Hi Wolfgang,
I have spotted the problem causing this error I face yesterday. Basically,
if I want to install the software including p4est, trilinos, dealii
successfully, I can only do module load gcc-related compilers (no
intel/2018 etc) before the installation. But there is another error
happening when I can actually run step-32 in parallel for testing by
typing mpirun -np 4 ./step-32 ./step-32.prm . How do I solve it?
[chueh5851a@clogin2 step-xx]$ make release
Scanning dependencies of target release
[100%] Switch CMAKE_BUILD_TYPE to Release
-- Autopilot invoked
-- Run $ make info to print a detailed help message
-- Configuring done
-- Generating done
-- Build files have been written to:
/home/chueh5851a/software/dealii/examples/step-xx
Scanning dependencies of target step-32
[100%] Building CXX object CMakeFiles/step-32.dir/step-32.cc.o
/home/chueh5851a/software/dealii/examples/step-xx/step-32.cc:874:25:
warning: ‘using ConstraintMatrix = class dealii::AffineConstraints<double>’
is deprecated [-Wdeprecated-declarations]
ConstraintMatrix stokes_constraints;
^~~~~~~~~~~~~~~~~~
In file included from
/home/chueh5851a/software/dealii/examples/step-xx/step-32.cc:40:0:
/home/chueh5851a/software/dealii/include/deal.II/lac/affine_constraints.h:65:70:
note: declared here
using ConstraintMatrix DEAL_II_DEPRECATED = AffineConstraints<double>;
^
/home/chueh5851a/software/dealii/examples/step-xx/step-32.cc:886:22:
warning: ‘using ConstraintMatrix = class dealii::AffineConstraints<double>’
is deprecated [-Wdeprecated-declarations]
ConstraintMatrix temperature_constraints;
^~~~~~~~~~~~~~~~~~~~~~~
In file included from
/home/chueh5851a/software/dealii/examples/step-xx/step-32.cc:40:0:
/home/chueh5851a/software/dealii/include/deal.II/lac/affine_constraints.h:65:70:
note: declared here
using ConstraintMatrix DEAL_II_DEPRECATED = AffineConstraints<double>;
^
Linking CXX executable step-32
[100%] Built target step-32
Built target release
[chueh5851a@clogin2 step-xx]$ mpirun -np 4 ./step-32 ./step-32.prm
[clogin2:87394] *** Process received signal ***
[clogin2:87394] Signal: Segmentation fault (11)
[clogin2:87394] Signal code: Address not mapped (1)
[clogin2:87394] Failing at address: 0xc8dce218
[clogin2:87395] *** Process received signal ***
[clogin2:87396] *** Process received signal ***
[clogin2:87396] Signal: Segmentation fault (11)
[clogin2:87396] Signal code: Address not mapped (1)
[clogin2:87396] Failing at address: 0xc8dce218
[clogin2:87397] *** Process received signal ***
[clogin2:87397] Signal: Segmentation fault (11)
[clogin2:87397] Signal code: Address not mapped (1)
[clogin2:87397] Failing at address: 0xc8dce218
[clogin2:87395] Signal: Segmentation fault (11)
[clogin2:87395] Signal code: Address not mapped (1)
[clogin2:87395] Failing at address: 0xc8dce218
[clogin2:87394] [ 0] [clogin2:87397] [ 0] [clogin2:87396] [ 0]
/usr/lib64/libc.so.6(+0x35250)[0x2aaac949d250]
[clogin2:87396] [clogin2:87395] [ 0]
/usr/lib64/libc.so.6(+0x35250)[0x2aaac949d250]
[clogin2:87394] [ 1] /usr/lib64/libc.so.6(+0x35250)[0x2aaac949d250]
[clogin2:87397] [ 1] [ 1]
/pkg/openmpi/3.0.0/gcc/6.3.0/lib64/libmpi.so.40(PMPI_Comm_size+0x42)[0x2aaac8a02bd2]
[clogin2:87396] [ 2]
/pkg/openmpi/3.0.0/gcc/6.3.0/lib64/libmpi.so.40(PMPI_Comm_size+0x42)[0x2aaac8a02bd2]
[clogin2:87397] [ 2] /home/chueh5851a/software/p4est-2.0/FAST/lib/
libp4est-2.0.so(p4est_comm_parallel_env_get_info+0xf)[0x2aaac7aea8bf]
[clogin2:87397] [ 3] /usr/lib64/libc.so.6(+0x35250)[0x2aaac949d250]
[clogin2:87395] [ 1]
/pkg/openmpi/3.0.0/gcc/6.3.0/lib64/libmpi.so.40(PMPI_Comm_size+0x42)[0x2aaac8a02bd2]
[clogin2:87394] [ 2] /home/chueh5851a/software/p4est-2.0/FAST/lib/
libp4est-2.0.so(p4est_comm_parallel_env_get_info+0xf)[0x2aaac7aea8bf]
[clogin2:87394] [ 3] /home/chueh5851a/software/p4est-2.0/FAST/lib/
libp4est-2.0.so(p4est_comm_parallel_env_get_info+0xf)[0x2aaac7aea8bf]
[clogin2:87396] [ 3] /home/chueh5851a/software/p4est-2.0/FAST/lib/
libp4est-2.0.so(p4est_new_ext+0xbd)[0x2aaac7ad9bcd]
[clogin2:87396] [ 4] /home/chueh5851a/software/p4est-2.0/FAST/lib/
libp4est-2.0.so(p4est_new_ext+0xbd)[0x2aaac7ad9bcd]
[clogin2:87394] [ 4] /home/chueh5851a/software/p4est-2.0/FAST/lib/
libp4est-2.0.so(p4est_new_ext+0xbd)[0x2aaac7ad9bcd]
[clogin2:87397] [ 4]
/pkg/openmpi/3.0.0/gcc/6.3.0/lib64/libmpi.so.40(PMPI_Comm_size+0x42)[0x2aaac8a02bd2]
[clogin2:87395] [ 2] /home/chueh5851a/software/p4est-2.0/FAST/lib/
libp4est-2.0.so(p4est_comm_parallel_env_get_info+0xf)[0x2aaac7aea8bf]
[clogin2:87395] [ 3] /home/chueh5851a/software/p4est-2.0/FAST/lib/
libp4est-2.0.so(p4est_new_ext+0xbd)[0x2aaac7ad9bcd]
[clogin2:87395] [ 4]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii8parallel11distributed13TriangulationILi2ELi2EE31copy_new_triangulation_to_p4estESt17integral_constantIiLi2EE+0xbe5)[0x2aaab26ff125]
[clogin2:87396] [ 5]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii8parallel11distributed13TriangulationILi2ELi2EE31copy_new_triangulation_to_p4estESt17integral_constantIiLi2EE+0xbe5)[0x2aaab26ff125]
[clogin2:87394] [ 5]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii8parallel11distributed13TriangulationILi2ELi2EE31copy_new_triangulation_to_p4estESt17integral_constantIiLi2EE+0xbe5)[0x2aaab26ff125]
[clogin2:87397] [ 5]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii8parallel11distributed13TriangulationILi2ELi2EE31copy_new_triangulation_to_p4estESt17integral_constantIiLi2EE+0xbe5)[0x2aaab26ff125]
[clogin2:87395] [ 5]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii8parallel11distributed13TriangulationILi2ELi2EE20create_triangulationERKSt6vectorINS_5PointILi2EdEESaIS6_EERKS4_INS_8CellDataILi2EEESaISC_EERKNS_11SubCellDataE+0x26)[0x2aaab272ef56]
[clogin2:87397] [ 6]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii8parallel11distributed13TriangulationILi2ELi2EE20create_triangulationERKSt6vectorINS_5PointILi2EdEESaIS6_EERKS4_INS_8CellDataILi2EEESaISC_EERKNS_11SubCellDataE+0x26)[0x2aaab272ef56]
[clogin2:87396] [ 6]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii8parallel11distributed13TriangulationILi2ELi2EE20create_triangulationERKSt6vectorINS_5PointILi2EdEESaIS6_EERKS4_INS_8CellDataILi2EEESaISC_EERKNS_11SubCellDataE+0x26)[0x2aaab272ef56]
[clogin2:87394] [ 6]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii8parallel11distributed13TriangulationILi2ELi2EE20create_triangulationERKSt6vectorINS_5PointILi2EdEESaIS6_EERKS4_INS_8CellDataILi2EEESaISC_EERKNS_11SubCellDataE+0x26)[0x2aaab272ef56]
[clogin2:87395] [ 6]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii13GridGenerator11hyper_shellILi2EEEvRNS_13TriangulationIXT_EXT_EEERKNS_5PointIXT_EdEEddjb+0x433)[0x2aaab1edf9c3]
[clogin2:87394] [ 7]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii13GridGenerator11hyper_shellILi2EEEvRNS_13TriangulationIXT_EXT_EEERKNS_5PointIXT_EdEEddjb+0x433)[0x2aaab1edf9c3]
[clogin2:87397] [ 7]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii13GridGenerator11hyper_shellILi2EEEvRNS_13TriangulationIXT_EXT_EEERKNS_5PointIXT_EdEEddjb+0x433)[0x2aaab1edf9c3]
[clogin2:87396] [ 7]
/home/chueh5851a/software/dealii/lib/libdeal_II.so.9.1.0-pre(_ZN6dealii13GridGenerator11hyper_shellILi2EEEvRNS_13TriangulationIXT_EXT_EEERKNS_5PointIXT_EdEEddjb+0x433)[0x2aaab1edf9c3]
[clogin2:87395] [ 7]
./step-32(_ZN6Step3221BoussinesqFlowProblemILi2EE3runEv+0x62)[0x4c9822]
[clogin2:87395] [ 8]
./step-32(_ZN6Step3221BoussinesqFlowProblemILi2EE3runEv+0x62)[0x4c9822]
[clogin2:87396] [ 8]
./step-32(_ZN6Step3221BoussinesqFlowProblemILi2EE3runEv+0x62)[0x4c9822]
[clogin2:87394] [ 8] ./step-32(main+0x8f)[0x474f9f]
[clogin2:87394]
./step-32(_ZN6Step3221BoussinesqFlowProblemILi2EE3runEv+0x62)[0x4c9822]
[clogin2:87397] [ 8] ./step-32(main+0x8f)[0x474f9f]
[clogin2:87395] [ 9]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2aaac9489b35]
[clogin2:87395] [10] ./step-32(main+0x8f)[0x474f9f]
[clogin2:87396] [ 9]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2aaac9489b35]
[clogin2:87396] [10] [ 9]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2aaac9489b35]
[clogin2:87394] [10] ./step-32[0x4751da]
./step-32(main+0x8f)[0x474f9f]
[clogin2:87397] [ 9]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2aaac9489b35]
[clogin2:87397] [10] [clogin2:87394] *** End of error message ***
./step-32[0x4751da]
[clogin2:87395] *** End of error message ***
./step-32[0x4751da]
[clogin2:87396] *** End of error message ***
./step-32[0x4751da]
[clogin2:87397] *** End of error message ***
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node clogin2 exited on
signal 11 (Segmentation fault).
--------------------------------------------------------------------------
Sincerely,
Chih-Che
On Tue, Oct 23, 2018 at 12:16 PM Wolfgang Bangerth <bange...@colostate.edu>
wrote:
> On 10/22/18 8:09 AM, Chih-Che Chueh wrote:
> > -- Could NOT find MPI_C (missing: MPI_C_WORKS)
> > -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS)
> > -- Could NOT find MPI_Fortran (missing: MPI_Fortran_WORKS)
> > -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND
> MPI_Fortran_FOUND)
> > -- Performing Test MPI_HAVE_MPI_SEEK_SET
> > -- Performing Test MPI_HAVE_MPI_SEEK_SET - Failed
> > -- MPI_MPI_H not found! Call:
>
> Chih-Che,
> Well, it apparently can't find anything about the MPI system. Can you take
> a
> look into the CMakeFiles/CMakeErrors.log file to see what the error
> messages
> related to all of the MPI stuff are?
>
> Best
> W.
>
> --
> ------------------------------------------------------------------------
> Wolfgang Bangerth email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
> https://groups.google.com/d/forum/dealii?hl=en
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--
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see
https://groups.google.com/d/forum/dealii?hl=en
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