On Thu, Oct 17, 2013 at 1:07 PM, Matthew Knepley <[email protected]> wrote:
> On Thu, Oct 17, 2013 at 3:42 AM, Bishesh Khanal <[email protected]>wrote: > >> >> >> >> On Wed, Oct 16, 2013 at 8:04 PM, Satish Balay <[email protected]> wrote: >> >>> On Wed, 16 Oct 2013, Matthew Knepley wrote: >>> >>> > You can also try running under MPICH, which can be valgrind clean. >>> >>> Actually --download-mpich would configure/install mpich with appropriate >>> flags to be valgrind clean. >>> >> >> In my laptop (but not in the cluster, please look at the second part of >> this reply below for the cluster case) that's how I configured petsc and >> ran it under mpich. The following errors (which I do not understand what >> they mean) was reported by valgrind when using the mpich of the petsc in my >> laptop: Here is the command I used and the error: >> > > This is harmless, and as you can see it comes from gfortran initialization. > > >> (Note: petsc is an alias in my .bashrc: alias >> petsc='/home/bkhanal/Documents/softwares/petsc-3.4.3/bin/petscmpiexec' >> >> petsc -n 2 valgrind src/AdLemMain -pc_type fieldsplit -pc_fieldsplit_type >> schur -pc_fieldsplit_dm_splits 0 -pc_fieldsplit_0_fields 0,1,2 >> -pc_fieldsplit_1_fields 3 -fieldsplit_0_pc_type hypre >> -fieldsplit_0_ksp_converged_reason -ksp_converged_reason >> ==3106== Memcheck, a memory error detector >> ==3106== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al. >> ==3106== Using Valgrind-3.6.1 and LibVEX; rerun with -h for copyright info >> ==3107== Memcheck, a memory error detector >> ==3107== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al. >> ==3107== Using Valgrind-3.6.1 and LibVEX; rerun with -h for copyright info >> ==3107== Command: src/AdLemMain -pc_type fieldsplit -pc_fieldsplit_type >> schur -pc_fieldsplit_dm_splits 0 -pc_fieldsplit_0_fields 0,1,2 >> -pc_fieldsplit_1_fields 3 -fieldsplit_0_pc_type hypre >> -fieldsplit_0_ksp_converged_reason -ksp_converged_reason >> ==3107== >> ==3106== Command: src/AdLemMain -pc_type fieldsplit -pc_fieldsplit_type >> schur -pc_fieldsplit_dm_splits 0 -pc_fieldsplit_0_fields 0,1,2 >> -pc_fieldsplit_1_fields 3 -fieldsplit_0_pc_type hypre >> -fieldsplit_0_ksp_converged_reason -ksp_converged_reason >> ==3106== >> ==3107== Conditional jump or move depends on uninitialised value(s) >> ==3107== at 0x32EEED9BCE: ??? (in /usr/lib64/libgfortran.so.3.0.0) >> ==3107== by 0x32EEED9155: ??? (in /usr/lib64/libgfortran.so.3.0.0) >> ==3107== by 0x32EEE185D7: ??? (in /usr/lib64/libgfortran.so.3.0.0) >> ==3107== by 0x32ECC0F195: call_init.part.0 (in /lib64/ld-2.14.90.so) >> ==3107== by 0x32ECC0F272: _dl_init (in /lib64/ld-2.14.90.so) >> ==3107== by 0x32ECC01719: ??? (in /lib64/ld-2.14.90.so) >> ==3107== by 0xE: ??? >> ==3107== by 0x7FF0003EE: ??? >> ==3107== by 0x7FF0003FC: ??? >> ==3107== by 0x7FF000405: ??? >> ==3107== by 0x7FF000410: ??? >> ==3107== by 0x7FF000424: ??? >> ==3107== >> ==3107== Conditional jump or move depends on uninitialised value(s) >> ==3107== at 0x32EEED9BD9: ??? (in /usr/lib64/libgfortran.so.3.0.0) >> ==3107== by 0x32EEED9155: ??? (in /usr/lib64/libgfortran.so.3.0.0) >> ==3107== by 0x32EEE185D7: ??? (in /usr/lib64/libgfortran.so.3.0.0) >> ==3107== by 0x32ECC0F195: call_init.part.0 (in /lib64/ld-2.14.90.so) >> ==3107== by 0x32ECC0F272: _dl_init (in /lib64/ld-2.14.90.so) >> ==3107== by 0x32ECC01719: ??? (in /lib64/ld-2.14.90.so) >> ==3107== by 0xE: ??? >> ==3107== by 0x7FF0003EE: ??? >> ==3107== by 0x7FF0003FC: ??? >> ==3107== by 0x7FF000405: ??? >> ==3107== by 0x7FF000410: ??? >> ==3107== by 0x7FF000424: ??? >> ==3107== >> dmda of size: (8,8,8) >> >> using schur complement >> >> using user defined split >> Linear solve converged due to CONVERGED_ATOL iterations 0 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 3 >> Linear solve converged due to CONVERGED_RTOL iterations 1 >> ==3106== >> ==3106== HEAP SUMMARY: >> ==3106== in use at exit: 187,709 bytes in 1,864 blocks >> ==3106== total heap usage: 112,891 allocs, 111,027 frees, 19,838,487 >> bytes allocated >> ==3106== >> ==3107== >> ==3107== HEAP SUMMARY: >> ==3107== in use at exit: 212,357 bytes in 1,870 blocks >> ==3107== total heap usage: 112,701 allocs, 110,831 frees, 19,698,341 >> bytes allocated >> ==3107== >> ==3106== LEAK SUMMARY: >> ==3106== definitely lost: 0 bytes in 0 blocks >> ==3106== indirectly lost: 0 bytes in 0 blocks >> ==3106== possibly lost: 0 bytes in 0 blocks >> ==3106== still reachable: 187,709 bytes in 1,864 blocks >> ==3106== suppressed: 0 bytes in 0 blocks >> ==3106== Rerun with --leak-check=full to see details of leaked memory >> ==3106== >> ==3106== For counts of detected and suppressed errors, rerun with: -v >> ==3106== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 2 from 2) >> ==3107== LEAK SUMMARY: >> ==3107== definitely lost: 0 bytes in 0 blocks >> ==3107== indirectly lost: 0 bytes in 0 blocks >> ==3107== possibly lost: 0 bytes in 0 blocks >> ==3107== still reachable: 212,357 bytes in 1,870 blocks >> ==3107== suppressed: 0 bytes in 0 blocks >> ==3107== Rerun with --leak-check=full to see details of leaked memory >> ==3107== >> ==3107== For counts of detected and suppressed errors, rerun with: -v >> ==3107== Use --track-origins=yes to see where uninitialised values come >> from >> ==3107== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 2 from 2) >> >> In the above example, the solver iterates and gives results. >> >> Now the case in cluster: I had to configure petsc with the option: >> --with-mpi-dir=/opt/openmpi-gcc/current/ , that's how the cluster >> administrators asked me to install to get petsc running in many nodes of >> the clusters. I had tried on my own to configure with --download-mpich in >> the cluster too, but could not succeed with some errors. If you really >> think the errors could be from this configuration, I would retry to install >> with the petscmpich; please let me know. >> And the valgrind errors for the case where program terminates without >> completing normally (big sized domain), it has following errors just before >> abrupt termination: >> >> ... lots of other errors and then warnings such as: >> > > This appears to be a bug in OpenMPI, which would not be all that > surprising. First, you can try running > in the debugger and extracting a stack trace from the SEGV. > Just to make sure that I understood what you said before I talk with the cluster administrators: The program crashes only for a bigger domain size. Even in the cluster, it does not crash for the domain size up to a certain size. So I need to run in the debugger for the case when it crashes to get the stack trace from the SEGV, right ? I do not know how to attach a debugger when submitting a job to the cluster if that is possible at all! Or are you asking me to run the program in the debugger in my laptop for the biggest size ? (I have not tried running the code for the biggest size in my laptop fearing it might take forever) > Then you could > > 1) Get the admin to install MPICH > > 2) Try running a PETSc example on the cluster > > 3) Try running on another machine > > Matt > > >> ==55437== Warning: set address range perms: large range [0xc4369040, >> 0xd6abb670) (defined) >> ==55438== Warning: set address range perms: large range [0xc4369040, >> 0xd6a6cd00) (defined) >> ==37183== Warning: set address range perms: large range [0xc4369040, >> 0xd69f57d8) (defined) >> ==37182== Warning: set address range perms: large range [0xc4369040, >> 0xd6a474f0) (defined) >> mpiexec: killing job... >> >> >> In between there are several errors such as: >> ==59334== Use of uninitialised value of size 8 >> ==59334== at 0xD5B3704: mca_pml_ob1_send_request_put >> (pml_ob1_sendreq.c:1217) >> ==59334== by 0xE1EF01A: btl_openib_handle_incoming >> (btl_openib_component.c:3092) >> ==59334== by 0xE1F03E9: btl_openib_component_progress >> (btl_openib_component.c:3634) >> ==59334== by 0x81CF16A: opal_progress (opal_progress.c:207) >> ==59334== by 0x81153AC: ompi_request_default_wait_all (condition.h:92) >> ==59334== by 0xF4C25DD: ompi_coll_tuned_sendrecv_actual >> (coll_tuned_util.c:54) >> ==59334== by 0xF4C91FD: >> ompi_coll_tuned_allgatherv_intra_neighborexchange (coll_tuned_util.h:57) >> ==59334== by 0x8121783: PMPI_Allgatherv (pallgatherv.c:139) >> ==59334== by 0x5156D19: ISAllGather (iscoloring.c:502) >> ==59334== by 0x57A6B78: MatGetSubMatrix_MPIAIJ (mpiaij.c:3607) >> ==59334== by 0x532DB36: MatGetSubMatrix (matrix.c:7297) >> ==59334== by 0x5B97725: PCSetUp_FieldSplit(_p_PC*) (fieldsplit.c:524) >> >> >> >> >> >> >>> >>> Satish >>> >> >> > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener >
