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atlas-orca plugin for Atlas, providing support for ORCA grids and mesh generation

License: Apache License 2.0

CMake 7.15% C++ 90.77% C 0.30% Python 1.78%

atlas-orca's People

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twsearle djdavies2 raguridan matthewrmshin mircovalentiniecmwf

atlas-orca's Issues

NETCDF_LIBRARIES keeps appending

What happened?

Things seem to be working for me, but doing incremental builds of atlas-orca results in the NETCDF_LIBRARIES cmake variable being appended, and so it keeps growing with each incremental build. The builds still work, but it would be nice if it didn't happen.

What are the steps to reproduce the bug?

atlas-orca is included in a bundle, the bundle isn't public unfortunately.

There is a find_package( NetCDF REQUIRED COMPONENTS C CXX Fortran ) in the bundle CMakelists.txt, I don't know if that makes a difference?

Version

develop

Platform (OS and architecture)

Cray

Relevant log output

-- Adding bundle project atlas-orca
-- ---------------------------------------------------------
-- �[32m[atlas-orca] (0.1.1) [37615b6]�[m
-- Feature TESTS enabled
-- Found OpenMP: TRUE (found version "4.5") found components: CXX 
-- Found NetCDF: /home/d00/darth/opt/bb-stack/cray_gnu-v28/include (found version "4.9.2") found components: CXX Fortran 
-- FindNetCDF defines targets:
--   - NetCDF_VERSION [4.9.2]
--   - NetCDF_PARALLEL [TRUE]
--   - NetCDF_C_CONFIG_EXECUTABLE [/home/d00/darth/opt/bb-stack/cray_gnu-v28/bin/nc-config]
--   - NetCDF::NetCDF_C [SHARED] [Root: /home/d00/darth/opt/bb-stack/cray_gnu-v28] Lib: /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so 
--   - NetCDF_CXX_CONFIG_EXECUTABLE [/home/d00/darth/opt/bb-stack/cray_gnu-v28/bin/ncxx4-config]
--   - NetCDF::NetCDF_CXX [SHARED] [Root: /home/d00/darth/opt/bb-stack/cray_gnu-v28] Lib: /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so 
--   - NetCDF_Fortran_CONFIG_EXECUTABLE [/home/d00/darth/opt/bb-stack/cray_gnu-v28/bin/nf-config]
--   - NetCDF::NetCDF_Fortran [SHARED] [Root: /home/d00/darth/opt/bb-stack/cray_gnu-v28] Lib: /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so 
-- atlas-orca FOUND NetCDF (found version "4.9.2")
--    NetCDF_INCLUDE_DIRS : [/home/d00/darth/opt/bb-stack/cray_gnu-v28/include]
--    NETCDF_LIBRARIES : [/home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdf_c++4.so /home/d00/darth/opt/bb-stack/cray_gnu-v28/lib64/libnetcdff.so]
-- Feature NETCDF enabled

Accompanying data

No response

Organisation

Met Office

Cannot build atlas-orca standalone; cannot find NetCDF

I am trying to build atlas-orca standalone, it is failing like this:

CMake Error at /home/h01/frwd/cylc-run/mi-be204/share/installs/ecbuild/share/ecbuild/cmake/ecbuild_log.cmake:190 (message):
�[1;35mCRITICAL - Feature NETCDF cannot be enabled -- following required
packages weren't found: NetCDF�[m
Call Stack (most recent call first):
/home/h01/frwd/cylc-run/mi-be204/share/installs/ecbuild/share/ecbuild/cmake/ecbuild_add_option.cmake:260 (ecbuild_critical)
src/apps/atlas-orca-convert/CMakeLists.txt:16 (ecbuild_add_option)

My NetCDF is built in separate directories for C, C++ and Fortran. The relevant NetCDF -config scripts are in the $PATH.

I think this can be fixed by using a tweaked find NetCDF script (such as that used by jedi-cmake) but is there another alternative?

Using ATLAS_DATA_PATH no longer works

What happened?

Nightly tests at the met office failed with:

Downloading https://get.ecmwf.int/repository/atlas/grids/orca/v0/ORCA2_T.atlas to /home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/share/atlas/grids/orca/unknown/ORCA2_T.atlas ...
[31mTest "test orca grid iterator (section: ORCA2_T)" failed with unhandled eckit::Exception: Could not download file from url https://get.ecmwf.int/repository/atlas/grids/orca/v0/ORCA2_T.atlas @  (/home/h05/tsearle/cylc-run/bb_mo_test/share/mo-bundle/atlas-orca/src/atlas-orca/util/OrcaDataFile.h +92 OrcaDataFile)
....

We are using the ATLAS_DATA_PATH environment variable to define the path to our local cache of grid data as our operational systems are isolated from the internet. We suspect the issue might be related to yesterdays change in: f0b9d2d

It looks like this changes some URLs which now are not in the search path:
https://github.com/ecmwf/atlas-orca/blob/develop/src/atlas-orca/util/ComputeCachedPath.h#L49

What are the steps to reproduce the bug?

Run atlas-orca tests without the grid data cached and without connection to the internet.

Version

v0.0.1

Platform (OS and architecture)

Met Office HPC

Relevant log output

Running section "ORCA2_T" ...
Downloading https://get.ecmwf.int/repository/atlas/grids/orca/v0/ORCA2_T.atlas to /home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/share/atlas/grids/orca/unknown/ORCA2_T.atlas ...
[0] �[31mTest "test orca grid iterator (section: ORCA2_T)" failed with unhandled eckit::Exception: Could not download file from url https://get.ecmwf.int/repository/atlas/grids/orca/v0/ORCA2_T.atlas @  (/home/h05/tsearle/cylc-run/bb_mo_test/share/mo-bundle/atlas-orca/src/atlas-orca/util/OrcaDataFile.h +92 OrcaDataFile)�[0m
[0]     Stack trace: backtrace [2] stack has 18 addresses
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/lib/libeckit.so+eckit::BackTrace::dump[abi:cxx11]())0x1b0 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/lib/libeckit.so+eckit::Exception::Exception(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, eckit::CodeLocation const&))0x92 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/lib/libatlas.so.0.32+atlas::throw_Exception(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, eckit::CodeLocation const&))0x26 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/lib/libatlas-orca.so+atlas::orca::OrcaDataFile::OrcaDataFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&))0x1e2c 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/lib/libatlas-orca.so+atlas::grid::detail::grid::Orca::Orca(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, atlas::util::Config const&))0x49f 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/lib/libatlas-orca.so+atlas::grid::detail::grid::Orca::Orca(atlas::util::Config const&))0xb4 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/lib/libatlas-orca.so+atlas::grid::detail::grid::OrcaGridBuilder::create(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, atlas::util::Config const&) const)0x25e 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/lib/libatlas.so.0.32+atlas::grid::detail::grid::Grid::create(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, atlas::util::Config const&))0x50 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/lib/libatlas.so.0.32+atlas::Grid::Grid(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, atlas::Domain const&))0xbc 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/lib/libatlas-orca.so+atlas::OrcaGrid::OrcaGrid(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&))0x2e 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/atlas-orca/src/tests/atlas_test_orca_grid) 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/atlas-orca/src/tests/atlas_test_orca_grid) 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/atlas-orca/src/tests/atlas_test_orca_grid) 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/atlas-orca/src/tests/atlas_test_orca_grid) 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/atlas-orca/src/tests/atlas_test_orca_grid) 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/atlas-orca/src/tests/atlas_test_orca_grid) 
[0] (/usr/lib64/libc.so.6+__libc_start_main)0xf5 
[0] (/home/h05/tsearle/cylc-run/bb_mo_test/share/build-mo-spice_gnu/atlas-orca/src/tests/atlas_test_orca_grid)

Accompanying data

No response

Organisation

MetOffice

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