[MOAB-dev] Error message when compiling the mbcoupler_test.cpp
Jie Wu
jie.voo at gmail.com
Fri May 13 13:31:36 CDT 2016
Hi Vijay,
Deleting the auto-installed packages under sandbox before issue new configurations works good! No error message emerged until I input the command make check, which is as following.
Do you have any idea for this problem?
Best,
Jie
PASS: reorder_test
FAIL: test_prog_opt
PASS: coords_connect_iterate
PASS: elem_eval_test
PASS: spatial_locator_test
PASS: test_boundbox
PASS: adj_moab_test
PASS: uref_mesh_test
PASS: verdict_test
PASS: test_Matrix3
PASS: mbfacet_test
PASS: gttool_test
PASS: cropvol_test
FAIL: mergemesh_test
PASS: mbground_test
PASS: lloyd_smoother_test
============================================================================
Testsuite summary for MOAB 4.9.2pre
============================================================================
# TOTAL: 36
# PASS: 34
# SKIP: 0
# XFAIL: 0
# FAIL: 2
# XPASS: 0
# ERROR: 0
============================================================================
See test/test-suite.log
Please report to moab-dev at mcs.anl.gov
============================================================================
make[4]: *** [test-suite.log] Error 1
make[3]: *** [check-TESTS] Error 2
make[2]: *** [check-am] Error 2
make[1]: *** [check-recursive] Error 1
make: *** [check-recursive] Error 1
> On May 13, 2016, at 1:08 PM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>
> Jie, since you now changed the compilers used to configure the stack,
> I would advise deleting the auto-installed packages under sandbox
> directory and then re-configuring. This will force the rebuild of
> HDF5/NetCDF packages with the parallel MPI compilers and you should
> get the HDF5-parallel support enabled after that. Makes sense ?
>
> Vijay
>
> On Fri, May 13, 2016 at 11:27 AM, Jie Wu <jie.voo at gmail.com> wrote:
>> Hi Vijay,
>>
>> Thank you for your reply. The new configuration do works. Here shows the
>> command I inputed and the message while I input: make check.
>>
>> dyn-160-39-10-173:moab jiewu$ ./configure --with-mpi=/usr/local
>> CC=/usr/local/bin/mpicc CXX=/usr/local/bin/mpic++ FC=/usr/local/bin/mpif90
>> F77=/usr/local/bin/mpif77 --download-metis --download-hdf5 --download-netcdf
>> --enable-docs --with-doxygen=/Applications/Doxygen.app/Contents/Resources/
>>
>> The results are
>>
>> configure: WARNING:
>> *************************************************************************
>> * MOAB has been configured with parallel and HDF5 support
>> * but the configured HDF5 library does not support parallel IO.
>> * Some parallel IO capabilities will be disabled.
>> *************************************************************************
>>
>> After that, I inputted the command, make -j4, and then command make check.
>> Here are the results it shows
>>
>> /Applications/Xcode.app/Contents/Developer/usr/bin/make check-TESTS
>> PASS: elem_util_test
>> PASS: element_test
>> FAIL: datacoupler_test
>> FAIL: mbcoupler_test
>> FAIL: parcoupler_test
>> ============================================================================
>> Testsuite summary for MOAB 4.9.2pre
>> ============================================================================
>> # TOTAL: 5
>> # PASS: 2
>> # SKIP: 0
>> # XFAIL: 0
>> # FAIL: 3
>> # XPASS: 0
>> # ERROR: 0
>> ============================================================================
>> See tools/mbcoupler/test-suite.log
>> Please report to moab-dev at mcs.anl.gov
>> ============================================================================
>> make[4]: *** [test-suite.log] Error 1
>> make[3]: *** [check-TESTS] Error 2
>> make[2]: *** [check-am] Error 2
>> make[1]: *** [check-recursive] Error 1
>> make: *** [check-recursive] Error 1
>>
>> Then I was trying to run the mbcouple_test with command
>> dyn-160-39-10-173:mbcoupler jiewu$ mpiexec -np 2 mbcoupler_test -meshes
>> /Users/wujie/SourceCode/moab/MeshFiles/unittest/64bricks_1khex.h5m
>> /Users/wujie/SourceCode/moab/MeshFiles/unittest/64bricks_12ktet.h5m -itag
>> vertex_field -outfile dum.h5m
>> Now the results look like,
>>
>> [0]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]MOAB ERROR: MOAB not configured with parallel HDF5 support!
>> [0]MOAB ERROR: set_up_read() line 355 in src/io/ReadHDF5.cpp
>> [0]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]MOAB ERROR: NULL file handle.!
>> [0]MOAB ERROR: is_error() line 133 in src/io/ReadHDF5.hpp
>> [1]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [1]MOAB ERROR: MOAB not configured with parallel HDF5 support!
>> [1]MOAB ERROR: set_up_read() line 355 in src/io/ReadHDF5.cpp
>> [1]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [1]MOAB ERROR: NULL file handle.!
>> [1]MOAB ERROR: is_error() line 133 in src/io/ReadHDF5.hpp
>> [0]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]MOAB ERROR: Failed to load file after trying all possible readers!
>> [0]MOAB ERROR: serial_load_file() line 635 in src/Core.cpp
>> [0]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]MOAB ERROR: Failed in step PARALLEL READ PART!
>> [0]MOAB ERROR: load_file() line 553 in src/parallel/ReadParallel.cpp
>> [0]MOAB ERROR: load_file() line 252 in src/parallel/ReadParallel.cpp
>> [0]MOAB ERROR: load_file() line 515 in src/Core.cpp
>> [1]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [1]MOAB ERROR: Failed to load file after trying all possible readers!
>> [1]MOAB ERROR: serial_load_file() line 635 in src/Core.cpp
>> [1]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [1]MOAB ERROR: Failed in step PARALLEL READ PART!
>> [1]MOAB ERROR: load_file() line 553 in src/parallel/ReadParallel.cpp
>> [0]MOAB ERROR: main() line 172 in mbcoupler_test.cpp
>> [1]MOAB ERROR: load_file() line 252 in src/parallel/ReadParallel.cpp
>> [1]MOAB ERROR: load_file() line 515 in src/Core.cpp
>> [1]MOAB ERROR: main() line 172 in mbcoupler_test.cpp
>> --------------------------------------------------------------------------
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 16.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> --------------------------------------------------------------------------
>> [dyn-160-39-11-172.dyn.columbia.edu:26361] 1 more process has sent help
>> message help-mpi-api.txt / mpi-abort
>> [dyn-160-39-11-172.dyn.columbia.edu:26361] Set MCA parameter
>> "orte_base_help_aggregate" to 0 to see all help / error messages
>> The other excitable file in mbcoupler folder, like ./element_test now can
>> run successfully.
>>
>> Any direction for this was deeply appreciated!
>>
>> Best,
>> Jie
>>
>>
>> On May 13, 2016, at 11:54 AM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>>
>> I also forgot to mention that you can be more explicit in the
>> specification of compilers during configuration, if you really want.
>> This would avoid headaches since the user specified wrappers will
>> directly be used. For example:
>>
>> ./configure --with-mpi=/usr/local CC=/usr/local/bin/mpicc
>> CXX=/usr/local/bin/mpic++ FC=/usr/local/bin/mpif90
>> F77=/usr/local/bin/mpif77 <OTHER_CONFIGURE_OPTIONS>
>>
>> Vijay
>>
>> On Fri, May 13, 2016 at 10:52 AM, Vijay S. Mahadevan <vijay.m at gmail.com>
>> wrote:
>>
>> Please use --with-mpi=/usr/local as the configure option. If you have
>> MPI pre-installed, either through PETSc or natively in your system,
>> always try to re-use that to maintain consistency. This will help
>> avoid mix-up of MPI implementations when you try to launch a parallel
>> job later.
>>
>> Let us know if the new configuration works.
>>
>> Vijay
>>
>> On Thu, May 12, 2016 at 6:32 PM, Jie Wu <jie.voo at gmail.com> wrote:
>>
>> Thank you very much for your reply. I search in my src/moab/MOABConfig.h
>> file, and I did not find the MOAB_HAVE_MPI. So I think the MOAB on my laptop
>> cannot run in parallel yet.
>>
>> I have this from my terminal.
>>
>> dyn-160-39-10-173:moab jiewu$ which mpic++
>> /usr/local/bin/mpic++
>>
>> But I cannot get anything by inputing which mpi. So I don’t know where the
>> mpi is in my laptop.
>>
>> dyn-160-39-10-173:moab jiewu$ which mpi
>>
>> I have petsc installed which has mpich, and linking that directory to the
>> MOAB configure option also did not work.
>>
>> Should I install mpi solely? I am afraid it might conflict with the one
>> installed in petsc.
>>
>> Is there any method that the mpi could be installed with MOAB automatically,
>> or maybe other proper manner? Thanks a lot!
>>
>> Best,
>> Jie
>>
>>
>> On May 12, 2016, at 6:11 PM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>>
>> Can you send the config.log. Looks like MPI is not getting enabled
>> (possibly), even with --dowload-mpich. Or you can check
>> src/moab/MOABConfig.h in your build directory and grep for
>> MOAB_HAVE_MPI.
>>
>> Vijay
>>
>> On Thu, May 12, 2016 at 4:46 PM, Jie Wu <jie.voo at gmail.com> wrote:
>>
>> Hi Iulian,
>>
>> Thanks for your reply. I think my configure is with mpi. Here is my
>> configure command
>>
>> dyn-160-39-10-173:moab jiewu$ ./configure --download-metis
>> --download-hdf5 --download-netcdf --download-mpich --enable-docs
>> --with-doxygen=/Applications/Doxygen.app/Contents/Resources/
>>
>> Best,
>> Jie
>>
>> On May 12, 2016, at 5:43 PM, Grindeanu, Iulian R. <iulian at mcs.anl.gov>
>> wrote:
>>
>> Hi Jie,
>> Did you configure with mpi? What is your configure command?
>>
>> Iulian
>> ________________________________
>> From: moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on behalf
>> of Jie Wu [jie.voo at gmail.com]
>> Sent: Thursday, May 12, 2016 4:23 PM
>> To: moab-dev at mcs.anl.gov
>> Subject: [MOAB-dev] Error message when compiling the mbcoupler_test.cpp
>>
>> Hi all,
>>
>> My name is Jie and I am part of computational mechanics group at civil
>> engineering dept. of Columbia university.
>>
>> I am working on large deformation problems which may lead mesh distortions
>> and a re-meshing become necessary.
>>
>> I would like to compile mbcoupler_test.cpp to learn how it transfer the
>> variables from old to the new mesh.
>>
>> Now I can successfully compile the codes in build/examples and they works
>> good! But I cannot compile the codes in folder build/tools/mbcoupler by
>> following the instructions in build/tools/readme.tools, which shows error
>> message like following.
>>
>> Do you have any idea for this problem? Thanks a lot!
>>
>> Best,
>> Jie
>>
>> DataCoupler.cpp:136:25: error: member access into incomplete
>> type 'moab::ParallelComm'
>> if (myPcomm && myPcomm->size() > 1) {
>> ^
>> ./DataCoupler.hpp:34:7: note: forward declaration of
>> 'moab::ParallelComm'
>> class ParallelComm;
>> ^
>> DataCoupler.cpp:161:12: error: member access into incomplete
>> type 'moab::ParallelComm'
>> myPcomm->proc_config().crystal_router()->gs_tran...
>> ^
>> ./DataCoupler.hpp:34:7: note: forward declaration of
>> 'moab::ParallelComm'
>> class ParallelComm;
>> ^
>> DataCoupler.cpp:187:12: error: member access into incomplete
>> type 'moab::ParallelComm'
>> myPcomm->proc_config().crystal_router()->gs_tran...
>> ^
>> ./DataCoupler.hpp:34:7: note: forward declaration of
>> 'moab::ParallelComm'
>> class ParallelComm;
>> ^
>> 3 errors generated.
>> make[2]: *** [DataCoupler.lo] Error 1
>> make[2]: *** Waiting for unfinished jobs....
>> Coupler.cpp:344:45: error: no member named 'gs_transfer' in
>> 'moab::gs_data::crystal_data'
>> (myPc->proc_config().crystal_router())->gs_trans...
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> Coupler.cpp:388:45: error: no member named 'gs_transfer' in
>> 'moab::gs_data::crystal_data'
>> (myPc->proc_config().crystal_router())->gs_trans...
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> Coupler.cpp:611:45: error: no member named 'gs_transfer' in
>> 'moab::gs_data::crystal_data'
>> (myPc->proc_config().crystal_router())->gs_trans...
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> Coupler.cpp:638:43: error: no member named 'gs_transfer' in
>> 'moab::gs_data::crystal_data'
>> myPc->proc_config().crystal_router()->gs_transfe...
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> 4 errors generated.
>> make[2]: *** [Coupler.lo] Error 1
>> make[1]: *** [all-recursive] Error 1
>> make: *** [all-recursive] Error 1
>>
>>
>>
>>
>>
>>
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