3.7.10 hffdb5ce_100_cpython conda-forge
python_abi 3.7 2_cp37m conda-forge
readline 8.1 h46c0cb4_0 conda-forge
setuptools 49.6.0 py37h89c1867_3 conda-forge
sqlite 3.36.0 h9cd32fc_0 conda-forge
sysroot_linux-64 2.12 he073ed8_14 conda-forge
tk 8.6.10 h21135ba_1 conda-forge
wheel 0.36.2 pyhd3deb0d_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
conda
and system ( conda info
):
$ conda info
active environment : ucx
active env location : /raid/charlesb/miniconda3/envs/ucx
shell level : 2
user config file : /home/nfs/charlesb/.condarc
populated config files : /home/nfs/charlesb/.condarc
conda version : 4.10.3
conda-build version : not installed
python version : 3.8.5.final.0
virtual packages : __cuda=11.2=0
__linux=4.15.0=0
__glibc=2.27=0
__unix=0=0
__archspec=1=x86_64
base environment : /raid/charlesb/miniconda3 (writable)
conda av data dir : /raid/charlesb/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/rapidsai-nightly/linux-64
https://conda.anaconda.org/rapidsai-nightly/noarch
https://conda.anaconda.org/rapidsai/linux-64
https://conda.anaconda.org/rapidsai/noarch
https://conda.anaconda.org/nvidia/linux-64
https://conda.anaconda.org/nvidia/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /raid/charlesb/miniconda3/pkgs
/home/nfs/charlesb/.conda/pkgs
envs directories : /raid/charlesb/miniconda3/envs
/home/nfs/charlesb/.conda/envs
platform : linux-64
user-agent : conda/4.10.3 requests/2.24.0 CPython/3.8.5 Linux/4.15.0-76-generic ubuntu/18.04.4 glibc/2.27
UID:GID : 10232:10004
netrc file : None
offline mode : False
Issue:
The solver doesn't appear to pull the latest build
(base) root@53232016349f:/# conda create -n mpi_test2 -c conda-forge python=3.7 openmpi openmpi-mpicc
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /opt/conda/envs/mpi_test2
added / updated specs:
- openmpi
- openmpi-mpicc
- python=3.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | conda_forge 3 KB conda-forge
_openmp_mutex-4.5 | 1_gnu 22 KB conda-forge
binutils_impl_linux-64-2.34| h2122c62_9 9.2 MB conda-forge
binutils_linux-64-2.34 | h47ac705_27 22 KB conda-forge
gcc_impl_linux-64-7.5.0 | hda68d29_13 42.7 MB conda-forge
gcc_linux-64-7.5.0 | hf34d7eb_27 23 KB conda-forge
kernel-headers_linux-64-2.6.32| h77966d4_13 707 KB conda-forge
ld_impl_linux-64-2.34 | hc38a660_9 612 KB conda-forge
libffi-3.2.1 | he1b5a44_1007 47 KB conda-forge
libgcc-ng-9.3.0 | h24d8f2e_16 7.8 MB conda-forge
libgfortran-ng-7.5.0 | hdf63c60_16 1.3 MB conda-forge
libgomp-9.3.0 | h24d8f2e_16 378 KB conda-forge
libstdcxx-ng-9.3.0 | hdf63c60_16 4.0 MB conda-forge
mpi-1.0 | openmpi 4 KB conda-forge
ncurses-6.2 | he1b5a44_1 993 KB conda-forge
openmpi-4.0.5 | hdf1f1ad_1 3.9 MB conda-forge
openmpi-mpicc-4.0.5 | h516909a_1 8 KB conda-forge
pip-20.2.3 | py_0 1.1 MB conda-forge
python-3.7.8 |h6f2ec95_1_cpython 53.1 MB conda-forge
readline-8.0 | he28a2e2_2 281 KB conda-forge
setuptools-49.6.0 | py37hc8dfbb8_0 948 KB conda-forge
sqlite-3.33.0 | h4cf870e_0 1.4 MB conda-forge
sysroot_linux-64-2.12 | h77966d4_13 30.2 MB conda-forge
tk-8.6.10 | hed695b0_0 3.2 MB conda-forge
wheel-0.35.1 | pyh9f0ad1d_0 29 KB conda-forge
xz-5.2.5 | h516909a_1 343 KB conda-forge
zlib-1.2.11 | h516909a_1009 106 KB conda-forge
------------------------------------------------------------
Total: 162.4 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h2122c62_9
binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-h47ac705_27
ca-certificates conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
certifi conda-forge/linux-64::certifi-2020.6.20-py37hc8dfbb8_0
gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.5.0-hda68d29_13
gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.5.0-hf34d7eb_27
kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-2.6.32-h77966d4_13
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-hc38a660_9
libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
libgcc-ng conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_16
libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_16
libgomp conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_16
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_16
mpi conda-forge/linux-64::mpi-1.0-openmpi
ncurses conda-forge/linux-64::ncurses-6.2-he1b5a44_1
openmpi conda-forge/linux-64::openmpi-4.0.5-hdf1f1ad_1
openmpi-mpicc conda-forge/linux-64::openmpi-mpicc-4.0.5-h516909a_1
openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_1
pip conda-forge/noarch::pip-20.2.3-py_0
python conda-forge/linux-64::python-3.7.8-h6f2ec95_1_cpython
python_abi conda-forge/linux-64::python_abi-3.7-1_cp37m
readline conda-forge/linux-64::readline-8.0-he28a2e2_2
setuptools conda-forge/linux-64::setuptools-49.6.0-py37hc8dfbb8_0
sqlite conda-forge/linux-64::sqlite-3.33.0-h4cf870e_0
sysroot_linux-64 conda-forge/noarch::sysroot_linux-64-2.12-h77966d4_13
tk conda-forge/linux-64::tk-8.6.10-hed695b0_0
wheel conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
xz conda-forge/linux-64::xz-5.2.5-h516909a_1
zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1009
Proceed ([y]/n)? n
CondaSystemExit: Exiting.
Here is what is available.
(base) root@53232016349f:/# conda search gcc_impl_linux-64
Loading channels: done
# Name Version Build Channel
gcc_impl_linux-64 7.3.0 hd420e75_4 conda-forge
gcc_impl_linux-64 7.3.0 hd420e75_5 conda-forge
gcc_impl_linux-64 7.5.0 hda68d29_10 conda-forge
gcc_impl_linux-64 7.5.0 hda68d29_11 conda-forge
gcc_impl_linux-64 7.5.0 hda68d29_12 conda-forge
gcc_impl_linux-64 7.5.0 hda68d29_13 conda-forge
gcc_impl_linux-64 7.5.0 hdb87b24_14 conda-forge
gcc_impl_linux-64 7.5.0 hdb87b24_15 conda-forge
gcc_impl_linux-64 7.5.0 hdb87b24_16 conda-forge
gcc_impl_linux-64 8.4.0 h4f5b6c9_14 conda-forge
gcc_impl_linux-64 8.4.0 h4f5b6c9_15 conda-forge
gcc_impl_linux-64 8.4.0 h4f5b6c9_16 conda-forge
gcc_impl_linux-64 9.3.0 ha2fd2e4_14 conda-forge
gcc_impl_linux-64 9.3.0 ha2fd2e4_15 conda-forge
gcc_impl_linux-64 9.3.0 ha2fd2e4_16 conda-forge
gcc_impl_linux-64 9.3.0 hda68d29_11 conda-forge
gcc_impl_linux-64 9.3.0 hda68d29_12 conda-forge
gcc_impl_linux-64 9.3.0 hda68d29_13 conda-forge
When you specify gcc_impl_linux-64=7.5.0
at the command line, it works correctly.
Note that builds past 13 have extra and more complicated deps due to the cross-compiling PRs.
gcc_impl_linux-64-7.3.0-hd420e75_4.tar.bz2 ['libgcc-ng 5.4.*|7.2.*|7.3.*|8.2.*|9.1.*|9.2.*', 'libstdcxx-ng 5.4.*|7.2.*|7.3.*|8.2.*|9.1.*|9.2.*', 'libgfortran 5.4.*|7.2.*|7.3.*|8.2.*|9.1.*|9.2.*', 'libgomp 5.4.*|7.2.*|7.3.*|8.2.*|9.1.*|9.2.*', 'binutils_impl_linux-64 <2.34', 'ld_impl_linux-64 <2.34', 'sysroot_linux-64 ==99999999999'] ['binutils_impl_linux-64 >=2.31.1', 'libgcc-ng >=7.3.0', 'libgomp >=7.3.0', 'libstdcxx-ng >=7.3.0']
gcc_impl_linux-64-7.3.0-hd420e75_5.tar.bz2 ['libgcc-ng 5.4.*|7.2.*|7.3.*|8.2.*|9.1.*|9.2.*', 'libstdcxx-ng 5.4.*|7.2.*|7.3.*|8.2.*|9.1.*|9.2.*', 'libgfortran 5.4.*|7.2.*|7.3.*|8.2.*|9.1.*|9.2.*', 'libgomp 5.4.*|7.2.*|7.3.*|8.2.*|9.1.*|9.2.*', 'binutils_impl_linux-64 <2.34', 'ld_impl_linux-64 <2.34', 'sysroot_linux-64 ==99999999999'] ['binutils_impl_linux-64 >=2.31.1', 'libgcc-ng >=7.3.0', 'libgomp >=7.3.0', 'libstdcxx-ng >=7.3.0']
gcc_impl_linux-64-7.5.0-hda68d29_10.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-ng >=7.5.0', 'libgomp >=7.5.0', 'libstdcxx-ng >=7.5.0', 'sysroot_linux-64']
gcc_impl_linux-64-7.5.0-hda68d29_11.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-ng >=7.5.0', 'libgomp >=7.5.0', 'libstdcxx-ng >=7.5.0', 'sysroot_linux-64']
gcc_impl_linux-64-7.5.0-hda68d29_12.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-ng >=7.5.0', 'libgomp >=7.5.0', 'libstdcxx-ng >=7.5.0', 'sysroot_linux-64']
gcc_impl_linux-64-7.5.0-hda68d29_13.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-ng >=7.5.0', 'libgomp >=7.5.0', 'libstdcxx-ng >=7.5.0', 'sysroot_linux-64']
gcc_impl_linux-64-7.5.0-hdb87b24_14.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-devel_linux-64 7.5.0 h42c25f5_14', 'libgcc-ng >=4.9', 'libgcc-ng >=7.5.0', 'libgomp >=7.5.0', 'libstdcxx-ng >=4.9', 'libstdcxx-ng >=7.5.0', 'sysroot_linux-64']
gcc_impl_linux-64-7.5.0-hdb87b24_15.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-devel_linux-64 7.5.0 h42c25f5_15', 'libgcc-ng >=4.9', 'libgcc-ng >=7.5.0', 'libgomp >=7.5.0', 'libstdcxx-ng >=4.9', 'libstdcxx-ng >=7.5.0', 'sysroot_linux-64']
gcc_impl_linux-64-7.5.0-hdb87b24_16.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-devel_linux-64 7.5.0 h42c25f5_16', 'libgcc-ng >=4.9', 'libgcc-ng >=7.5.0', 'libgomp >=7.5.0', 'libstdcxx-ng >=4.9', 'libstdcxx-ng >=7.5.0', 'sysroot_linux-64']
gcc_impl_linux-64-8.4.0-h4f5b6c9_14.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-devel_linux-64 8.4.0 h3b9816e_14', 'libgcc-ng >=4.9', 'libgcc-ng >=8.4.0', 'libgomp >=8.4.0', 'libstdcxx-ng >=4.9', 'libstdcxx-ng >=8.4.0', 'sysroot_linux-64']
gcc_impl_linux-64-8.4.0-h4f5b6c9_15.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-devel_linux-64 8.4.0 h3b9816e_15', 'libgcc-ng >=4.9', 'libgcc-ng >=8.4.0', 'libgomp >=8.4.0', 'libstdcxx-ng >=4.9', 'libstdcxx-ng >=8.4.0', 'sysroot_linux-64']
gcc_impl_linux-64-8.4.0-h4f5b6c9_16.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-devel_linux-64 8.4.0 h3b9816e_16', 'libgcc-ng >=4.9', 'libgcc-ng >=8.4.0', 'libgomp >=8.4.0', 'libstdcxx-ng >=4.9', 'libstdcxx-ng >=8.4.0', 'sysroot_linux-64']
gcc_impl_linux-64-9.3.0-ha2fd2e4_14.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-devel_linux-64 9.3.0 hfd08b2a_14', 'libgcc-ng >=4.9', 'libgcc-ng >=9.3.0', 'libgomp >=9.3.0', 'libstdcxx-ng >=4.9', 'libstdcxx-ng >=9.3.0', 'sysroot_linux-64']
gcc_impl_linux-64-9.3.0-ha2fd2e4_15.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-devel_linux-64 9.3.0 hfd08b2a_15', 'libgcc-ng >=4.9', 'libgcc-ng >=9.3.0', 'libgomp >=9.3.0', 'libstdcxx-ng >=4.9', 'libstdcxx-ng >=9.3.0', 'sysroot_linux-64']
gcc_impl_linux-64-9.3.0-ha2fd2e4_16.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-devel_linux-64 9.3.0 hfd08b2a_16', 'libgcc-ng >=4.9', 'libgcc-ng >=9.3.0', 'libgomp >=9.3.0', 'libstdcxx-ng >=4.9', 'libstdcxx-ng >=9.3.0', 'sysroot_linux-64']
gcc_impl_linux-64-9.3.0-hda68d29_11.tar.bz2 None ['binutils_impl_linux-64 >=2.31.1', 'libgcc-ng >=9.3.0', 'libgomp >=9.3.0', 'libstdcxx-ng >=9.3.0', 'sysroot_linux-64']
The columns here are the package, constrains and depends.
conda list
):
$ conda list
(base) root@53232016349f:/# conda list
# packages in environment at /opt/conda:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 0_gnu conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.1 py_0 conda-forge
bzip2 1.0.8 h516909a_2 conda-forge
c-ares 1.16.1 h516909a_3 conda-forge
ca-certificates 2020.6.20 hecda079_0 conda-forge
certifi 2020.6.20 py37hc8dfbb8_0 conda-forge
cffi 1.13.2 py37h8022711_0 conda-forge
chardet 3.0.4 py37_1003 conda-forge
conda 4.8.4 py37hc8dfbb8_2 conda-forge
conda-package-handling 1.6.0 py37h516909a_1 conda-forge
cryptography 2.8 py37h72c5cf5_1 conda-forge
decorator 4.4.2 py_0 conda-forge
icu 64.2 he1b5a44_1 conda-forge
idna 2.8 py37_1000 conda-forge
ipython 5.8.0 py37_1 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
krb5 1.17.1 hfafb76e_3 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_8 conda-forge
libarchive 3.3.3 hc3f970e_1004 conda-forge
libcurl 7.71.1 hcdd3856_5 conda-forge
libedit 3.1.20191231 h46ee950_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
libiconv 1.16 h516909a_0 conda-forge
libnghttp2 1.41.0 h8cfc5f6_2 conda-forge
libsolv 0.7.14 h8b12597_5 conda-forge
libssh2 1.9.0 hab1572f_5 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
lz4-c 1.8.3 he1b5a44_1001 conda-forge
lzo 2.10 h516909a_1000 conda-forge
mamba 0.5.1 py37h782c684_0 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
openssl 1.1.1g h516909a_1 conda-forge
pexpect 4.8.0 py37hc8dfbb8_1 conda-forge
pickleshare 0.7.5 py37hc8dfbb8_1001 conda-forge
pip 20.0.2 py_2 conda-forge
prompt_toolkit 1.0.15 py_1 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
pycosat 0.6.3 py37h516909a_1002 conda-forge
pycparser 2.19 py37_1 conda-forge
pygments 2.6.1 py_0 conda-forge
pyopenssl 19.1.0 py37_0 conda-forge
pysocks 1.7.1 py37_0 conda-forge
python 3.7.6 h357f687_2 conda-forge
python_abi 3.7 1_cp37m conda-forge
rapidjson 1.1.0 he1b5a44_1002 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.22.0 py37_1 conda-forge
ruamel_yaml 0.15.80 py37h516909a_1000 conda-forge
setuptools 45.2.0 py37_0 conda-forge
simplegeneric 0.8.1 py_1 conda-forge
six 1.14.0 py37_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
tqdm 4.42.1 py_0 conda-forge
traitlets 5.0.4 py_0 conda-forge
urllib3 1.25.7 py37_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_1 conda-forge
wheel 0.34.2 py_1 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
yaml 0.2.2 h516909a_1 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
zstd 1.3.3 1 conda-forge
conda
and system ( conda info
):
$ conda info
(base) root@53232016349f:/# conda info
active environment : base
active env location : /opt/conda
shell level : 1
user config file : /root/.condarc
populated config files : /opt/conda/.condarc
conda version : 4.8.4
conda-build version : not installed
python version : 3.7.6.final.0
virtual packages : __glibc=2.27
base environment : /opt/conda (writable)
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /opt/conda/pkgs
/root/.conda/pkgs
envs directories : /opt/conda/envs
/root/.conda/envs
platform : linux-64
user-agent : conda/4.8.4 requests/2.22.0 CPython/3.7.6 Linux/4.19.76-linuxkit ubuntu/18.04.5 glibc/2.27
UID:GID : 0:0
netrc file : None
offline mode : False
Issue:
I use the cxx-compiler
(gcc 9.3, linux-64, micromamba) to compile and sanitize (with -fsanitize=address
) some code, which used to work well.
Now, installing cxx-compiler
installs gcc 9.3 but libgcc-ng
11.1.0 and I get a linker error
/home/runner/micromamba/envs/undefined/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lasan
Reverting to libgcc-ng
9.3 solves the issue.
Is this the correct behaviour, or should gcc and libgcc-ng
be the same version?
conda list
):
$ conda list
List of packages in environment: "/root/micromamba/envs/ecole"
Name Version Build Channel
──────────────────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge/linux-64
_openmp_mutex 4.5 1_gnu conda-forge/linux-64
alabaster 0.7.12 py_0 conda-forge/noarch
ampl-mp 3.1.0 h616b090_1004 conda-forge/linux-64
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge/noarch
attrs 21.2.0 pyhd8ed1ab_0 conda-forge/noarch
babel 2.9.1 pyh44b312d_0 conda-forge/noarch
backcall 0.2.0 pyh9f0ad1d_0 conda-forge/noarch
backports 1.0 py_2 conda-forge/noarch
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge/noarch
binutils 2.36.1 hdd6e379_1 conda-forge/linux-64
binutils_impl_linux-64 2.36.1 h193b22a_1 conda-forge/linux-64
binutils_linux-64 2.36 hf3e587d_33 conda-forge/linux-64
black 21.7b0 pyhd8ed1ab_0 conda-forge/noarch
bleach 3.3.1 pyhd8ed1ab_0 conda-forge/noarch
breathe 4.30.0 pyhd8ed1ab_0 conda-forge/noarch
brotlipy 0.7.0 py39h3811e60_1001 conda-forge/linux-64
bzip2 1.0.8 h7f98852_4 conda-forge/linux-64
c-ares 1.17.1 h7f98852_1 conda-forge/linux-64
c-compiler 1.2.0 h7f98852_0 conda-forge/linux-64
ca-certificates 2021.5.30 ha878542_0 conda-forge/linux-64
catch2 2.13.6 h4bd325d_0 conda-forge/linux-64
ccache 4.3 haef5404_1 conda-forge/linux-64
certifi 2021.5.30 py39hf3d152e_0 conda-forge/linux-64
cffi 1.14.6 py39he32792d_0 conda-forge/linux-64
cfgv 3.3.0 pyhd8ed1ab_0 conda-forge/noarch
chardet 4.0.0 py39hf3d152e_1 conda-forge/linux-64
charset-normalizer 2.0.0 pyhd8ed1ab_0 conda-forge/noarch
clang 11.1.0 ha770c72_1 conda-forge/linux-64
clang-11 11.1.0 default_ha53f305_1 conda-forge/linux-64
clang-tools 11.1.0 default_ha53f305_1 conda-forge/linux-64
clangxx 11.1.0 default_ha53f305_1 conda-forge/linux-64
cli11 2.0.0 h9c3ff4c_0 conda-forge/linux-64
click 8.0.1 py39hf3d152e_0 conda-forge/linux-64
cmake 3.21.1 h8897547_0 conda-forge/linux-64
cmarkgfm 0.6.0 py39h3811e60_0 conda-forge/linux-64
colorama 0.4.4 pyh9f0ad1d_0 conda-forge/noarch
cppad 20210000.6 h9c3ff4c_0 conda-forge/linux-64
cryptography 3.4.7 py39hbca0aa6_0 conda-forge/linux-64
cxx-compiler 1.2.0 h4bd325d_0 conda-forge/linux-64
dataclasses 0.8 pyhc8e2a94_1 conda-forge/noarch
dbus 1.13.6 h48d8840_2 conda-forge/linux-64
decorator 5.0.9 pyhd8ed1ab_0 conda-forge/noarch
distlib 0.3.2 pyhd8ed1ab_0 conda-forge/noarch
distro 1.5.0 pyh9f0ad1d_0 conda-forge/noarch
docutils 0.16 py39hf3d152e_3 conda-forge/linux-64
doxygen 1.9.1 hb166930_1 conda-forge/linux-64
editdistance-s 1.0.0 py39h1a9c180_1 conda-forge/linux-64
expat 2.4.1 h9c3ff4c_0 conda-forge/linux-64
filelock 3.0.12 pyh9f0ad1d_0 conda-forge/noarch
fmt 8.0.1 h4bd325d_0 conda-forge/linux-64
gcc_impl_linux-64 9.3.0 h70c0ae5_19 conda-forge/linux-64
gcc_linux-64 9.3.0 hf25ea35_33 conda-forge/linux-64
gettext 0.19.8.1 h0b5b191_1005 conda-forge/linux-64
glib 2.68.3 h9c3ff4c_0 conda-forge/linux-64
glib-tools 2.68.3 h9c3ff4c_0 conda-forge/linux-64
gmp 6.2.1 h58526e2_0 conda-forge/linux-64
gxx_impl_linux-64 9.3.0 hd87eabc_19 conda-forge/linux-64
gxx_linux-64 9.3.0 h3fbe746_33 conda-forge/linux-64
identify 2.2.11 pyhd8ed1ab_0 conda-forge/noarch
idna 3.1 pyhd3deb0d_0 conda-forge/noarch
imagesize 1.2.0 py_0 conda-forge/noarch
importlib-metadata 4.6.1 py39hf3d152e_0 conda-forge/linux-64
importlib_metadata 4.6.1 hd8ed1ab_0 conda-forge/noarch
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge/noarch
ipopt 3.14.2 h7ede334_0 conda-forge/linux-64
ipython 7.25.0 py39hef51801_1 conda-forge/linux-64
ipython_genutils 0.2.0 py_1 conda-forge/noarch
jedi 0.18.0 py39hf3d152e_2 conda-forge/linux-64
jeepney 0.7.0 pyhd8ed1ab_0 conda-forge/noarch
jinja2 3.0.1 pyhd8ed1ab_0 conda-forge/noarch
kernel-headers_linux-64 2.6.32 he073ed8_14 conda-forge/noarch
keyring 23.0.1 py39hf3d152e_0 conda-forge/linux-64
krb5 1.19.1 hcc1bbae_0 conda-forge/linux-64
ld_impl_linux-64 2.36.1 hea4e1c9_1 conda-forge/linux-64
libblas 3.9.0 9_openblas conda-forge/linux-64
libcblas 3.9.0 9_openblas conda-forge/linux-64
libclang-cpp11.1 11.1.0 default_ha53f305_1 conda-forge/linux-64
libcurl 7.78.0 h2574ce0_0 conda-forge/linux-64
libedit 3.1.20191231 he28a2e2_2 conda-forge/linux-64
libev 4.33 h516909a_1 conda-forge/linux-64
libffi 3.3 h58526e2_2 conda-forge/linux-64
libgcc-devel_linux-64 9.3.0 h7864c58_19 conda-forge/linux-64
libgcc-ng 11.1.0 hc902ee8_2 conda-forge/linux-64
libgfortran-ng 11.1.0 h69a702a_0 conda-forge/linux-64
libgfortran5 11.1.0 h6c583b3_0 conda-forge/linux-64
libglib 2.68.3 h3e27bee_0 conda-forge/linux-64
libgomp 11.1.0 hc902ee8_2 conda-forge/linux-64
libiconv 1.16 h516909a_0 conda-forge/linux-64
liblapack 3.9.0 9_openblas conda-forge/linux-64
libllvm11 11.1.0 hf817b99_2 conda-forge/linux-64
libnghttp2 1.43.0 h812cca2_0 conda-forge/linux-64
libopenblas 0.3.15 pthreads_h8fe5266_1 conda-forge/linux-64
libssh2 1.9.0 ha56f1ee_6 conda-forge/linux-64
libstdcxx-devel_linux-64 9.3.0 hb016644_19 conda-forge/linux-64
libstdcxx-ng 11.1.0 h56837e0_2 conda-forge/linux-64
libuv 1.42.0 h7f98852_0 conda-forge/linux-64
lz4-c 1.9.3 h9c3ff4c_0 conda-forge/linux-64
make 4.3 hd18ef5c_1 conda-forge/linux-64
markupsafe 2.0.1 py39h3811e60_0 conda-forge/linux-64
matplotlib-inline 0.1.2 pyhd8ed1ab_2 conda-forge/noarch
metis 5.1.0 h58526e2_1006 conda-forge/linux-64
more-itertools 8.8.0 pyhd8ed1ab_0 conda-forge/noarch
mumps-include 5.2.1 ha770c72_10 conda-forge/linux-64
mumps-seq 5.2.1 h47a8eb5_10 conda-forge/linux-64
mypy_extensions 0.4.3 py39hf3d152e_3 conda-forge/linux-64
ncurses 6.2 h58526e2_4 conda-forge/linux-64
ninja 1.10.2 h4bd325d_0 conda-forge/linux-64
nodeenv 1.6.0 pyhd8ed1ab_0 conda-forge/noarch
numpy 1.21.1 py39hdbf815f_0 conda-forge/linux-64
openssl 1.1.1k h7f98852_0 conda-forge/linux-64
packaging 21.0 pyhd8ed1ab_0 conda-forge/noarch
parso 0.8.2 pyhd8ed1ab_0 conda-forge/noarch
pathspec 0.9.0 pyhd8ed1ab_0 conda-forge/noarch
pcre 8.45 h9c3ff4c_0 conda-forge/linux-64
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge/noarch
pickleshare 0.7.5 py39hde42818_1002 conda-forge/linux-64
pip 21.2.1 pyhd8ed1ab_0 conda-forge/noarch
pkginfo 1.7.1 pyhd8ed1ab_0 conda-forge/noarch
pluggy 0.13.1 py39hf3d152e_4 conda-forge/linux-64
pre-commit 2.13.0 py39hf3d152e_0 conda-forge/linux-64
prompt-toolkit 3.0.19 pyha770c72_0 conda-forge/noarch
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge/noarch
py 1.10.0 pyhd3deb0d_0 conda-forge/noarch
pybind11 2.7.0 py39h1a9c180_0 conda-forge/linux-64
pybind11-global 2.7.0 py39h1a9c180_0 conda-forge/linux-64
pycparser 2.20 pyh9f0ad1d_2 conda-forge/noarch
pygments 2.9.0 pyhd8ed1ab_0 conda-forge/noarch
pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge/noarch
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge/noarch
pyscipopt 3.2.2 py39he80948d_0 conda-forge/linux-64
pysocks 1.7.1 py39hf3d152e_3 conda-forge/linux-64
pytest 6.2.4 py39hf3d152e_0 conda-forge/linux-64
pytest-helpers-namespace 2021.4.29 pyhd8ed1ab_0 conda-forge/noarch
python 3.9.6 h49503c6_1_cpython conda-forge/linux-64
python_abi 3.9 2_cp39 conda-forge/linux-64
pytz 2021.1 pyhd8ed1ab_0 conda-forge/noarch
pyyaml 5.4.1 py39h3811e60_0 conda-forge/linux-64
readline 8.1 h46c0cb4_0 conda-forge/linux-64
readme_renderer 27.0 pyh9f0ad1d_0 conda-forge/noarch
regex 2021.7.6 py39h3811e60_0 conda-forge/linux-64
requests 2.26.0 pyhd8ed1ab_0 conda-forge/noarch
requests-toolbelt 0.9.1 py_0 conda-forge/noarch
rfc3986 1.5.0 pyhd8ed1ab_0 conda-forge/noarch
rhash 1.4.1 h7f98852_0 conda-forge/linux-64
scikit-build 0.11.1 py39he80948d_2 conda-forge/linux-64
scip 7.0.3 hf5bcbcd_1 conda-forge/linux-64
scotch 6.0.9 h3858553_1 conda-forge/linux-64
secretstorage 3.3.1 py39hf3d152e_0 conda-forge/linux-64
setuptools 49.6.0 py39hf3d152e_3 conda-forge/linux-64
six 1.16.0 pyh6c4a22f_0 conda-forge/noarch
snowballstemmer 2.1.0 pyhd8ed1ab_0 conda-forge/noarch
sphinx 4.0.3 pyh6c4a22f_0 conda-forge/noarch
sphinx_rtd_theme 0.5.2 pyhd8ed1ab_1 conda-forge/noarch
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge/noarch
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge/noarch
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge/noarch
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge/noarch
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge/noarch
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_0 conda-forge/noarch
sqlite 3.36.0 h9cd32fc_0 conda-forge/linux-64
sysroot_linux-64 2.12 he073ed8_14 conda-forge/noarch
tbb 2020.2 h4bd325d_4 conda-forge/linux-64
tk 8.6.10 h21135ba_1 conda-forge/linux-64
toml 0.10.2 pyhd8ed1ab_0 conda-forge/noarch
tomli 1.1.0 pyhd8ed1ab_0 conda-forge/noarch
tqdm 4.61.2 pyhd8ed1ab_1 conda-forge/noarch
traitlets 5.0.5 py_0 conda-forge/noarch
twine 3.4.2 pyhd8ed1ab_0 conda-forge/noarch
typed-ast 1.4.3 py39h3811e60_0 conda-forge/linux-64
typing_extensions 3.10.0.0 pyha770c72_0 conda-forge/noarch
tzdata 2021a he74cb21_1 conda-forge/noarch
urllib3 1.26.6 pyhd8ed1ab_0 conda-forge/noarch
virtualenv 20.4.7 py39hf3d152e_0 conda-forge/linux-64
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge/noarch
webencodings 0.5.1 py_1 conda-forge/noarch
wheel 0.36.2 pyhd3deb0d_0 conda-forge/noarch
xsimd 7.5.0 h4bd325d_1 conda-forge/linux-64
xtensor 0.23.10 h4bd325d_0 conda-forge/linux-64
xtensor-python 0.25.3 py39h5472131_0 conda-forge/linux-64
xtl 0.7.2 h4bd325d_1 conda-forge/linux-64
xz 5.2.5 h516909a_1 conda-forge/linux-64
yaml 0.2.5 h516909a_0 conda-forge/linux-64
zipp 3.5.0 pyhd8ed1ab_0 conda-forge/noarch
zlib 1.2.11 h516909a_1010 conda-forge/linux-64
zstd 1.5.0 ha95c52a_0 conda-forge/linux-64
conda
and system ( conda info
):
$ conda info
__
__ ______ ___ ____ _____ ___ / /_ ____ _
/ / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
/ /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
/ .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
/_/
environment : ecole (active)
env location : /root/micromamba/envs/ecole
user config files : /root/.mambarc
populated config files :
micromamba version : 0.15.2
virtual packages : __unix=0=0
__linux=5.10.7=0
__glibc=2.31=0
__archspec=1=x86_64
base environment : /root/micromamba
platform : linux-64
xref: https://tracker.ceph.com/issues/51147
xref: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100985
Bad backport as a result of: gcc-mirror/gcc@6f06be1#diff-64cabf812b3706ffd3c5ab7c6048c3617a406f029631d0427d3cfb896fd8dbf3R32
Possible bugfix:
diff --git a/gcc/config/aarch64/arm_acle.h b/gcc/config/aarch64/arm_acle.h
index 29880793bdc..e3185d58a15 100644
--- a/gcc/config/aarch64/arm_acle.h
+++ b/gcc/config/aarch64/arm_acle.h
@@ -29,10 +29,6 @@
#include <stdint.h>
-#ifdef __cplusplus
-extern "C" {
-#endif
-
#pragma GCC push_options
#pragma GCC target ("arch=armv8.3-a")
__extension__ static __inline int32_t __attribute__ ((__always_inline__))
Hello,
I am trying to understand - what all tests and validation are recommended to bring up conda compiler for new architecture.
There are test stage
in meta.yaml for gcc,g++ , others in ctng-compilers-feedstock
and below test coverage in build.sh
.
ctng-compilers-feedstock/recipe/build.sh
Line 112 in 883e60a
# pushd .build/${CHOST}/build/build-cc-gcc-final
# make -k check || true
# popd
are above tests strictly recommended for new architecture ? Any suggestion would really help.
Thank you !
Reference of work:
conda/conda#9791
This is working:
conda create -n test-build6 compilers 'gxx_impl_linux-64=7.5.0=*_6' 'gfortran_impl_linux-64=7.5.0=*_6' pip
conda activate test-build6
pip wheel git+https://github.com/johnlees/glmnet_python.git@94101a0d88cc8a5505e61d97df552b6e5defab7a
While this fails:
conda create -y -n test-build7 compilers 'gxx_impl_linux-64=7.5.0=*_7' 'gfortran_impl_linux-64=7.5.0=*_7' pip
conda activate test-build7
pip wheel git+https://github.com/johnlees/glmnet_python.git@94101a0d88cc8a5505e61d97df552b6e5defab7a
with the following error:
…
copying glmnet_python/loadGlmLib.py -> build/lib.linux-x86_64-3.8/glmnet_python
running build_ext
/home/uwe/miniconda3/envs/test-build7/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lquadmath
collect2: error: ld returned 1 exit status
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-req-build-h1hnpswb/setup.py", line 41, in <module>
setup(name='glmnet_python',
File "/home/uwe/miniconda3/envs/test-build7/lib/python3.8/site-packages/setuptools/__init__.py", line 161, in setup
return distutils.core.setup(**attrs)
File "/home/uwe/miniconda3/envs/test-build7/lib/python3.8/distutils/core.py", line 148, in setup
dist.run_commands()
File "/home/uwe/miniconda3/envs/test-build7/lib/python3.8/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/home/uwe/miniconda3/envs/test-build7/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/home/uwe/miniconda3/envs/test-build7/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 223, in run
self.run_command('build')
File "/home/uwe/miniconda3/envs/test-build7/lib/python3.8/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/uwe/miniconda3/envs/test-build7/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/home/uwe/miniconda3/envs/test-build7/lib/python3.8/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/home/uwe/miniconda3/envs/test-build7/lib/python3.8/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/uwe/miniconda3/envs/test-build7/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-req-build-h1hnpswb/setup.py", line 22, in run
self.build_extension(ext)
File "/tmp/pip-req-build-h1hnpswb/setup.py", line 35, in build_extension
subprocess.check_call(['gfortran', ext.input] + gfortran_args, cwd=self.build_temp, env=env)
File "/home/uwe/miniconda3/envs/test-build7/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['gfortran', '/tmp/pip-req-build-h1hnpswb/glmnet_python/GLMnet.f', '-fPIC', '-fdefault-real-8', '-shared', '-o', '/tmp/pip-req-build-h1hnpswb/glmnet_python/GLMnet.so']' returned non-zero exit status 1.
----------------------------------------
ERROR: Failed building wheel for glmnet-python
Running setup.py clean for glmnet-python
Failed to build glmnet-python
GCC 14 finally finished <chrono>
support (search for P0355R7 here).
We'll need to set _GLIBCXX_ZONEINFO_DIR=$PREFIX/share/zoneinfo
(see here), to point to our own tzdata
, assuming relocation works correctly for the embedded path there. Otherwise we could patch the zoneinfo_dir_override
function to directly load the path from $CONDA_PREFIX
.
When we were working with the Continuum folks during the development of conda-build 3, my colleagues and I suggested rather strongly that -I $PREFIX/include
and the 4 required linking arguments -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -Wl,-disable-new-dtags -L $PREFIX/lib
be built into the configuration of GCC so that when someone does a conda install gcc
and then tries to build something with gcc
it operates like one would expect, treating the conda environment like the 'local' include and lib path and setting things appropriately to use RPATH everywhere.
I don't recall why Ray and Michael stuck with setting *FLAGS
in the activation scripts. To their credit, we have been able to get very far with that. However, to continue polishing the end-user experience, I feel that we should still continue to use the activation scripts for building packages but that their use should be optional for users who just want to compile their own code using conda to install the prerequisites of a C/C++ development environment.
Since you guys moved away from ctng, it is probably easier to do this now. Also, it looks like LLVM/clang has the ability to define configuration files and accomplish the equivalent behavior as the spec-file chicanery required to get the RPATHS by default in GCC. Again, I think it's time to make this work.
@conda-forge/ctng-compilers folks, I'm interested to hear your feedback. I have recipe changes building locally that I'm going to Q/A a bit before opening a PR.
Released today
x86_64-conda-linux-gnu-c++: internal compiler error: Segmentation fault signal terminated program as
Please submit a full bug report,
with preprocessed source if appropriate.
See https://github.com/conda-forge/ctng-compilers-feedstock/issues/new/choose for instructions.
make: *** [/home/twise/projects/moose/framework/build.mk:150: /home/twise/projects/moose/framework/build/unity_src/postprocessors_Unity.x86_64-conda-linux-gnu.opt.lo] Error 1
# packages in environment at /home/twise/mambaforge3/envs/moose:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_sysroot_linux-64_curr_repodata_hack 3 h69a702a_14 conda-forge
alsa-lib 1.2.8 h166bdaf_0 conda-forge
aom 3.5.0 h27087fc_0 conda-forge
arrow-cpp 10.0.1 h3e2b116_4_cpu conda-forge
astroid 3.1.0 py310hff52083_0 conda-forge
atk-1.0 2.38.0 hd4edc92_1 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
autoconf 2.71 pl5321h2b4cb7a_1 conda-forge
automake 1.16.5 pl5321ha770c72_0 conda-forge
aws-c-auth 0.6.21 h774e2f3_1 conda-forge
aws-c-cal 0.5.20 hd3b2fe5_3 conda-forge
aws-c-common 0.8.5 h166bdaf_0 conda-forge
aws-c-compression 0.2.16 hf5f93bc_0 conda-forge
aws-c-event-stream 0.2.16 h52dae97_0 conda-forge
aws-c-http 0.6.29 hf21410f_0 conda-forge
aws-c-io 0.13.11 h4f448d1_2 conda-forge
aws-c-mqtt 0.7.13 hefb3e95_10 conda-forge
aws-c-s3 0.2.1 h2b8044a_2 conda-forge
aws-c-sdkutils 0.1.7 hf5f93bc_0 conda-forge
aws-checksums 0.1.14 h6027aba_0 conda-forge
aws-crt-cpp 0.18.16 h89864ff_5 conda-forge
aws-sdk-cpp 1.9.379 hc894300_6 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
binutils_impl_linux-64 2.39 he00db2b_1 conda-forge
binutils_linux-64 2.39 h5fc0e48_13 conda-forge
bison 3.4 h58526e2_1 conda-forge
blosc 1.21.5 h0f2a231_0 conda-forge
brotli 1.0.9 h166bdaf_9 conda-forge
brotli-bin 1.0.9 h166bdaf_9 conda-forge
brotli-python 1.0.9 py310hd8f1fbe_9 conda-forge
brunsli 0.1 h9c3ff4c_0 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.28.1 hd590300_0 conda-forge
c-blosc2 2.12.0 hb4ffafa_0 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cairo 1.16.0 ha61ee94_1014 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cfitsio 4.1.0 hd9d235c_0 conda-forge
charls 2.3.4 h9c3ff4c_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
clang 12.0.1 ha770c72_0 conda-forge
clang-12 12.0.1 default_ha53f305_0 conda-forge
clang-format 14.0.6 default_h7634d5b_1 conda-forge
clang-format-14 14.0.6 default_h7634d5b_1 conda-forge
clang-tools 12.0.1 default_ha53f305_0 conda-forge
clangxx 12.0.1 default_ha53f305_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge
cmake 3.25.1 h816a3e0_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
contourpy 1.2.1 py310hd41b1e2_0 conda-forge
curl 7.86.0 h7bff187_1 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
cytoolz 0.12.3 py310h2372a71_0 conda-forge
dask-core 2024.4.2 pyhd8ed1ab_0 conda-forge
dav1d 1.0.0 h166bdaf_1 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
deepdiff 7.0.1 pyhd8ed1ab_0 conda-forge
dill 0.3.8 pyhd8ed1ab_0 conda-forge
double-conversion 3.2.0 h27087fc_1 conda-forge
eigen 3.4.0 h00ab1b0_0 conda-forge
elfutils 0.188 hde5d1a3_1 conda-forge
expat 2.6.2 h59595ed_0 conda-forge
ffmpeg 4.4.2 gpl_h8dda1f0_112 conda-forge
fftw 3.3.10 nompi_hc118613_108 conda-forge
flex 2.6.4 h58526e2_1004 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.51.0 py310h2372a71_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
fsspec 2024.3.1 pyhca7485f_0 conda-forge
gcc 10.4.0 hb92f740_13 conda-forge
gcc_impl_linux-64 10.4.0 h5231bdf_19 conda-forge
gcc_linux-64 10.4.0 h9215b83_13 conda-forge
gdk-pixbuf 2.42.8 hff1cb4f_1 conda-forge
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
gfortran 10.4.0 h0c96582_13 conda-forge
gfortran_impl_linux-64 10.4.0 h7d168d2_19 conda-forge
gfortran_linux-64 10.4.0 h69d5af5_13 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
git-lfs 3.5.1 ha770c72_0 conda-forge
gitdb 4.0.11 pyhd8ed1ab_0 conda-forge
gitpython 3.1.43 pyhd8ed1ab_0 conda-forge
gl2ps 1.4.2 h0708190_0 conda-forge
glew 2.1.0 h9c3ff4c_2 conda-forge
glib 2.80.0 hf2295e7_6 conda-forge
glib-tools 2.80.0 hde27a5a_6 conda-forge
glog 0.6.0 h6f12383_0 conda-forge
gmp 6.3.0 h59595ed_1 conda-forge
gmpy2 2.1.2 py310h3ec546c_1 conda-forge
gnutls 3.7.9 hb077bed_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
graphviz 7.0.5 h2e5815a_0 conda-forge
gst-plugins-base 1.21.3 h4243ec0_1 conda-forge
gstreamer 1.21.3 h25f0c4b_1 conda-forge
gstreamer-orc 0.4.38 hd590300_0 conda-forge
gtk2 2.24.33 h90689f9_2 conda-forge
gts 0.7.6 h977cf35_4 conda-forge
gxx 10.4.0 hb92f740_13 conda-forge
gxx_impl_linux-64 10.4.0 h5231bdf_19 conda-forge
gxx_linux-64 10.4.0 h6e491c6_13 conda-forge
harfbuzz 6.0.0 h8e241bc_0 conda-forge
hdf4 4.2.15 h9772cbc_5 conda-forge
hdf5 1.12.1 mpi_mpich_h08b82f9_4 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.7 pyhd8ed1ab_0 conda-forge
imagecodecs 2022.7.31 py310hfa28e48_1 conda-forge
imagecodecs-lite 2019.12.3 py310h1f7b6fc_7 conda-forge
imageio 2.34.1 pyh4b66e23_0 conda-forge
importlib-metadata 7.1.0 pyha770c72_0 conda-forge
importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge
isort 5.13.2 pyhd8ed1ab_0 conda-forge
jack 1.9.22 h11f4161_0 conda-forge
jinja2 3.1.3 pyhd8ed1ab_0 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
jsoncpp 1.9.5 h4bd325d_1 conda-forge
jxrlib 1.1 hd590300_3 conda-forge
kernel-headers_linux-64 3.10.0 h4a8ded7_14 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py310hd41b1e2_1 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
latexcodec 2.0.1 pyh9f0ad1d_0 conda-forge
lazy_loader 0.4 pyhd8ed1ab_0 conda-forge
lcms2 2.14 h6ed2654_0 conda-forge
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20220623.0 cxx17_h05df665_6 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libarchive 3.6.2 hc8874e4_0 conda-forge
libarrow 10.0.1 hee49ebd_4_cpu conda-forge
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libavif 0.10.1 h5cdd6b5_2 conda-forge
libblas 3.9.0 22_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_9 conda-forge
libbrotlidec 1.0.9 h166bdaf_9 conda-forge
libbrotlienc 1.0.9 h166bdaf_9 conda-forge
libcap 2.66 ha37c62d_0 conda-forge
libcblas 3.9.0 22_linux64_openblas conda-forge
libclang 15.0.7 default_h127d8a8_5 conda-forge
libclang-cpp12 12.0.1 default_ha53f305_4 conda-forge
libclang-cpp14 14.0.6 default_h7634d5b_1 conda-forge
libclang13 15.0.7 default_h5d6823c_5 conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcups 2.3.3 h3e49a29_2 conda-forge
libcurl 7.86.0 h7bff187_1 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.13 h166bdaf_0 conda-forge
libdrm 2.4.120 hd590300_0 conda-forge
libdrm-cos7-x86_64 2.4.97 h9b0a68f_1105 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-devel_linux-64 10.4.0 hd38fd1e_19 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgd 2.3.3 h18fbbfe_3 conda-forge
libgettextpo 0.22.5 h59595ed_2 conda-forge
libgettextpo-devel 0.22.5 h59595ed_2 conda-forge
libgfortran-ng 13.1.0 h69a702a_0 conda-forge
libgfortran5 13.1.0 h15d22d2_0 conda-forge
libglib 2.80.0 hf2295e7_6 conda-forge
libglu 9.0.0 he1b5a44_1001 conda-forge
libglvnd-cos7-x86_64 1.0.1 h9b0a68f_1105 conda-forge
libglvnd-glx-cos7-x86_64 1.0.1 h9b0a68f_1105 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
libgoogle-cloud 2.5.0 h5d50b59_1 conda-forge
libgpg-error 1.48 h71f35ed_0 conda-forge
libgrpc 1.51.1 h05bd8bd_0 conda-forge
libhwloc 2.9.1 hd6dc26d_0 conda-forge
libice-cos7-x86_64 1.0.9 h9b0a68f_1105 conda-forge
libice-devel-cos7-x86_64 1.0.9 h9b0a68f_1105 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libidn2 2.3.7 hd590300_0 conda-forge
liblapack 3.9.0 22_linux64_openblas conda-forge
libllvm12 12.0.1 hf817b99_2 conda-forge
libllvm14 14.0.6 hcd5def8_4 conda-forge
libllvm15 15.0.7 hadd5161_1 conda-forge
libmicrohttpd 0.9.77 h97afed2_0 conda-forge
libnetcdf 4.8.1 mpi_mpich_hcdf9059_2 conda-forge
libnghttp2 1.51.0 hdcd2b5c_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpciaccess 0.18 hd590300_0 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libpq 15.1 hf695f80_1 conda-forge
libprotobuf 3.21.12 hfc55251_2 conda-forge
librsvg 2.54.4 h7abd40a_0 conda-forge
libsanitizer 10.4.0 h5246dfb_19 conda-forge
libsm-cos7-x86_64 1.2.2 h9b0a68f_1105 conda-forge
libsm-devel-cos7-x86_64 1.2.2 h9b0a68f_1105 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsqlite 3.45.2 h2797004_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-devel_linux-64 10.4.0 hd38fd1e_19 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libsystemd0 252 h2a991cd_0 conda-forge
libtasn1 4.19.0 h166bdaf_0 conda-forge
libtheora 1.1.1 h7f98852_1005 conda-forge
libthrift 0.16.0 h491838f_2 conda-forge
libtiff 4.4.0 h0e0dad5_3 conda-forge
libtool 2.4.7 h27087fc_0 conda-forge
libudev1 253 h0b41bf4_0 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libutf8proc 2.8.0 h166bdaf_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.48.0 hd590300_0 conda-forge
libva 2.18.0 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libvpx 1.11.0 h9c3ff4c_3 conda-forge
libwebp 1.2.4 h522a892_0 conda-forge
libwebp-base 1.2.4 h166bdaf_0 conda-forge
libx11-common-cos7-x86_64 1.6.7 h9b0a68f_1105 conda-forge
libx11-cos7-x86_64 1.6.7 h9b0a68f_1105 conda-forge
libx11-devel-cos7-x86_64 1.6.7 h9b0a68f_1105 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxext-cos7-x86_64 1.3.3 h9b0a68f_1105 conda-forge
libxext-devel-cos7-x86_64 1.3.3 h9b0a68f_1105 conda-forge
libxkbcommon 1.5.0 h79f4944_1 conda-forge
libxml2 2.10.3 hca2bb57_4 conda-forge
libxslt 1.1.37 h873f0b0_0 conda-forge
libxt-cos7-x86_64 1.1.5 h9b0a68f_1105 conda-forge
libxt-devel-cos7-x86_64 1.1.5 h9b0a68f_1105 conda-forge
libzip 1.9.2 hc869a4a_1 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
libzopfli 1.0.3 h9c3ff4c_0 conda-forge
livereload 2.6.3 pyh9f0ad1d_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
loguru 0.7.2 py310hff52083_1 conda-forge
lxml 4.9.2 py310hbdc0903_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h516909a_1000 conda-forge
m4 1.4.18 h516909a_1001 conda-forge
make 4.3 hd18ef5c_1 conda-forge
mako 1.3.3 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py310h2372a71_0 conda-forge
matplotlib 3.8.4 py310hff52083_0 conda-forge
matplotlib-base 3.8.4 py310h62c0568_0 conda-forge
mccabe 0.7.0 pyhd8ed1ab_0 conda-forge
mesa-khr-devel-cos7-x86_64 18.3.4 h9b0a68f_1105 conda-forge
mesa-libgl-cos7-x86_64 18.3.4 h9b0a68f_1105 conda-forge
mesa-libgl-devel-cos7-x86_64 18.3.4 h9b0a68f_1105 conda-forge
mesa-libglapi-cos7-x86_64 18.3.4 h9b0a68f_1105 conda-forge
mesalib 23.0.0 h0fe20ba_0 conda-forge
mock 5.1.0 pyhd8ed1ab_0 conda-forge
moose-dev 2024.04.12 build_0 https://conda.software.inl.gov/public
moose-libmesh 2024.04.03 build_1 https://conda.software.inl.gov/public
moose-libmesh-vtk 9.2.6 build_9 https://conda.software.inl.gov/public
moose-mpich 4.0.2 build_16 https://conda.software.inl.gov/public
moose-peacock 2023.04.11 hb6770a3_0 https://conda.software.inl.gov/public
moose-petsc 3.20.3 build_1 https://conda.software.inl.gov/public
moose-tools 2024.04.12 h4a78fc2_0 https://conda.software.inl.gov/public
moose-wasp 2024.03.15 build_0 https://conda.software.inl.gov/public
mpc 1.3.1 hfe3b2da_0 conda-forge
mpfr 4.2.1 h9458935_1 conda-forge
mpg123 1.32.6 h59595ed_0 conda-forge
mpi 1.0 mpich conda-forge
mpich 4.0.2 h846660c_100 conda-forge
mpich-mpicc 4.0.2 hb600da9_100 conda-forge
mpich-mpicxx 4.0.2 h166bdaf_100 conda-forge
mpich-mpifort 4.0.2 h924138e_100 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.32 h14678bc_0 conda-forge
mysql-libs 8.0.32 h54cf53e_0 conda-forge
ncurses 6.4.20240210 h59595ed_0 conda-forge
nettle 3.9.1 h7ab15ed_0 conda-forge
networkx 3.3 pyhd8ed1ab_1 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.98 h1d7d5a4_0 conda-forge
numpy 1.26.4 py310hb13e2d6_0 conda-forge
openh264 2.3.1 hcb278e6_2 conda-forge
openjpeg 2.5.0 h7d73246_1 conda-forge
openssl 1.1.1w hd590300_0 conda-forge
orc 1.8.2 hfdbbad2_2 conda-forge
ordered-set 4.1.0 pyhd8ed1ab_0 conda-forge
orjson 3.10.1 py310hcb5633a_0 conda-forge
p11-kit 0.24.1 hc5aa10d_0 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
pandas 2.2.2 py310hcc13569_0 conda-forge
pango 1.50.14 hd33c08f_0 conda-forge
parquet-cpp 1.5.1 2 conda-forge
partd 1.4.1 pyhd8ed1ab_0 conda-forge
pcre2 10.43 hcad00b1_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pillow 9.2.0 py310h454ad03_3 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
pkg-config 0.29.2 h36c2ea0_1008 conda-forge
platformdirs 4.2.0 pyhd8ed1ab_0 conda-forge
ply 3.11 pyhd8ed1ab_2 conda-forge
proj 9.0.1 h93bde94_1 conda-forge
psycopg2 2.9.3 py310h416cc33_2 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pugixml 1.11.4 h59595ed_1 conda-forge
pulseaudio 16.1 h4ab2085_1 conda-forge
pyaml 24.4.0 pyhd8ed1ab_0 conda-forge
pyarrow 10.0.1 py310hf2f6370_4_cpu conda-forge
pybtex 0.24.0 pyhd8ed1ab_2 conda-forge
pycobertura 3.3.1 pyhd8ed1ab_0 conda-forge
pyflakes 3.2.0 pyhd8ed1ab_0 conda-forge
pylatexenc 2.10 pyhd8ed1ab_0 conda-forge
pylint 3.1.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pyqt 5.15.7 py310hab646b1_3 conda-forge
pyqt5-sip 12.11.0 py310heca2aa9_3 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.8 h257c98d_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.10 4_cp310 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pywavelets 1.4.1 py310h1f7b6fc_1 conda-forge
pyyaml 6.0.1 py310h2372a71_1 conda-forge
qt-main 5.15.6 h25460bb_4 conda-forge
re2 2022.06.01 h27087fc_1 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rhash 1.4.3 hd590300_2 conda-forge
ruamel.yaml 0.18.6 py310h2372a71_0 conda-forge
ruamel.yaml.clib 0.2.8 py310h2372a71_0 conda-forge
s2n 1.3.30 hae46d1a_0 conda-forge
scikit-image 0.22.0 py310hcc13569_2 conda-forge
scipy 1.13.0 py310hb13e2d6_0 conda-forge
setuptools 59.8.0 py310hff52083_1 conda-forge
sip 6.7.12 py310hc6cd4ac_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smmap 5.0.0 pyhd8ed1ab_0 conda-forge
snappy 1.1.10 hdb0a2a9_1 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sqlite 3.45.2 h2c6b66d_0 conda-forge
svt-av1 1.4.1 hcb278e6_0 conda-forge
sympy 1.12 pypyh9d50eac_103 conda-forge
sysroot_linux-64 2.17 h4a8ded7_14 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
tbb 2021.9.0 hf52228f_0 conda-forge
tbb-devel 2021.9.0 hf52228f_0 conda-forge
tifffile 2022.10.10 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tomlkit 0.12.4 pyha770c72_0 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tornado 6.4 py310h2372a71_0 conda-forge
typing-extensions 4.11.0 hd8ed1ab_0 conda-forge
typing_extensions 4.11.0 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
unicodedata2 15.1.0 py310h2372a71_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
utfcpp 4.0.5 ha770c72_0 conda-forge
vtk 9.1.0 qt_py310hb71b3df_211 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
x264 1!164.3095 h166bdaf_2 conda-forge
x265 3.5 h924138e_3 conda-forge
xcb-util 0.4.0 h516909a_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h516909a_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h516909a_0 conda-forge
xkeyboard-config 2.38 h0b41bf4_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-damageproto 1.2.1 h7f98852_1002 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-glproto 1.4.17 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.8.4 h0b41bf4_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdamage 1.1.5 h7f98852_1 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxrandr 1.5.2 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.3.0 hd590300_0 conda-forge
xorg-randrproto 1.5.0 h7f98852_1001 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-util-macros 1.19.3 h7f98852_0 conda-forge
xorg-x11-proto-devel-cos7-x86_64 2018.4 h9b0a68f_1105 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zfp 0.5.5 h9c3ff4c_8 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
active environment : moose
active env location : /home/twise/mambaforge3/envs/moose
shell level : 2
user config file : /home/twise/.condarc
populated config files : /home/twise/mambaforge3/.condarc
/home/twise/.condarc
conda version : 24.1.2
conda-build version : not installed
python version : 3.10.14.final.0
solver : libmamba (default)
virtual packages : __archspec=1=skylake
__conda=24.1.2=0
__cuda=11.4=0
__glibc=2.35=0
__linux=6.5.0=0
__unix=0=0
base environment : /home/twise/mambaforge3 (writable)
conda av data dir : /home/twise/mambaforge3/etc/conda
conda av metadata url : None
channel URLs : https://conda.software.inl.gov/public/linux-64
https://conda.software.inl.gov/public/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/twise/mambaforge3/pkgs
/home/twise/.conda/pkgs
envs directories : /home/twise/mambaforge3/envs
/home/twise/.conda/envs
platform : linux-64
user-agent : conda/24.1.2 requests/2.31.0 CPython/3.10.14 Linux/6.5.0-28-generic ubuntu/22.04.4 glibc/2.35 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.7
UID:GID : 1000:1000
netrc file : None
offline mode : False
cc @beckermr
In Matplotlib, we're running into an issue when using conda-forge compilers that some symbols in compiled extensions are missing.
A straightforward reproducer is to do the following:
$ git clone https://github.com/matplotlib/matplotlib
$ micromamba create -f environment.yml compilers
$ pip install --no-build-isolation --editable .
$ python -c 'import matplotlib'
which ends up failing as:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/elliott/code/matplotlib/lib/matplotlib/__init__.py", line 159, in <module>
from . import _api, _version, cbook, _docstring, rcsetup
File "/home/elliott/code/matplotlib/lib/matplotlib/rcsetup.py", line 28, in <module>
from matplotlib.colors import Colormap, is_color_like
File "/home/elliott/code/matplotlib/lib/matplotlib/colors.py", line 57, in <module>
from matplotlib import _api, _cm, cbook, scale
File "/home/elliott/code/matplotlib/lib/matplotlib/scale.py", line 22, in <module>
from matplotlib.ticker import (
File "/home/elliott/code/matplotlib/lib/matplotlib/ticker.py", line 144, in <module>
from matplotlib import transforms as mtransforms
File "/home/elliott/code/matplotlib/lib/matplotlib/transforms.py", line 49, in <module>
from matplotlib._path import (
ImportError: /home/elliott/code/matplotlib/build/cp39/src/_path.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZN3agg10curve3_div4initEdddddd
This missing symbol (_ZN3agg10curve3_div4initEdddddd
= agg::curve3_div::init(double, double, double, double, double, double)
) is part of a static library that is built into the extension shared library, except it disappeared with the conda-forge compilers. If you build the library with verbose settings (by passing --config-settings=compile-args=-v -v
to pip
), then you can find a warning somewhere in there that points to gcc-ar
plugins:
...
[58/101] rm -f extern/agg24-svn/libagg.a && /home/elliott/micromamba/envs/mpl-dev2/bin/x86_64-conda-linux-gnu-ar csrDT extern/agg24-svn/libagg.a extern/agg24-svn/libagg.a.p/src_agg_bezier_arc.cpp.o extern/agg24-svn/libagg.a.p/src_agg_curves.cpp.o extern/agg24-svn/libagg.a.p/src_agg_image_filters.cpp.o extern/agg24-svn/libagg.a.p/src_agg_trans_affine.cpp.o extern/agg24-svn/libagg.a.p/src_agg_vcgen_contour.cpp.o extern/agg24-svn/libagg.a.p/src_agg_vcgen_dash.cpp.o extern/agg24-svn/libagg.a.p/src_agg_vcgen_stroke.cpp.o extern/agg24-svn/libagg.a.p/src_agg_vpgen_segmentator.cpp.o
/home/elliott/micromamba/envs/mpl-dev2/bin/x86_64-conda-linux-gnu-ar: extern/agg24-svn/libagg.a.p/src_agg_bezier_arc.cpp.o: plugin needed to handle lto object
...
[61/101] rm -f extern/ttconv/libttconv.a && /home/elliott/micromamba/envs/mpl-dev2/bin/x86_64-conda-linux-gnu-ar csrDT extern/ttconv/libttconv.a extern/ttconv/libttconv.a.p/pprdrv_tt2.cpp.o extern/ttconv/libttconv.a.p/pprdrv_tt.cpp.o extern/ttconv/libttconv.a.p/ttutil.cpp.o
/home/elliott/micromamba/envs/mpl-dev2/bin/x86_64-conda-linux-gnu-ar: extern/ttconv/libttconv.a.p/pprdrv_tt2.cpp.o: plugin needed to handle lto object
...
[71/101] rm -f subprojects/freetype-2.6.1/libfreetype.a && /home/elliott/micromamba/envs/mpl-dev2/bin/x86_64-conda-linux-gnu-ar csrDT subprojects/freetype-2.6.1/libfreetype.a subprojects/freetype-2.6.1/libfreetype.a.p/src_autofit_autofit.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftbase.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftbbox.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftbdf.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftbitmap.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftcid.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftfntfmt.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftfstype.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftgasp.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftglyph.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftgxval.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftinit.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftlcdfil.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftmm.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftotval.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftpatent.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftpfr.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftstroke.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftsynth.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftsystem.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_fttype1.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftwinfnt.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_bdf_bdf.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_bzip2_ftbzip2.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_cache_ftcache.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_cff_cff.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_cid_type1cid.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_gzip_ftgzip.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_lzw_ftlzw.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_pcf_pcf.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_pfr_pfr.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_psaux_psaux.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_pshinter_pshinter.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_psnames_psnames.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_raster_raster.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_sfnt_sfnt.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_smooth_smooth.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_truetype_truetype.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_type1_type1.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_type42_type42.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_winfonts_winfnt.c.o subprojects/freetype-2.6.1/libfreetype.a.p/src_base_ftdebug.c.o
/home/elliott/micromamba/envs/mpl-dev2/bin/x86_64-conda-linux-gnu-ar: subprojects/freetype-2.6.1/libfreetype.a.p/src_autofit_autofit.c.o: plugin needed to handle lto object
...
[74/101] rm -f subprojects/qhull-8.0.2/libqhull_r.a && /home/elliott/micromamba/envs/mpl-dev2/bin/x86_64-conda-linux-gnu-ar csrDT subprojects/qhull-8.0.2/libqhull_r.a subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_geom2_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_geom_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_global_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_io_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_libqhull_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_mem_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_merge_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_poly2_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_poly_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_qset_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_random_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_rboxlib_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_stat_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_usermem_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_userprintf_rbox_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_userprintf_r.c.o subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_user_r.c.o
/home/elliott/micromamba/envs/mpl-dev2/bin/x86_64-conda-linux-gnu-ar: subprojects/qhull-8.0.2/libqhull_r.a.p/src_libqhull_r_geom2_r.c.o: plugin needed to handle lto object
While I as able to reproduce locally, this also appears on the update to the feedstock at conda-forge/matplotlib-feedstock#373.
cc @jakirkham and @dopplershift
Name Version Build Channel
─────────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
accessible-pygments 0.0.4 pyhd8ed1ab_0 conda-forge
adwaita-icon-theme 46.2 unix_0 conda-forge
alabaster 0.7.16 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.11 hd590300_1 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
at-spi2-atk 2.38.0 h0630a04_3 conda-forge
at-spi2-core 2.40.3 h0630a04_0 conda-forge
atk-1.0 2.38.0 h04ea711_2 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
binutils 2.40 h4852527_2 conda-forge
binutils_impl_linux-64 2.40 ha1999f0_2 conda-forge
binutils_linux-64 2.40 hdade7a5_3 conda-forge
black 23.12.1 py39hf3d152e_0 conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py39h3d6467e_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.28.1 hd590300_0 conda-forge
c-compiler 1.7.0 hd590300_1 conda-forge
ca-certificates 2024.6.2 hbcca054_0 conda-forge
cachetools 5.3.3 pyhd8ed1ab_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
cairocffi 1.7.0 pypyhd8ed1ab_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py39h7a31438_0 conda-forge
cfgv 3.3.1 pyhd8ed1ab_0 conda-forge
chardet 5.2.0 py39hf3d152e_1 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
colorspacious 1.1.2 pyh24bf2e0_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
compilers 1.7.0 ha770c72_1 conda-forge
contourpy 1.2.1 py39h7633fee_0 conda-forge
coverage 7.5.3 py39hd3abc70_0 conda-forge
cxx-compiler 1.7.0 h00ab1b0_1 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.8.1 py39h3d6467e_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
distlib 0.3.8 pyhd8ed1ab_0 conda-forge
docutils 0.21.2 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
epoxy 1.5.10 h166bdaf_1 conda-forge
exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge
execnet 2.1.1 pyhd8ed1ab_0 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.6.2 h59595ed_0 conda-forge
filelock 3.14.0 pyhd8ed1ab_0 conda-forge
flake8 7.0.0 pyhd8ed1ab_0 conda-forge
flake8-docstrings 1.7.0 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_2 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.53.0 py39hd3abc70_0 conda-forge
fortran-compiler 1.7.0 heb67821_1 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fribidi 1.0.10 h516909a_0 conda-forge
gcc 12.3.0 h915e2ae_7 conda-forge
gcc_impl_linux-64 12.3.0 h58ffeeb_7 conda-forge
gcc_linux-64 12.3.0 h6477408_3 conda-forge
gdk-pixbuf 2.42.12 hb9ae30d_0 conda-forge
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
gfortran 12.3.0 h915e2ae_7 conda-forge
gfortran_impl_linux-64 12.3.0 h1645026_7 conda-forge
gfortran_linux-64 12.3.0 h617cb40_3 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
glib 2.80.2 hf974151_0 conda-forge
glib-tools 2.80.2 hb6ce0ca_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
graphviz 11.0.0 hc68bbd7_0 conda-forge
gst-plugins-base 1.24.4 h9ad1361_0 conda-forge
gstreamer 1.24.4 haf2f30d_0 conda-forge
gtk2 2.24.33 h280cfa0_4 conda-forge
gtk3 3.24.42 h6d40eaa_0 conda-forge
gtk4 4.12.1 h0210e61_3 conda-forge
gts 0.7.6 h977cf35_4 conda-forge
gxx 12.3.0 h915e2ae_7 conda-forge
gxx_impl_linux-64 12.3.0 h2a574ab_7 conda-forge
gxx_linux-64 12.3.0 h4a1b8e8_3 conda-forge
harfbuzz 8.5.0 hfac3d4d_0 conda-forge
hicolor-icon-theme 0.17 ha770c72_2 conda-forge
icu 73.2 h59595ed_0 conda-forge
identify 2.5.36 pyhd8ed1ab_0 conda-forge
idna 3.7 pyhd8ed1ab_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.1.0 pyha770c72_0 conda-forge
importlib-resources 6.4.0 pyhd8ed1ab_0 conda-forge
importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.3 pyhd33586a_0 conda-forge
ipython 8.18.1 pyh707e725_3 conda-forge
ipywidgets 8.1.3 pyhd8ed1ab_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 py39hf3d152e_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge
jupyterlab_widgets 3.0.11 pyhd8ed1ab_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_17 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py39h7633fee_1 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_2 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libblas 3.9.0 22_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 22_linux64_openblas conda-forge
libclang-cpp15 15.0.7 default_h127d8a8_5 conda-forge
libclang13 18.1.6 default_h5d6823c_0 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.8.0 hca28451_0 conda-forge
libdeflate 1.20 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-devel_linux-64 12.3.0 h0223996_107 conda-forge
libgcc-ng 13.2.0 h77fa898_7 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgd 2.3.3 h119a65a_9 conda-forge
libgettextpo 0.22.5 h59595ed_2 conda-forge
libgettextpo-devel 0.22.5 h59595ed_2 conda-forge
libgfortran-ng 13.2.0 h69a702a_7 conda-forge
libgfortran5 13.2.0 hca663fb_7 conda-forge
libgirepository 1.80.1 h003a4f0_0 conda-forge
libglib 2.80.2 hf974151_0 conda-forge
libgomp 13.2.0 h77fa898_7 conda-forge
libgpg-error 1.49 h4f305b6_0 conda-forge
libgraphene 1.10.8 hc02c970_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 22_linux64_openblas conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
libllvm18 18.1.6 hb77312f_0 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libpq 16.3 ha72fbe1_0 conda-forge
librsvg 2.58.0 hadf69e7_1 conda-forge
libsanitizer 12.3.0 hb8811af_7 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsodium 1.0.18 h516909a_1 conda-forge
libsqlite 3.45.3 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-devel_linux-64 12.3.0 h0223996_107 conda-forge
libstdcxx-ng 13.2.0 hc0a3c3a_7 conda-forge
libsystemd0 255 h3516f8a_1 conda-forge
libtiff 4.6.0 h1dd3fc0_3 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 he1b5a44_0 conda-forge
libwebp 1.4.0 h2c329e2_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.7.0 h662e7e4_0 conda-forge
libxml2 2.12.7 hc051c1a_1 conda-forge
libzlib 1.3.1 h4ab18f5_1 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
markupsafe 2.1.5 py39hd1e30aa_0 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
mccabe 0.7.0 pyhd8ed1ab_0 conda-forge
meson 1.4.0 pyhd8ed1ab_0 conda-forge
meson-python 0.16.0 pyh0c530f3_0 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
mpg123 1.32.6 h59595ed_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mypy_extensions 1.0.0 pyha770c72_0 conda-forge
mysql-common 8.3.0 hf1915f5_4 conda-forge
mysql-libs 8.3.0 hca2cd23_4 conda-forge
nbclient 0.10.0 pyhd8ed1ab_0 conda-forge
nbconvert 7.16.4 hd8ed1ab_0 conda-forge
nbconvert-core 7.16.4 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.16.4 hd8ed1ab_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
ncurses 6.5 h59595ed_0 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
ninja 1.12.1 h297d8ca_0 conda-forge
nodeenv 1.9.1 pyhd8ed1ab_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.100 hca3bf56_0 conda-forge
numpy 1.26.4 py39h474f0d3_0 conda-forge
numpydoc 1.7.0 pyhd8ed1ab_1 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openssl 3.3.1 h4ab18f5_0 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
pandas 2.2.2 py39hfc16268_1 conda-forge
pandoc 3.2 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
pango 1.52.2 ha41ecd1_0 conda-forge
parso 0.8.4 pyhd8ed1ab_0 conda-forge
pathspec 0.12.1 pyhd8ed1ab_0 conda-forge
pcre2 10.43 hcad00b1_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.3.0 py39h90c7501_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
pkg-config 0.29.2 h516909a_1008 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge
pluggy 1.5.0 pyhd8ed1ab_0 conda-forge
ply 3.11 pyhd8ed1ab_2 conda-forge
pre-commit 3.7.1 pyha770c72_0 conda-forge
prompt-toolkit 3.0.46 pyha770c72_0 conda-forge
psutil 5.9.8 py39hd1e30aa_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio-client 17.0 hb77b528_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pybind11 2.12.0 py39h7633fee_0 conda-forge
pybind11-global 2.12.0 py39h7633fee_0 conda-forge
pycairo 1.26.0 py39hc92de75_0 conda-forge
pycodestyle 2.11.1 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pydata-sphinx-theme 0.15.3 pyhd8ed1ab_0 conda-forge
pydocstyle 6.3.0 pyhd8ed1ab_0 conda-forge
pyflakes 3.2.0 pyhd8ed1ab_0 conda-forge
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pygobject 3.48.2 py39hb25b1be_0 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pyproject-api 1.6.1 pyhd8ed1ab_0 conda-forge
pyproject-metadata 0.8.0 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py39h52134e7_5 conda-forge
pyqt5-sip 12.12.2 py39h3d6467e_5 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytest 8.2.2 pyhd8ed1ab_0 conda-forge
pytest-cov 5.0.0 pyhd8ed1ab_0 conda-forge
pytest-rerunfailures 14.0 pyhd8ed1ab_0 conda-forge
pytest-timeout 2.3.1 pyhd8ed1ab_1 conda-forge
pytest-xdist 3.5.0 pyhd8ed1ab_0 conda-forge
python 3.9.19 h0755675_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.19.1 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.9 4_cp39 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py39hd1e30aa_1 conda-forge
pyzmq 26.0.3 py39ha1047a2_0 conda-forge
qt-main 5.15.8 hc9dc06e_21 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.35.1 pyhd8ed1ab_0 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
rpds-py 0.18.1 py39ha68c5e3_0 conda-forge
setuptools 70.0.0 pyhd8ed1ab_0 conda-forge
setuptools-scm 8.1.0 pyhd8ed1ab_0 conda-forge
setuptools_scm 8.1.0 hd8ed1ab_0 conda-forge
sip 6.7.12 py39h3d6467e_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sphinx 7.3.7 pyhd8ed1ab_0 conda-forge
sphinx-copybutton 0.5.2 pyhd8ed1ab_0 conda-forge
sphinx-design 0.5.0 pyhd8ed1ab_0 conda-forge
sphinx-gallery 0.16.0 pyhd8ed1ab_0 conda-forge
sphinx-tags 0.3.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 1.0.8 pyhd8ed1ab_0 conda-forge
sphinxcontrib-devhelp 1.0.6 pyhd8ed1ab_0 conda-forge
sphinxcontrib-htmlhelp 2.0.5 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-qthelp 1.0.7 pyhd8ed1ab_0 conda-forge
sphinxcontrib-serializinghtml 1.1.10 pyhd8ed1ab_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
sysroot_linux-64 2.12 he073ed8_17 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.4 py39hd1e30aa_0 conda-forge
tox 4.15.0 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
typing-extensions 4.12.1 hd8ed1ab_0 conda-forge
typing_extensions 4.12.1 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
ukkonen 1.0.1 py39h7633fee_4 conda-forge
unicodedata2 15.1.0 py39hd1e30aa_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
virtualenv 20.26.2 pyhd8ed1ab_0 conda-forge
wayland 1.23.0 h5291e77_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.11 pyhd8ed1ab_0 conda-forge
wxpython 4.2.1 py39h3eb26e4_6 conda-forge
wxwidgets 3.2.5 h91e79f6_0 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.41 hd590300_0 conda-forge
xorg-compositeproto 0.4.2 h7f98852_1001 conda-forge
xorg-damageproto 1.2.1 h516909a_1002 conda-forge
xorg-fixesproto 5.0 h14c3975_1002 conda-forge
xorg-inputproto 2.3.2 h14c3975_1002 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.9 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxcomposite 0.4.6 h0b41bf4_1 conda-forge
xorg-libxcursor 1.2.0 h0b41bf4_1 conda-forge
xorg-libxdamage 1.1.5 h7f98852_1 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxinerama 1.1.5 h27087fc_0 conda-forge
xorg-libxrandr 1.5.2 h7f98852_1 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-libxxf86vm 1.1.5 h0b41bf4_0 conda-forge
xorg-randrproto 1.5.0 h516909a_1001 conda-forge
xorg-recordproto 1.14.2 h516909a_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-util-macros 1.19.3 h7f98852_0 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h516909a_1002 conda-forge
xorg-xineramaproto 1.2.1 h14c3975_1001 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zeromq 4.3.5 h75354e8_4 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 h4ab18f5_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
libmamba version : 1.5.6
micromamba version : 1.5.6
curl version : libcurl/8.6.0 OpenSSL/3.2.1 zlib/1.3.0.zlib-ng libidn2/2.3.7 nghttp2/1.59.0
libarchive version : libarchive 3.7.2 zlib/1.3.0.zlib-ng liblzma/5.4.6 bz2lib/1.0.8 liblz4/1.9.4 libzstd/1.5.6
envs directories : /home/elliott/micromamba/envs
package cache : /home/elliott/micromamba/pkgs
/home/elliott/.mamba/pkgs
environment : mpl-dev2 (active)
env location : /home/elliott/micromamba/envs/mpl-dev2
user config files : /home/elliott/.mambarc
populated config files :
virtual packages : __unix=0=0
__linux=6.8.11=0
__glibc=2.39=0
__archspec=1=x86_64-v3
channels :
base environment : /home/elliott/micromamba
platform : linux-64
Issue: With the environment below, I cannot compile a simple test program. Once I conda update -all
to a new env, getting the latest builds of the compilers, it works.
The updated env is
# packages in environment at /opt/conda:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
apipkg 1.5 py_0 conda-forge
apr 1.6.5 h516909a_2 conda-forge
asteval 0.9.16 pyh5ca1d4c_0 conda-forge
astropy 3.2.3 py37h516909a_0 conda-forge
atomicwrites 1.4.0 pyh9f0ad1d_0 conda-forge
attrs 19.3.0 py_0 conda-forge
binutils-meta 1.0.4 0 conda-forge
binutils_impl_linux-64 2.34 h53a641e_0 conda-forge
binutils_linux-64 2.34 hc952b39_20 conda-forge
blosc 1.15.0 hd408876_0 defaults
boost 1.69.0 py37h8619c78_1001 conda-forge
boost-cpp 1.69.0 ha2d47e9_1001 conda-forge
brotlipy 0.7.0 py37h8f50634_1000 conda-forge
bzip2 1.0.8 h516909a_2 conda-forge
c-compiler 1.0.4 h516909a_0 conda-forge
ca-certificates 2020.4.5.1 hecc5488_0 conda-forge
certifi 2020.4.5.1 py37hc8dfbb8_0 conda-forge
cffi 1.14.0 py37hd463f26_0 conda-forge
chardet 3.0.4 py37hc8dfbb8_1006 conda-forge
cmake 3.17.0 h28c56e5_0 conda-forge
conda 4.8.3 py37hc8dfbb8_1 conda-forge
conda-package-handling 1.6.0 py37h8f50634_2 conda-forge
coverage 5.1 py37h8f50634_0 conda-forge
cryptography 2.9.2 py37hb09aad4_0 conda-forge
curl 7.69.1 h33f0ec9_0 conda-forge
cxx-compiler 1.0.4 hc9558a2_0 conda-forge
cycler 0.10.0 py_2 conda-forge
dbus 1.13.6 he372182_0 conda-forge
deprecated 1.2.10 pyh9f0ad1d_0 conda-forge
doxygen 1.8.13 1 conda-forge
eigen 3.3.7 hc9558a2_1001 conda-forge
emcee 3.0.2 pyh5ca1d4c_0 conda-forge
esutil 0.6.4 py37hb3f55d8_0 conda-forge
execnet 1.7.1 py_0 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
fftw 3.3.8 nompi_h7f3a6c3_1110 conda-forge
fitsio 1.1.2 py37h04524ed_0 conda-forge
flake8 3.8.1 pyh9f0ad1d_0 conda-forge
flake8-polyfill 1.0.2 py_0 conda-forge
fontconfig 2.13.1 he4413a7_1000 conda-forge
freetype 2.10.2 he06d7ca_0 conda-forge
future 0.18.2 py37hc8dfbb8_1 conda-forge
galsim 2.2.2 py37hb745460_1 conda-forge
gcc_impl_linux-64 7.5.0 hd420e75_6 conda-forge
gcc_linux-64 7.5.0 h09487f9_20 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
git 2.26.2 pl526h5e3e691_0 conda-forge
glib 2.64.2 h6f030ca_1 conda-forge
gsl 2.6 h294904e_0 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
gxx_impl_linux-64 7.5.0 hdf63c60_6 conda-forge
gxx_linux-64 7.5.0 h09487f9_20 conda-forge
h5py 2.9.0 nompi_py37h513d04c_1104 conda-forge
hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge
healpy 1.12.10 py37hf476568_0 conda-forge
hypothesis 5.15.0 py_0 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 2.9 py_1 conda-forge
importlib-metadata 1.6.0 py37hc8dfbb8_0 conda-forge
importlib_metadata 1.6.0 0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
kiwisolver 1.2.0 py37h99015e2_0 conda-forge
krb5 1.17.1 h2fd8d38_0 conda-forge
ld_impl_linux-64 2.34 h53a641e_0 conda-forge
libapr 1.6.5 h516909a_2 conda-forge
libapriconv 1.2.2 h516909a_2 conda-forge
libaprutil 1.6.1 ha1d75be_2 conda-forge
libblas 3.8.0 16_openblas conda-forge
libcblas 3.8.0 16_openblas conda-forge
libcurl 7.69.1 hf7181ac_0 conda-forge
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.5.0 hdf63c60_6 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
libiconv 1.15 h516909a_1006 conda-forge
liblapack 3.8.0 16_openblas conda-forge
libllvm8 8.0.1 hc9558a2_0 conda-forge
libopenblas 0.3.9 h5ec1e0e_0 conda-forge
libpng 1.6.37 hed695b0_1 conda-forge
libssh2 1.9.0 hab1572f_2 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libuv 1.34.0 h516909a_0 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.9 h13577e0_2 conda-forge
llvm-openmp 10.0.0 hc9558a2_0 conda-forge
llvmlite 0.31.0 py37h5202443_1 conda-forge
lmfit 1.0.0 py_0 conda-forge
log4cxx 0.10.0 h66fa5af_2 conda-forge
lsstdesc.coord 1.2.1 py37h99015e2_0 conda-forge
lsstdesc.weaklensingdeblending 0.4 py37_0 conda-forge
m4 1.4.18 h14c3975_1001 conda-forge
make 4.3 h516909a_0 conda-forge
matplotlib 3.0.3 py37_1 conda-forge
matplotlib-base 3.0.3 py37h5f35d83_1 conda-forge
mccabe 0.6.1 py_1 conda-forge
meds 0.9.10 py37h03ebfcd_1 conda-forge
more-itertools 8.3.0 py_0 conda-forge
mpi 1.0 mpich conda-forge
mpi4py 3.0.3 py37h0c5ec45_1 conda-forge
mpich 3.3.1 hc856adb_1 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
ndarray 1.5.3 h75f6862_1 conda-forge
ngmix 1.3.7 py37_0 conda-forge
numba 0.48.0 py37hb3f55d8_0 conda-forge
numexpr 2.6.9 py37h637b7d7_1000 conda-forge
numpy 1.16.2 py37h8b7e671_1 conda-forge
openssl 1.1.1g h516909a_0 conda-forge
packaging 20.1 py_0 conda-forge
pandas 0.24.2 py37hb3f55d8_1 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pep8-naming 0.10.0 pyh9f0ad1d_0 conda-forge
perl 5.26.2 h516909a_1006 conda-forge
pip 20.1.1 pyh9f0ad1d_0 conda-forge
pluggy 0.13.1 py37hc8dfbb8_1 conda-forge
psutil 5.7.0 py37h8f50634_1 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
py 1.8.1 py_0 conda-forge
pybind11 2.2.4 py37hc9558a2_1001 conda-forge
pycodestyle 2.6.0 pyh9f0ad1d_0 conda-forge
pycosat 0.6.3 py37h8f50634_1004 conda-forge
pycparser 2.20 py_0 conda-forge
pyflakes 2.2.0 pyh9f0ad1d_0 conda-forge
pyopenssl 19.1.0 py_1 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyqt 5.9.2 py37hcca6a23_4 conda-forge
pysocks 1.7.1 py37hc8dfbb8_1 conda-forge
pytest 4.6.4 py37_0 conda-forge
pytest-arraydiff 0.3 py_0 conda-forge
pytest-astropy 0.7.0 py_0 conda-forge
pytest-astropy-header 0.1.2 py_0 conda-forge
pytest-cov 2.8.1 py_0 conda-forge
pytest-doctestplus 0.6.1 pyh9f0ad1d_0 conda-forge
pytest-flake8 1.0.6 pyh9f0ad1d_0 conda-forge
pytest-forked 1.1.2 py_0 conda-forge
pytest-openfiles 0.4.0 py_0 conda-forge
pytest-remotedata 0.3.1 py_0 conda-forge
pytest-runner 5.2 py_0 conda-forge
pytest-xdist 1.32.0 pyh9f0ad1d_0 conda-forge
python 3.7.6 h8356626_5_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.7 1_cp37m conda-forge
pytz 2020.1 pyh9f0ad1d_0 conda-forge
pyyaml 5.3.1 py37h8f50634_0 conda-forge
qt 5.9.7 h52cfd70_2 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.23.0 pyh8c360ce_2 conda-forge
rhash 1.3.6 h14c3975_1001 conda-forge
ruamel_yaml 0.15.80 py37h8f50634_1001 conda-forge
schwimmbad 0.3.1 py37hc8dfbb8_0 conda-forge
scikit-learn 0.20.3 py37ha8026db_1 conda-forge
scipy 1.2.1 py37h09a28d5_1 conda-forge
setuptools 46.4.0 py37hc8dfbb8_0 conda-forge
setuptools-scm 3.5.0 pyh9f0ad1d_2 conda-forge
setuptools_scm 3.5.0 2 conda-forge
sip 4.19.8 py37hf484d3e_1000 conda-forge
six 1.14.0 py_1 conda-forge
snappy 1.1.7 he1b5a44_1003 conda-forge
sortedcontainers 2.1.0 py_0 conda-forge
sqlalchemy 1.3.17 py37h8f50634_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
stackvana 2019.44w py37_0 stackvana
stackvana-core-impl 2019.44w py37hf484d3e_0 stackvana
starlink-ast 8.7.2 h516909a_0 conda-forge
tini 0.18.0 h14c3975_1001 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
toml 0.10.1 pyh9f0ad1d_0 conda-forge
tornado 6.0.4 py37h8f50634_1 conda-forge
tqdm 4.46.0 pyh9f0ad1d_0 conda-forge
treecorr 3.3.11 py37hf484d3e_1001 conda-forge
uncertainties 3.1.2 py37_0 conda-forge
urllib3 1.25.9 py_0 conda-forge
wcwidth 0.1.9 pyh9f0ad1d_0 conda-forge
wheel 0.34.2 py_1 conda-forge
wrapt 1.12.1 py37h8f50634_1 conda-forge
ws4py 0.5.1 py_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xpa 2.1.19 he1b5a44_0 conda-forge
xz 5.2.5 h516909a_0 conda-forge
yaml 0.2.4 h516909a_0 conda-forge
zipp 3.1.0 py_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
conda list
):
$ conda list
# packages in environment at /opt/conda:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 0_gnu conda-forge
apipkg 1.5 py_0 conda-forge
apr 1.6.5 h516909a_2 conda-forge
asteval 0.9.16 pyh5ca1d4c_0 conda-forge
astropy 3.2.3 py37h516909a_0 conda-forge
atomicwrites 1.3.0 py_0 conda-forge
attrs 19.3.0 py_0 conda-forge
binutils-meta 1.0.4 0 conda-forge
binutils_impl_linux-64 2.33.1 h53a641e_8 conda-forge
binutils_linux-64 2.33.1 h9595d00_17 conda-forge
blosc 1.15.0 hd408876_0 defaults
boost 1.69.0 py37h8619c78_1001 conda-forge
boost-cpp 1.69.0 ha2d47e9_1001 conda-forge
bzip2 1.0.8 h516909a_2 conda-forge
c-compiler 1.0.4 h516909a_0 conda-forge
ca-certificates 2020.4.5.1 hecc5488_0 conda-forge
certifi 2020.4.5.1 py37hc8dfbb8_0 conda-forge
cffi 1.13.2 py37h8022711_0 conda-forge
chardet 3.0.4 py37_1003 conda-forge
cmake 3.17.0 h28c56e5_0 conda-forge
conda 4.8.3 py37hc8dfbb8_1 conda-forge
conda-package-handling 1.6.0 py37h516909a_1 conda-forge
coverage 5.1 py37h8f50634_0 conda-forge
cryptography 2.8 py37h72c5cf5_1 conda-forge
curl 7.69.1 h33f0ec9_0 conda-forge
cxx-compiler 1.0.4 hc9558a2_0 conda-forge
cycler 0.10.0 py_2 conda-forge
dbus 1.13.6 he372182_0 conda-forge
deprecated 1.2.8 pyh9f0ad1d_0 conda-forge
doxygen 1.8.13 1 conda-forge
eigen 3.3.7 hc9558a2_1001 conda-forge
emcee 3.0.2 pyh5ca1d4c_0 conda-forge
entrypoints 0.3 py37hc8dfbb8_1001 conda-forge
esutil 0.6.4 py37hb3f55d8_0 conda-forge
execnet 1.7.1 py_0 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
fftw 3.3.8 nompi_h7f3a6c3_1110 conda-forge
fitsio 1.1.1 py37h2d70e6e_2 conda-forge
flake8 3.7.9 py37hc8dfbb8_1 conda-forge
flake8-polyfill 1.0.2 py_0 conda-forge
fontconfig 2.13.1 he4413a7_1000 conda-forge
freetype 2.10.1 he06d7ca_0 conda-forge
future 0.18.2 py37hc8dfbb8_1 conda-forge
galsim 2.2.2 py37hb745460_1 conda-forge
gcc_impl_linux-64 7.3.0 hd420e75_5 conda-forge
gcc_linux-64 7.3.0 h553295d_17 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
git 2.26.2 pl526h5e3e691_0 conda-forge
glib 2.64.2 h6f030ca_0 conda-forge
gsl 2.6 h294904e_0 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
gxx_impl_linux-64 7.3.0 hdf63c60_5 conda-forge
gxx_linux-64 7.3.0 h553295d_17 conda-forge
h5py 2.9.0 nompi_py37h513d04c_1104 conda-forge
hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge
healpy 1.12.10 py37hf476568_0 conda-forge
hypothesis 5.10.4 py_0 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 2.8 py37_1000 conda-forge
importlib-metadata 1.6.0 py37hc8dfbb8_0 conda-forge
importlib_metadata 1.6.0 0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
kiwisolver 1.2.0 py37h99015e2_0 conda-forge
krb5 1.17.1 h2fd8d38_0 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_8 conda-forge
libapr 1.6.5 h516909a_2 conda-forge
libapriconv 1.2.2 h516909a_2 conda-forge
libaprutil 1.6.1 ha1d75be_2 conda-forge
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libcurl 7.69.1 hf7181ac_0 conda-forge
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.3.0 hdf63c60_5 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
libiconv 1.15 h516909a_1006 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libllvm8 8.0.1 hc9558a2_0 conda-forge
libopenblas 0.3.7 h5ec1e0e_6 conda-forge
libpng 1.6.37 hed695b0_1 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libuv 1.34.0 h516909a_0 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.9 h13577e0_2 conda-forge
llvmlite 0.31.0 py37h5202443_1 conda-forge
lmfit 1.0.0 py_0 conda-forge
log4cxx 0.10.0 h66fa5af_2 conda-forge
lsstdesc.coord 1.2.1 py37h99015e2_0 conda-forge
lsstdesc.weaklensingdeblending 0.4 py37_0 conda-forge
m4 1.4.18 h14c3975_1001 conda-forge
make 4.3 h516909a_0 conda-forge
matplotlib 3.0.3 py37_1 conda-forge
matplotlib-base 3.0.3 py37h5f35d83_1 conda-forge
mccabe 0.6.1 py_1 conda-forge
meds 0.9.10 py37h03ebfcd_1 conda-forge
more-itertools 8.2.0 py_0 conda-forge
mpi 1.0 mpich conda-forge
mpi4py 3.0.3 py37h0c5ec45_1 conda-forge
mpich 3.3.1 hc856adb_1 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
ndarray 1.5.3 h75f6862_1 conda-forge
ngmix 1.3.7 py37_0 conda-forge
numba 0.48.0 py37hb3f55d8_0 conda-forge
numexpr 2.6.9 py37h637b7d7_1000 conda-forge
numpy 1.16.2 py37h8b7e671_1 conda-forge
openssl 1.1.1g h516909a_0 conda-forge
packaging 20.1 py_0 conda-forge
pandas 0.24.2 py37hb3f55d8_1 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pep8-naming 0.10.0 pyh9f0ad1d_0 conda-forge
perl 5.26.2 h516909a_1006 conda-forge
pip 20.0.2 py_2 conda-forge
pluggy 0.13.0 py37_0 conda-forge
psutil 5.7.0 py37h8f50634_1 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
py 1.8.1 py_0 conda-forge
pybind11 2.2.4 py37hc9558a2_1001 conda-forge
pycodestyle 2.5.0 py_0 conda-forge
pycosat 0.6.3 py37h516909a_1002 conda-forge
pycparser 2.19 py37_1 conda-forge
pyflakes 2.1.1 py_0 conda-forge
pyopenssl 19.1.0 py37_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyqt 5.9.2 py37hcca6a23_4 conda-forge
pysocks 1.7.1 py37_0 conda-forge
pytest 4.6.4 py37_0 conda-forge
pytest-arraydiff 0.3 py_0 conda-forge
pytest-astropy 0.7.0 py_0 conda-forge
pytest-astropy-header 0.1.2 py_0 conda-forge
pytest-cov 2.8.1 py_0 conda-forge
pytest-doctestplus 0.4.0 py_0 conda-forge
pytest-flake8 1.0.5 pyh9f0ad1d_0 conda-forge
pytest-forked 1.1.2 py_0 conda-forge
pytest-openfiles 0.4.0 py_0 conda-forge
pytest-remotedata 0.3.1 py_0 conda-forge
pytest-runner 5.2 py_0 conda-forge
pytest-xdist 1.31.0 py_0 conda-forge
python 3.7.6 h357f687_2 conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.7 1_cp37m conda-forge
pytz 2019.3 py_0 conda-forge
pyyaml 5.3.1 py37h8f50634_0 conda-forge
qt 5.9.7 h52cfd70_2 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.22.0 py37_1 conda-forge
rhash 1.3.6 h14c3975_1001 conda-forge
ruamel_yaml 0.15.80 py37h516909a_1000 conda-forge
schwimmbad 0.3.1 py37hc8dfbb8_0 conda-forge
scikit-learn 0.20.3 py37ha8026db_1 conda-forge
scipy 1.2.1 py37h09a28d5_1 conda-forge
setuptools 45.2.0 py37_0 conda-forge
setuptools-scm 3.5.0 py_1 conda-forge
setuptools_scm 3.5.0 1 conda-forge
sip 4.19.8 py37hf484d3e_1000 conda-forge
six 1.14.0 py37_0 conda-forge
snappy 1.1.7 he1b5a44_1003 conda-forge
sortedcontainers 2.1.0 py_0 conda-forge
sqlalchemy 1.3.16 py37h8f50634_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
stackvana 2019.44w py37_0 stackvana
stackvana-core-impl 2019.44w py37hf484d3e_0 stackvana
starlink-ast 8.7.2 h516909a_0 conda-forge
tini 0.18.0 h14c3975_1001 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
tornado 6.0.4 py37h8f50634_1 conda-forge
tqdm 4.42.1 py_0 conda-forge
treecorr 3.3.11 py37hf484d3e_1001 conda-forge
uncertainties 3.1.2 py37_0 conda-forge
urllib3 1.25.7 py37_0 conda-forge
wcwidth 0.1.9 pyh9f0ad1d_0 conda-forge
wheel 0.34.2 py_1 conda-forge
wrapt 1.12.1 py37h8f50634_1 conda-forge
ws4py 0.5.1 py_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xpa 2.1.19 he1b5a44_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
yaml 0.2.2 h516909a_1 conda-forge
zipp 3.1.0 py_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
conda
and system ( conda info
):
$ conda info
active environment : base
active env location : /opt/conda
shell level : 1
user config file : /root/.condarc
populated config files : /opt/conda/.condarc
/root/.condarc
conda version : 4.8.3
conda-build version : not installed
python version : 3.7.6.final.0
virtual packages : __glibc=2.27
base environment : /opt/conda (writable)
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /opt/conda/pkgs
/root/.conda/pkgs
envs directories : /opt/conda/envs
/root/.conda/envs
platform : linux-64
user-agent : conda/4.8.3 requests/2.22.0 CPython/3.7.6 Linux/4.19.76-linuxkit ubuntu/18.04.4 glibc/2.27
UID:GID : 0:0
netrc file : None
offline mode : False
No response
The new compilers work fine now, but the CDT packages don't work now.
@isuruf and @beckermr, My team is hitting a bug in GCC 7.3 on linux and we'd like to see conda-forge update to something that has it fixed. I see that you have some work in progress on the https://github.com/conda-forge/ctng-compilers-feedstock/tree/libgcc-and-libstdcxx-9 branch to get things updated to 9.2.
What's left to be done there? I don't see gcc 9.x packages on anaconda.org yet. Perhaps I'm looking in the wrong place. Could I or someone on my team help push it the rest of the way?
@conda-forge-admin, please update team
No response
It seems that Ubuntu 22.04 doesn't play well with openGL from conda-forge.
mamba create --name dev --channel conda-forge --override-channels matplotlib --yes
mamba activate dev
python -c "from matplotlib import pyplot as plt; plt.plot(range(5)); plt.show()"
libGL error: MESA-LOADER: failed to open iris: /usr/lib/dri/iris_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open iris: /usr/lib/dri/iris_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: swrast
While the plot shows up, other hardware accelerate stuff (like using vispy) doesn't work. I didn't know where else to post this so I figured I would post it to matplotlib since it seems to have rather high visibility into these issues.
# packages in environment at /home/mark/mambaforge/envs/dev:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
alsa-lib 1.2.3 h516909a_0 conda-forge
brotli 1.0.9 h166bdaf_7 conda-forge
brotli-bin 1.0.9 h166bdaf_7 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
certifi 2021.10.8 py310hff52083_2 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
expat 2.4.8 h27087fc_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.32.0 py310h5764c6d_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
gst-plugins-base 1.20.1 hcf0ee16_1 conda-forge
gstreamer 1.20.1 hd4edc92_1 conda-forge
icu 69.1 h9c3ff4c_0 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jpeg 9e h7f98852_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.2 py310hbf28c38_1 conda-forge
krb5 1.19.3 h08a2579_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 14_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_7 conda-forge
libbrotlidec 1.0.9 h166bdaf_7 conda-forge
libbrotlienc 1.0.9 h166bdaf_7 conda-forge
libcblas 3.9.0 14_linux64_openblas conda-forge
libclang 13.0.1 default_hc23dcda_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libevent 2.1.10 h28343ad_4 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 11.2.0 h1d223b6_15 conda-forge
libgfortran-ng 11.2.0 h69a702a_15 conda-forge
libgfortran5 11.2.0 h5c6108e_15 conda-forge
libglib 2.70.2 h174f98d_4 conda-forge
libgomp 11.2.0 h1d223b6_15 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 14_linux64_openblas conda-forge
libllvm13 13.0.1 hf817b99_2 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libpq 14.2 h676c864_0 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_15 conda-forge
libtiff 4.3.0 h542a066_3 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.12 h885dcf4_1 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
matplotlib 3.5.1 py310hff52083_0 conda-forge
matplotlib-base 3.5.1 py310h23f4a51_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.28 h26416b9_3 conda-forge
mysql-libs 8.0.28 hbc51c84_3 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
nspr 4.32 h9c3ff4c_1 conda-forge
nss 3.77 h2350873_0 conda-forge
numpy 1.22.3 py310h45f3432_2 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 3.0.2 h166bdaf_1 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pillow 9.1.0 py310he619898_0 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyparsing 3.0.8 pyhd8ed1ab_0 conda-forge
pyqt 5.12.3 py310hff52083_8 conda-forge
pyqt-impl 5.12.3 py310h1f8e252_8 conda-forge
pyqt5-sip 4.19.18 py310h122e73d_8 conda-forge
pyqtchart 5.12 py310hfcd6d55_8 conda-forge
pyqtwebengine 5.12.1 py310hfcd6d55_8 conda-forge
python 3.10.4 h2660328_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 2_cp310 conda-forge
qt 5.12.9 h1304e3e_6 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
setuptools 62.0.0 py310hff52083_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.37.1 h4ff8645_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tornado 6.1 py310h5764c6d_3 conda-forge
tzdata 2022a h191b570_0 conda-forge
unicodedata2 14.0.0 py310h5764c6d_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h166bdaf_1014 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
active environment : dev
active env location : /home/mark/mambaforge/envs/dev
shell level : 2
user config file : /home/mark/.condarc
populated config files : /home/mark/mambaforge/.condarc
/home/mark/.condarc
conda version : 4.12.0
conda-build version : 3.21.8
python version : 3.9.12.final.0
virtual packages : __linux=5.15.0=0
__glibc=2.35=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/mark/mambaforge (writable)
conda av data dir : /home/mark/mambaforge/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/mark.harfouche/linux-64
https://conda.anaconda.org/mark.harfouche/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/mark/mambaforge/pkgs
/home/mark/.conda/pkgs
envs directories : /home/mark/mambaforge/envs
/home/mark/.conda/envs
platform : linux-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/5.15.0-25-generic ubuntu/22.04 glibc/2.35
UID:GID : 1000:1000
netrc file : None
offline mode : False
xref: conda-forge/matplotlib-feedstock#318
My solution was to delete the files
libstdc++.so libstdc++.so.6 libstdc++.so.6.0.28-gdb.py libstdc++.so.6.0.29
And let things fall back on the the libstdc++.so
provided by ubuntu. seems to work :/
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