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: (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: ==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 >
