[MOAB-dev] Error message when compiling the mbcoupler_test.cpp
Jie Wu
jie.voo at gmail.com
Fri May 13 11:27:12 CDT 2016
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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