markus-goetz / hpdbscan Goto Github PK

Sender: LSF System <[email protected]>
...
Started at Sat Jul 10 21:30:59 2021
Terminated at Sat Jul 10 21:31:04 2021
Results reported at Sat Jul 10 21:31:04 2021

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
# this file was automaticly created by mpisubmit.pl script for edu-cmc-sqi20-05 #
#BSUB -n 1
#BSUB -W 00:15
#BSUB -o hpdbscan.%J.out
#BSUB -e hpdbscan.%J.err
OMP_NUM_THREADS=1 mpiexec ./hpdbscan -t 1 -i /home_edu/edu-cmc-sqi20/edu-cmc-sqi20-05/my/ClusterLog_HPDBSCAN/ClusterLog/test/scadi.h5 --input-dataset DBSCAN -o data.h5 --output-dataset CLUSTERS -e 1.3 -m 2

------------------------------------------------------------

Exited with exit code 139.

Resource usage summary:

    CPU time :                                   1.32 sec.
    Max Memory :                                 119 MB
    Average Memory :                             79.67 MB
    Total Requested Memory :                     -
    Delta Memory :                               -
    Max Swap :                                   -
    Max Processes :                              5
    Max Threads :                                13
    Run time :                                   9 sec.
    Turnaround time :                            5 sec.

The output (if any) follows:

Computing cell space
        Computing dimensions...[OK] in 0.000053
        Computing cells...     [OK] in 0.000047
        Sorting points...

PS:

Read file <hpdbscan.765884.err> for stderr output of this job.

[polus-c4-ib:94545:0:94545] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x3fab4042367150cd)
==== backtrace ====
 0 0x00000000000452c4 ucs_debug_cleanup()  ???:0
 1 0x0000000000013f30 GOMP_parallel()  ???:0
 2 0x00000000100554a0 SpatialIndex<double>::sort_by_cell()  /polusfs/home_edu/edu-cmc-sqi20/edu-cmc-sqi20-05/my/py/highly/gcc9/hpdbscan/include/spatial_index.h:200
 3 0x0000000010072224 SpatialIndex<double>::SpatialIndex()  /polusfs/home_edu/edu-cmc-sqi20/edu-cmc-sqi20-05/my/py/highly/gcc9/hpdbscan/include/spatial_index.h:593
 4 0x0000000010073498 HPDBSCAN::cluster<double>()  /polusfs/home_edu/edu-cmc-sqi20/edu-cmc-sqi20-05/my/py/highly/gcc9/hpdbscan/include/hpdbscan.h:373
 5 0x0000000010073ef0 HPDBSCAN::cluster()  /polusfs/home_edu/edu-cmc-sqi20/edu-cmc-sqi20-05/my/py/highly/gcc9/hpdbscan/include/hpdbscan.h:349
 6 0x000000001000719c main()  /polusfs/home_edu/edu-cmc-sqi20/edu-cmc-sqi20-05/my/py/highly/gcc9/hpdbscan/src/cli.cpp:94
 7 0x0000000000024980 generic_start_main.isra.0()  libc-start.c:0
 8 0x0000000000024b74 __libc_start_main()  ???:0
===================
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec noticed that process rank 0 with PID 0 on node polus-c4-ib exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------

GNU gdb (GDB) Red Hat Enterprise Linux 8.3-3.el7
Copyright (C) 2019 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
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For help, type "help".
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Reading symbols from ./hpdbscan...
[New LWP 94545]
[New LWP 94550]
[New LWP 94546]
[New LWP 94547]

warning: .dynamic section for "/lib64/libsz.so.2" is not at the expected address (wrong library or version mismatch?)

warning: .dynamic section for "/lib64/libstdc++.so.6" is not at the expected address (wrong library or version mismatch?)

warning: .dynamic section for "/lib64/libgomp.so.1" is not at the expected address (wrong library or version mismatch?)

warning: .dynamic section for "/lib64/libgcc_s.so.1" is not at the expected address (wrong library or version mismatch?)

warning: .dynamic section for "/lib64/libaec.so.0" is not at the expected address (wrong library or version mismatch?)

warning: .dynamic section for "/usr/lib64/libnuma.so.1" is not at the expected address (wrong library or version mismatch?)
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Core was generated by `./hpdbscan -t 1 -i /home_edu/edu-cmc-sqi20/edu-cmc-sqi20-05/my/ClusterLog_HPDBS'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x0000000010050974 in std::_Hashtable<unsigned long, std::pair<unsigned long const, std::atomic<unsigned long> >, std::allocator<std::pair<unsigned long const, std::atomic<un
signed long> > >, std::__detail::_Select1st, std::equal_to<unsigned long>, std::hash<unsigned long>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::
__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::_M_find_before_node (__code=0, __k=@0x3ffffc13dbe8: 0, __n=0, this=0x3ffffc13dd28)
    at /opt/rh/devtoolset-9/root/usr/include/c++/9/bits/hashtable.h:1532
1532        _Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal,
[Current thread is 1 (Thread 0x100000049500 (LWP 94545))]
Missing separate debuginfos, use: debuginfo-install glibc-2.17-196.el7_4.2.ppc64le hdf5-1.8.12-12.el7.ppc64le libaec-1.0.2-1.el7.ppc64le libgcc-4.8.5-44.el7.ppc64le libgomp-4.8.5
-44.el7.ppc64le libibcm-41mlnx1-OFED.4.1.0.1.0.43101.ppc64le libibverbs-41mlnx1-OFED.4.3.0.1.8.43101.ppc64le libmlx4-41mlnx1-OFED.4.1.0.1.0.43101.ppc64le libmlx5-41mlnx1-OFED.4.3
.0.2.1.43101.ppc64le libnl3-3.2.28-4.el7.ppc64le librdmacm-41mlnx1-OFED.4.2.0.1.3.43101.ppc64le librxe-41mlnx1-OFED.4.1.0.1.7.43101.ppc64le libstdc++-4.8.5-44.el7.ppc64le numactl
-libs-2.0.9-7.el7.ppc64le ucx-1.3.0-1.43101.ppc64le zlib-1.2.7-17.el7.ppc64le

(gdb) bt
#0  0x0000000010050974 in std::_Hashtable<unsigned long, std::pair<unsigned long const, std::atomic<unsigned long> >, std::allocator<std::pair<unsigned long const, std::atomic<unsigned long> > >, std::__detail::_Select1st, std::equal_to<unsigned long>, std::hash<unsigned long>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::_M_find_before_node (__code=0, __k=@0x3ffffc13dbe8: 0, __n=0, this=0x3ffffc13dd28)
    at /opt/rh/devtoolset-9/root/usr/include/c++/9/bits/hashtable.h:1532
#1  std::_Hashtable<unsigned long, std::pair<unsigned long const, std::atomic<unsigned long> >, std::allocator<std::pair<unsigned long const, std::atomic<unsigned long> > >, std::__detail::_Select1st, std::equal_to<unsigned long>, std::hash<unsigned long>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::_M_find_node (__c=0, __key=@0x3ffffc13dbe8: 0, __bkt=0, this=0x3ffffc13dd28)
    at /opt/rh/devtoolset-9/root/usr/include/c++/9/bits/hashtable.h:655
#2  std::__detail::_Map_base<unsigned long, std::pair<unsigned long const, std::atomic<unsigned long> >, std::allocator<std::pair<unsigned long const, std::atomic<unsigned long> > >, std::__detail::_Select1st, std::equal_to<unsigned long>, std::hash<unsigned long>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true>, true>::operator[] (this=0x3ffffc13dd28, __k=@0x3ffffc13dbe8: 0)
    at /opt/rh/devtoolset-9/root/usr/include/c++/9/bits/hashtable_policy.h:697
#3  0x0000000010055154 in std::unordered_map<unsigned long, std::atomic<unsigned long>, std::hash<unsigned long>, std::equal_to<unsigned long>, std::allocator<std::pair<unsigned long const, std::atomic<unsigned long> > > >::operator[] (__k=<optimized out>, this=<optimized out>) at /opt/rh/devtoolset-9/root/usr/include/c++/9/bits/unordered_map.h:984
#4  SpatialIndex<double>::_ZN12SpatialIndexIdE12sort_by_cellEv._omp_fn.0(void) ()
    at /polusfs/home_edu/edu-cmc-sqi20/edu-cmc-sqi20-05/my/py/highly/gcc9/hpdbscan/include/spatial_index.h:204
#5  0x0000100000853f30 in GOMP_parallel () from /lib64/libgomp.so.1
#6  0x00000000100554a0 in SpatialIndex<double>::sort_by_cell (this=0x3ffffc13e000)
    at /polusfs/home_edu/edu-cmc-sqi20/edu-cmc-sqi20-05/my/py/highly/gcc9/hpdbscan/include/spatial_index.h:195
#7  0x0000000010072224 in SpatialIndex<double>::SpatialIndex (this=0x3ffffc13e000, data=..., epsilon=<optimized out>) at /opt/rh/devtoolset-9/root/usr/include/c++/9/ostream:621
#8  0x0000000010073498 in HPDBSCAN::cluster<double> (this=0x3ffffc13e4d0, dataset=..., threads=<optimized out>)
    at /opt/rh/devtoolset-9/root/usr/include/c++/9/bits/basic_ios.h:390
#9  0x0000000010073ef0 in HPDBSCAN::cluster (this=0x3ffffc13e4d0, path=..., dataset=..., threads=<optimized out>)
    at /polusfs/home_edu/edu-cmc-sqi20/edu-cmc-sqi20-05/my/py/highly/gcc9/hpdbscan/include/hpdbscan.h:349
#10 0x000000001000719c in main (argc=<optimized out>, argv=<optimized out>) at /polusfs/home_edu/edu-cmc-sqi20/edu-cmc-sqi20-05/my/py/highly/gcc9/hpdbscan/include/cxxopts.h:838

mkdir build && cd build && cmake .. && make
-- The C compiler identification is GNU 11.4.0
-- The CXX compiler identification is GNU 11.4.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Checking for module 'mpi-c'
--   No package 'mpi-c' found
-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) 
-- Checking for module 'mpi-cxx'
--   No package 'mpi-cxx' found
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) 
-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) 
BUILDING WITHOUT MPI SUPPORT
-- Found OpenMP_C: -fopenmp (found suitable version "4.5", minimum required is "4.0") 
-- Found OpenMP_CXX: -fopenmp (found suitable version "4.5", minimum required is "4.0") 
-- Found OpenMP: TRUE (found suitable version "4.5", minimum required is "4.0")  
-- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program.
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so (found suitable version "1.10.7", minimum required is "1.8.10")  
-- Found SWIG: /usr/bin/swig4.0 (found version "4.0.2")  
-- Found PythonInterp: /home/fbenedet/my_env/bin/python (found version "3.10.12") 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so (found version "3.10.12") 
CMake Warning (dev) at /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (NUMPY) does
  not match the name of the calling package (NumPy).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/FindNumPy.cmake:28 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
  CMakeLists.txt:61 (FIND_PACKAGE)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found NUMPY: /home/fbenedet/my_env/lib/python3.10/site-packages/numpy/core/include  
-- Configuring done
-- Generating done
-- Build files have been written to: /media/fbenedet/My Passport/dbscan/hpdbscan-master/build
[ 16%] Building CXX object CMakeFiles/hpdbscan.dir/src/hpdbscan.cpp.o
[ 33%] Linking CXX shared library libhpdbscan.so
[ 33%] Built target hpdbscan
[ 50%] Building CXX object CMakeFiles/hpdbscan-bin.dir/src/cli.cpp.o
[ 66%] Linking CXX executable hpdbscan
[ 66%] Built target hpdbscan-bin
[ 83%] Building CXX object CMakeFiles/hpdbscan-binding.dir/hpdbscan_wrap.cpp.o
/media/fbenedet/My Passport/dbscan/hpdbscan-master/build/hpdbscan_wrap.cpp:3344:10: fatal error: numpy/arrayobject.h: No such file or directory
 3344 | #include <numpy/arrayobject.h>
      |          ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/hpdbscan-binding.dir/build.make:76: CMakeFiles/hpdbscan-binding.dir/hpdbscan_wrap.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:139: CMakeFiles/hpdbscan-binding.dir/all] Error 2
make: *** [Makefile:91: all] Error 2