February 2017 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Bump MOAB version?
by Vijay S. Mahadevan 02 Feb '17

02 Feb '17

Toby, I'll take a look at this today or tomorrow and push a fix. Will also work on submitting a PR with updated changes by next week. Vijay On Feb 2, 2017 08:21, "Tobin Isaac" <tisaac(a)uchicago.edu> wrote: FYI, the PETSc tests that use MOAB passed using MOAB commit f862b4c on my laptop, though when I had mpich debugging on there looks like there may have been some memory leaks that don't appear in other PETSc tests. (log attached) Cheers, Toby On Wed, Feb 01, 2017 at 03:22:18AM +0530, Vijay S. Mahadevan wrote: > Toby, thanks for the update. Yes, I recently updated the "petsc" > branch in MOAB to make sure that v4.9.2 is merged. Some of these > changes are needed for one of my upcoming PR's to improve DMMoab > support. I however have been on some international travel and haven't > found enough time to take care of this. > > Iulian, can you create a tarball that corresponds to the HEAD in petsc > branch (if not already available from the ftp site) ? > > Vijay > > PS: The macports errors are related to ESMF. They have their custom > version of MOAB (4.6.x) and so I'm unsure whether the port needs the > latest MOAB as its dependency. > > On Wed, Feb 1, 2017 at 3:07 AM, Tobin Isaac <tisaac(a)uchicago.edu> wrote: > > > > The commit of MOAB that we use in MAOB.py doesn't compile in gcc6 > > due to c++14 compatibility issues [1]. I checked out the latest petsc > > branch from their repo and it seems to compile. Can we ask them to > > host an updated tarball, too? > > > > [1] https://trac.macports.org/ticket/52427#comment:2 > > > > Toby

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Re: [petsc-dev] Fwd: no petsc on Edison
by Hong 02 Feb '17

02 Feb '17

Mark: Try '-matmatmult_via scalable' first. If this works, should we set it as default? Hong > > > On Thu, Feb 2, 2017 at 10:53 AM, Satish Balay <balay(a)mcs.anl.gov> wrote: > >> > [3404]PETSC ERROR: Memory allocated 0 Memory used by process 2537885696 >> > [3404]PETSC ERROR: Memory requested 657532760 >> >> So the process is currently using 2.5GB - and then made a malloc >> request for 650MB - and this failed? >> > > Yep, large but not garbage. > > >> >> How many 'tasks-per-node' are you using? Perhaps you need to reduce this >> number? >> > > Treb has run this job before and I think this code has been touched > recently ... I suggested that Treb try -matmatmult_via scalable > > Thanks, > > >> >> https://www.nersc.gov/users/computational-systems/edison/configuration/ >> 64GB/node >> <https://www.nersc.gov/users/computational-systems/edison/configuration/64GB…> >> => 5.3GB/process for tasks-per-node=12 [and 2.6GB/node for >> tasks-per-node=24] >> >> Satish >> >> On Wed, 1 Feb 2017, Mark Adams wrote: >> >> > We are getting this error on Edison. This problem has run before. This >> is >> > using maint from last week. >> > >> > I recall there are low memory options for mpiptap. I don't think we are >> > using them. >> > >> > Thanks, >> > >> > 3404]PETSC ERROR: --------------------- Error Message >> > -------------------------------------------------------------- >> > [3404]PETSC ERROR: Out of memory. This could be due to allocating >> > [3404]PETSC ERROR: too large an object or bleeding by not properly >> > [3404]PETSC ERROR: destroying unneeded objects. >> > [3404]PETSC ERROR: Memory allocated 0 Memory used by process 2537885696 >> > <(253)%20788-5696> >> >> > [3404]PETSC ERROR: Try running with -malloc_dump or -malloc_log for >> info. >> > [3404]PETSC ERROR: Memory requested 657532760 >> > [3404]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d >> ocumentation/faq.html >> > for trouble shooting. >> > [3404]PETSC ERROR: Petsc Release Version 3.7.5, unknown >> > [3404]PETSC ERROR: /tmp/targetExec on a arch-xc30-opt64-intel named >> > nid00713 by u6338 Wed Feb 1 16:15:09 2017 >> > [3404]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" >> > --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" >> > --download-parmetis --download-metis --download-hypre --with-ssl=0 >> > --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC >> > --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn >> > --with-fortranlib-autodetect=0 --with-shared-libraries=0 --with-x=0 >> > --with-mpiexec=srun LIBS=-lstdc++ --with-64-bit-indices >> > --prefix=/global/homes/m/madams/petsc_install/petsc-xc30-opt64-intel >> > PETSC_ARCH=arch-xc30-opt64-intel PETSC_DIR=/global/homes/m/mada >> > ms/petsc_install/petsc >> > [3404]PETSC ERROR: #1 MatMatMultNumeric_SeqAIJ_SeqAIJ() line 187 in >> > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/ >> seq/matmatmult.c >> > [3404]PETSC ERROR: #2 MatMatMultNumeric_SeqAIJ_SeqAIJ() line 187 in >> > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/ >> seq/matmatmult.c >> > [3404]PETSC ERROR: #3 MatPtAPNumeric_MPIAIJ_MPIAIJ() line 557 in >> > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/mpi/mpiptap.c >> > [3404]PETSC ERROR: #4 MatPtAP_MPIAIJ_MPIAIJ() line 110 in >> > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/mpi/mpiptap.c >> > [3404]PETSC ERROR: #5 MatPtAP() line 9150 in >> /global/u2/m/madams/petsc_inst >> > all/petsc/src/mat/interface/matrix.c >> > [3404]PETSC ERROR: #6 PCGAMGCreateLevel_GAMG() line 88 in >> > /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/gamg.c >> > [3404]PETSC ERROR: #7 PCSetUp_GAMG() line 611 in >> > /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/gamg.c >> > [3404]PETSC ERROR: #8 PCSetUp() line 968 in >> /global/u2/m/madams/petsc_inst >> > all/petsc/src/ksp/pc/interface/precon.c >> > [3404]PETSC ERROR: #9 KSPSetUp() line 390 in >> /global/u2/m/madams/petsc_inst >> > all/petsc/src/ksp/ksp/interface/itfunc.c >> > [3404]PETSC ERROR: #10 KSPSolve() line 599 in >> /global/u2/m/madams/petsc_inst >> > all/petsc/src/ksp/ksp/interface/itfunc.c >> > >> > [3406]PETSC ERROR: --------------------- Error Message >> > -------------------------------------------------------------- >> > [3406]PETSC ERROR: Out of memory. This could be due to allocating >> > [3406]PETSC ERROR: too large an object or bleeding by not properly >> > [3406]PETSC ERROR: destroying unneeded objects. >> > [3406]PETSC ERROR: Memory allocated 0 Memory used by process 2603798528 >> <(260)%20379-8528> >> > <(260)%20379-8528> >> > [3406]PETSC ERROR: Try running with -malloc_dump or -malloc_log for >> info. >> > [3406]PETSC ERROR: Memory requested 657532760 >> > [3406]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d >> ocumentation/faq.html >> > for trouble shooting. >> > [3406]PETSC ERROR: Petsc Release Version 3.7.5, unknown >> > [3406]PETSC ERROR: /tmp/targetExec on a arch-xc30-opt64-intel named >> > nid00713 by u6338 Wed Feb 1 16:15:09 2017 >> > [3406]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" >> > --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" >> > --download-parmetis --download-metis --download-hypre --with-ssl=0 >> > --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC >> > --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn >> > --with-fortranlib-autodetect=0 --with-shared-libraries=0 --with-x=0 >> > --with-mpiexec=srun LIBS=-lstdc++ --with-64-bit-indices >> > --prefix=/global/homes/m/madams/petsc_install/petsc-xc30-opt64-intel >> > PETSC_ARCH=arch-xc30-opt64-intel >> > PETSC_DIR=/global/homes/m/madams/petsc_[7940]PETSC >> > ERROR: - >> > >> >> >

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Re: [petsc-dev] Fwd: no petsc on Edison
by Hong 02 Feb '17

02 Feb '17

Mark: A quick check, I find that MatPtAP_MPIAIJ_MPIAI() set default algorithm as rap=PETSC_TRUE; /* do R=P^T locally, then C=R*A*P */ The crash occurs at 3404]PETSC ERROR: #1 MatMatMultNumeric_SeqAIJ_SeqAIJ() line 187 in /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/seq/matmatmult.c ierr = PetscCalloc1(B->cmap->N,&ab_dense); which is global column size P->N. I'll check if we can avoid this non-scalable approach. Meanwhile, can you try option '-matrap false' to use P^T*A*P? Hong We are getting this error on Edison. This problem has run before. This is > using maint from last week. > > I recall there are low memory options for mpiptap. I don't think we are > using them. > > Thanks, > > 3404]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [3404]PETSC ERROR: Out of memory. This could be due to allocating > [3404]PETSC ERROR: too large an object or bleeding by not properly > [3404]PETSC ERROR: destroying unneeded objects. > [3404]PETSC ERROR: Memory allocated 0 Memory used by process 2537885696 > <(253)%20788-5696> > [3404]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. > [3404]PETSC ERROR: Memory requested 657532760 > [3404]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [3404]PETSC ERROR: Petsc Release Version 3.7.5, unknown > [3404]PETSC ERROR: /tmp/targetExec on a arch-xc30-opt64-intel named > nid00713 by u6338 Wed Feb 1 16:15:09 2017 > [3404]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" > --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" > --download-parmetis --download-metis --download-hypre --with-ssl=0 > --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC > --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn > --with-fortranlib-autodetect=0 --with-shared-libraries=0 --with-x=0 > --with-mpiexec=srun LIBS=-lstdc++ --with-64-bit-indices > --prefix=/global/homes/m/madams/petsc_install/petsc-xc30-opt64-intel > PETSC_ARCH=arch-xc30-opt64-intel PETSC_DIR=/global/homes/m/mada > ms/petsc_install/petsc > [3404]PETSC ERROR: #1 MatMatMultNumeric_SeqAIJ_SeqAIJ() line 187 in > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/seq/matmatmult.c > [3404]PETSC ERROR: #2 MatMatMultNumeric_SeqAIJ_SeqAIJ() line 187 in > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/seq/matmatmult.c > [3404]PETSC ERROR: #3 MatPtAPNumeric_MPIAIJ_MPIAIJ() line 557 in > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/mpi/mpiptap.c > [3404]PETSC ERROR: #4 MatPtAP_MPIAIJ_MPIAIJ() line 110 in > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/mpi/mpiptap.c > [3404]PETSC ERROR: #5 MatPtAP() line 9150 in /global/u2/m/madams/petsc_inst > all/petsc/src/mat/interface/matrix.c > [3404]PETSC ERROR: #6 PCGAMGCreateLevel_GAMG() line 88 in > /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/gamg.c > [3404]PETSC ERROR: #7 PCSetUp_GAMG() line 611 in > /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/gamg.c > [3404]PETSC ERROR: #8 PCSetUp() line 968 in /global/u2/m/madams/petsc_inst > all/petsc/src/ksp/pc/interface/precon.c > [3404]PETSC ERROR: #9 KSPSetUp() line 390 in /global/u2/m/madams/petsc_inst > all/petsc/src/ksp/ksp/interface/itfunc.c > [3404]PETSC ERROR: #10 KSPSolve() line 599 in > /global/u2/m/madams/petsc_install/petsc/src/ksp/ksp/interface/itfunc.c > > [3406]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [3406]PETSC ERROR: Out of memory. This could be due to allocating > [3406]PETSC ERROR: too large an object or bleeding by not properly > [3406]PETSC ERROR: destroying unneeded objects. > [3406]PETSC ERROR: Memory allocated 0 Memory used by process 2603798528 > <(260)%20379-8528> > [3406]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. > [3406]PETSC ERROR: Memory requested 657532760 > [3406]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [3406]PETSC ERROR: Petsc Release Version 3.7.5, unknown > [3406]PETSC ERROR: /tmp/targetExec on a arch-xc30-opt64-intel named > nid00713 by u6338 Wed Feb 1 16:15:09 2017 > [3406]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" > --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" > --download-parmetis --download-metis --download-hypre --with-ssl=0 > --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC > --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn > --with-fortranlib-autodetect=0 --with-shared-libraries=0 --with-x=0 > --with-mpiexec=srun LIBS=-lstdc++ --with-64-bit-indices > --prefix=/global/homes/m/madams/petsc_install/petsc-xc30-opt64-intel > PETSC_ARCH=arch-xc30-opt64-intel PETSC_DIR=/global/homes/m/madams/petsc_[7940]PETSC > ERROR: - >

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Re: [petsc-dev] Fwd: no petsc on Edison
by Mark Adams 02 Feb '17

02 Feb '17

On Thu, Feb 2, 2017 at 10:53 AM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > [3404]PETSC ERROR: Memory allocated 0 Memory used by process 2537885696 > > [3404]PETSC ERROR: Memory requested 657532760 > > So the process is currently using 2.5GB - and then made a malloc > request for 650MB - and this failed? > Yep, large but not garbage. > > How many 'tasks-per-node' are you using? Perhaps you need to reduce this > number? > Treb has run this job before and I think this code has been touched recently ... I suggested that Treb try -matmatmult_via scalable Thanks, > > https://www.nersc.gov/users/computational-systems/edison/configuration/ > 64GB/node => 5.3GB/process for tasks-per-node=12 [and 2.6GB/node for > tasks-per-node=24] > > Satish > > On Wed, 1 Feb 2017, Mark Adams wrote: > > > We are getting this error on Edison. This problem has run before. This is > > using maint from last week. > > > > I recall there are low memory options for mpiptap. I don't think we are > > using them. > > > > Thanks, > > > > 3404]PETSC ERROR: --------------------- Error Message > > -------------------------------------------------------------- > > [3404]PETSC ERROR: Out of memory. This could be due to allocating > > [3404]PETSC ERROR: too large an object or bleeding by not properly > > [3404]PETSC ERROR: destroying unneeded objects. > > [3404]PETSC ERROR: Memory allocated 0 Memory used by process 2537885696 > > <(253)%20788-5696> > > [3404]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. > > [3404]PETSC ERROR: Memory requested 657532760 > > [3404]PETSC ERROR: See http://www.mcs.anl.gov/petsc/ > documentation/faq.html > > for trouble shooting. > > [3404]PETSC ERROR: Petsc Release Version 3.7.5, unknown > > [3404]PETSC ERROR: /tmp/targetExec on a arch-xc30-opt64-intel named > > nid00713 by u6338 Wed Feb 1 16:15:09 2017 > > [3404]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" > > --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" > > --download-parmetis --download-metis --download-hypre --with-ssl=0 > > --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC > > --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn > > --with-fortranlib-autodetect=0 --with-shared-libraries=0 --with-x=0 > > --with-mpiexec=srun LIBS=-lstdc++ --with-64-bit-indices > > --prefix=/global/homes/m/madams/petsc_install/petsc-xc30-opt64-intel > > PETSC_ARCH=arch-xc30-opt64-intel PETSC_DIR=/global/homes/m/mada > > ms/petsc_install/petsc > > [3404]PETSC ERROR: #1 MatMatMultNumeric_SeqAIJ_SeqAIJ() line 187 in > > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/ > aij/seq/matmatmult.c > > [3404]PETSC ERROR: #2 MatMatMultNumeric_SeqAIJ_SeqAIJ() line 187 in > > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/ > aij/seq/matmatmult.c > > [3404]PETSC ERROR: #3 MatPtAPNumeric_MPIAIJ_MPIAIJ() line 557 in > > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/mpi/mpiptap.c > > [3404]PETSC ERROR: #4 MatPtAP_MPIAIJ_MPIAIJ() line 110 in > > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/mpi/mpiptap.c > > [3404]PETSC ERROR: #5 MatPtAP() line 9150 in > /global/u2/m/madams/petsc_inst > > all/petsc/src/mat/interface/matrix.c > > [3404]PETSC ERROR: #6 PCGAMGCreateLevel_GAMG() line 88 in > > /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/gamg.c > > [3404]PETSC ERROR: #7 PCSetUp_GAMG() line 611 in > > /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/gamg.c > > [3404]PETSC ERROR: #8 PCSetUp() line 968 in > /global/u2/m/madams/petsc_inst > > all/petsc/src/ksp/pc/interface/precon.c > > [3404]PETSC ERROR: #9 KSPSetUp() line 390 in > /global/u2/m/madams/petsc_inst > > all/petsc/src/ksp/ksp/interface/itfunc.c > > [3404]PETSC ERROR: #10 KSPSolve() line 599 in > /global/u2/m/madams/petsc_inst > > all/petsc/src/ksp/ksp/interface/itfunc.c > > > > [3406]PETSC ERROR: --------------------- Error Message > > -------------------------------------------------------------- > > [3406]PETSC ERROR: Out of memory. This could be due to allocating > > [3406]PETSC ERROR: too large an object or bleeding by not properly > > [3406]PETSC ERROR: destroying unneeded objects. > > [3406]PETSC ERROR: Memory allocated 0 Memory used by process 2603798528 > > <(260)%20379-8528> > > [3406]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. > > [3406]PETSC ERROR: Memory requested 657532760 > > [3406]PETSC ERROR: See http://www.mcs.anl.gov/petsc/ > documentation/faq.html > > for trouble shooting. > > [3406]PETSC ERROR: Petsc Release Version 3.7.5, unknown > > [3406]PETSC ERROR: /tmp/targetExec on a arch-xc30-opt64-intel named > > nid00713 by u6338 Wed Feb 1 16:15:09 2017 > > [3406]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" > > --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" > > --download-parmetis --download-metis --download-hypre --with-ssl=0 > > --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC > > --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn > > --with-fortranlib-autodetect=0 --with-shared-libraries=0 --with-x=0 > > --with-mpiexec=srun LIBS=-lstdc++ --with-64-bit-indices > > --prefix=/global/homes/m/madams/petsc_install/petsc-xc30-opt64-intel > > PETSC_ARCH=arch-xc30-opt64-intel > > PETSC_DIR=/global/homes/m/madams/petsc_[7940]PETSC > > ERROR: - > > > >

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Re: [petsc-dev] Fwd: no petsc on Edison
by Satish Balay 02 Feb '17

02 Feb '17

> [3404]PETSC ERROR: Memory allocated 0 Memory used by process 2537885696 > [3404]PETSC ERROR: Memory requested 657532760 So the process is currently using 2.5GB - and then made a malloc request for 650MB - and this failed? How many 'tasks-per-node' are you using? Perhaps you need to reduce this number? https://www.nersc.gov/users/computational-systems/edison/configuration/ 64GB/node => 5.3GB/process for tasks-per-node=12 [and 2.6GB/node for tasks-per-node=24] Satish On Wed, 1 Feb 2017, Mark Adams wrote: > We are getting this error on Edison. This problem has run before. This is > using maint from last week. > > I recall there are low memory options for mpiptap. I don't think we are > using them. > > Thanks, > > 3404]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [3404]PETSC ERROR: Out of memory. This could be due to allocating > [3404]PETSC ERROR: too large an object or bleeding by not properly > [3404]PETSC ERROR: destroying unneeded objects. > [3404]PETSC ERROR: Memory allocated 0 Memory used by process 2537885696 > <(253)%20788-5696> > [3404]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. > [3404]PETSC ERROR: Memory requested 657532760 > [3404]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [3404]PETSC ERROR: Petsc Release Version 3.7.5, unknown > [3404]PETSC ERROR: /tmp/targetExec on a arch-xc30-opt64-intel named > nid00713 by u6338 Wed Feb 1 16:15:09 2017 > [3404]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" > --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" > --download-parmetis --download-metis --download-hypre --with-ssl=0 > --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC > --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn > --with-fortranlib-autodetect=0 --with-shared-libraries=0 --with-x=0 > --with-mpiexec=srun LIBS=-lstdc++ --with-64-bit-indices > --prefix=/global/homes/m/madams/petsc_install/petsc-xc30-opt64-intel > PETSC_ARCH=arch-xc30-opt64-intel PETSC_DIR=/global/homes/m/mada > ms/petsc_install/petsc > [3404]PETSC ERROR: #1 MatMatMultNumeric_SeqAIJ_SeqAIJ() line 187 in > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/seq/matmatmult.c > [3404]PETSC ERROR: #2 MatMatMultNumeric_SeqAIJ_SeqAIJ() line 187 in > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/seq/matmatmult.c > [3404]PETSC ERROR: #3 MatPtAPNumeric_MPIAIJ_MPIAIJ() line 557 in > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/mpi/mpiptap.c > [3404]PETSC ERROR: #4 MatPtAP_MPIAIJ_MPIAIJ() line 110 in > /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/mpi/mpiptap.c > [3404]PETSC ERROR: #5 MatPtAP() line 9150 in /global/u2/m/madams/petsc_inst > all/petsc/src/mat/interface/matrix.c > [3404]PETSC ERROR: #6 PCGAMGCreateLevel_GAMG() line 88 in > /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/gamg.c > [3404]PETSC ERROR: #7 PCSetUp_GAMG() line 611 in > /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/gamg.c > [3404]PETSC ERROR: #8 PCSetUp() line 968 in /global/u2/m/madams/petsc_inst > all/petsc/src/ksp/pc/interface/precon.c > [3404]PETSC ERROR: #9 KSPSetUp() line 390 in /global/u2/m/madams/petsc_inst > all/petsc/src/ksp/ksp/interface/itfunc.c > [3404]PETSC ERROR: #10 KSPSolve() line 599 in /global/u2/m/madams/petsc_inst > all/petsc/src/ksp/ksp/interface/itfunc.c > > [3406]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [3406]PETSC ERROR: Out of memory. This could be due to allocating > [3406]PETSC ERROR: too large an object or bleeding by not properly > [3406]PETSC ERROR: destroying unneeded objects. > [3406]PETSC ERROR: Memory allocated 0 Memory used by process 2603798528 > <(260)%20379-8528> > [3406]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. > [3406]PETSC ERROR: Memory requested 657532760 > [3406]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [3406]PETSC ERROR: Petsc Release Version 3.7.5, unknown > [3406]PETSC ERROR: /tmp/targetExec on a arch-xc30-opt64-intel named > nid00713 by u6338 Wed Feb 1 16:15:09 2017 > [3406]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" > --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" > --download-parmetis --download-metis --download-hypre --with-ssl=0 > --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC > --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn > --with-fortranlib-autodetect=0 --with-shared-libraries=0 --with-x=0 > --with-mpiexec=srun LIBS=-lstdc++ --with-64-bit-indices > --prefix=/global/homes/m/madams/petsc_install/petsc-xc30-opt64-intel > PETSC_ARCH=arch-xc30-opt64-intel > PETSC_DIR=/global/homes/m/madams/petsc_[7940]PETSC > ERROR: - >

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Re: [petsc-dev] Fwd: no petsc on Edison
by Mark Adams 01 Feb '17

01 Feb '17

We are getting this error on Edison. This problem has run before. This is using maint from last week. I recall there are low memory options for mpiptap. I don't think we are using them. Thanks, 3404]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [3404]PETSC ERROR: Out of memory. This could be due to allocating [3404]PETSC ERROR: too large an object or bleeding by not properly [3404]PETSC ERROR: destroying unneeded objects. [3404]PETSC ERROR: Memory allocated 0 Memory used by process 2537885696 <(253)%20788-5696> [3404]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [3404]PETSC ERROR: Memory requested 657532760 [3404]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [3404]PETSC ERROR: Petsc Release Version 3.7.5, unknown [3404]PETSC ERROR: /tmp/targetExec on a arch-xc30-opt64-intel named nid00713 by u6338 Wed Feb 1 16:15:09 2017 [3404]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" --download-parmetis --download-metis --download-hypre --with-ssl=0 --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn --with-fortranlib-autodetect=0 --with-shared-libraries=0 --with-x=0 --with-mpiexec=srun LIBS=-lstdc++ --with-64-bit-indices --prefix=/global/homes/m/madams/petsc_install/petsc-xc30-opt64-intel PETSC_ARCH=arch-xc30-opt64-intel PETSC_DIR=/global/homes/m/mada ms/petsc_install/petsc [3404]PETSC ERROR: #1 MatMatMultNumeric_SeqAIJ_SeqAIJ() line 187 in /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/seq/matmatmult.c [3404]PETSC ERROR: #2 MatMatMultNumeric_SeqAIJ_SeqAIJ() line 187 in /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/seq/matmatmult.c [3404]PETSC ERROR: #3 MatPtAPNumeric_MPIAIJ_MPIAIJ() line 557 in /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/mpi/mpiptap.c [3404]PETSC ERROR: #4 MatPtAP_MPIAIJ_MPIAIJ() line 110 in /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/mpi/mpiptap.c [3404]PETSC ERROR: #5 MatPtAP() line 9150 in /global/u2/m/madams/petsc_inst all/petsc/src/mat/interface/matrix.c [3404]PETSC ERROR: #6 PCGAMGCreateLevel_GAMG() line 88 in /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/gamg.c [3404]PETSC ERROR: #7 PCSetUp_GAMG() line 611 in /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/gamg.c [3404]PETSC ERROR: #8 PCSetUp() line 968 in /global/u2/m/madams/petsc_inst all/petsc/src/ksp/pc/interface/precon.c [3404]PETSC ERROR: #9 KSPSetUp() line 390 in /global/u2/m/madams/petsc_inst all/petsc/src/ksp/ksp/interface/itfunc.c [3404]PETSC ERROR: #10 KSPSolve() line 599 in /global/u2/m/madams/petsc_inst all/petsc/src/ksp/ksp/interface/itfunc.c [3406]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [3406]PETSC ERROR: Out of memory. This could be due to allocating [3406]PETSC ERROR: too large an object or bleeding by not properly [3406]PETSC ERROR: destroying unneeded objects. [3406]PETSC ERROR: Memory allocated 0 Memory used by process 2603798528 <(260)%20379-8528> [3406]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [3406]PETSC ERROR: Memory requested 657532760 [3406]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [3406]PETSC ERROR: Petsc Release Version 3.7.5, unknown [3406]PETSC ERROR: /tmp/targetExec on a arch-xc30-opt64-intel named nid00713 by u6338 Wed Feb 1 16:15:09 2017 [3406]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" --download-parmetis --download-metis --download-hypre --with-ssl=0 --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn --with-fortranlib-autodetect=0 --with-shared-libraries=0 --with-x=0 --with-mpiexec=srun LIBS=-lstdc++ --with-64-bit-indices --prefix=/global/homes/m/madams/petsc_install/petsc-xc30-opt64-intel PETSC_ARCH=arch-xc30-opt64-intel PETSC_DIR=/global/homes/m/madams/petsc_[7940]PETSC ERROR: -

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Re: [petsc-dev] Bump MOAB version?
by Tobin Isaac 01 Feb '17

01 Feb '17

FYI, the PETSc tests that use MOAB passed using MOAB commit f862b4c on my laptop, though when I had mpich debugging on there looks like there may have been some memory leaks that don't appear in other PETSc tests. (log attached) Cheers, Toby On Wed, Feb 01, 2017 at 03:22:18AM +0530, Vijay S. Mahadevan wrote: > Toby, thanks for the update. Yes, I recently updated the "petsc" > branch in MOAB to make sure that v4.9.2 is merged. Some of these > changes are needed for one of my upcoming PR's to improve DMMoab > support. I however have been on some international travel and haven't > found enough time to take care of this. > > Iulian, can you create a tarball that corresponds to the HEAD in petsc > branch (if not already available from the ftp site) ? > > Vijay > > PS: The macports errors are related to ESMF. They have their custom > version of MOAB (4.6.x) and so I'm unsure whether the port needs the > latest MOAB as its dependency. > > On Wed, Feb 1, 2017 at 3:07 AM, Tobin Isaac <tisaac(a)uchicago.edu> wrote: > > > > The commit of MOAB that we use in MAOB.py doesn't compile in gcc6 > > due to c++14 compatibility issues [1]. I checked out the latest petsc > > branch from their repo and it seems to compile. Can we ask them to > > host an updated tarball, too? > > > > [1] https://trac.macports.org/ticket/52427#comment:2 > > > > Toby

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Re: [petsc-dev] Bump MOAB version?
by Tobin Isaac 31 Jan '17

31 Jan '17

Thanks, Vijay. I don't know about ESMF, either, I just reproduced the error building petsc today. Cheers, Toby On Wed, Feb 01, 2017 at 03:22:18AM +0530, Vijay S. Mahadevan wrote: > Toby, thanks for the update. Yes, I recently updated the "petsc" > branch in MOAB to make sure that v4.9.2 is merged. Some of these > changes are needed for one of my upcoming PR's to improve DMMoab > support. I however have been on some international travel and haven't > found enough time to take care of this. > > Iulian, can you create a tarball that corresponds to the HEAD in petsc > branch (if not already available from the ftp site) ? > > Vijay > > PS: The macports errors are related to ESMF. They have their custom > version of MOAB (4.6.x) and so I'm unsure whether the port needs the > latest MOAB as its dependency. > > On Wed, Feb 1, 2017 at 3:07 AM, Tobin Isaac <tisaac(a)uchicago.edu> wrote: > > > > The commit of MOAB that we use in MAOB.py doesn't compile in gcc6 > > due to c++14 compatibility issues [1]. I checked out the latest petsc > > branch from their repo and it seems to compile. Can we ask them to > > host an updated tarball, too? > > > > [1] https://trac.macports.org/ticket/52427#comment:2 > > > > Toby

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Problem with PetscObjectOptionsBegin
by Matthew Knepley 31 Jan '17

31 Jan '17

Here it is: #define PetscObjectOptionsBegin(obj) 0; do { \ PetscOptionItems PetscOptionsObjectBase;\ PetscOptionItems *PetscOptionsObject = &PetscOptionsObjectBase; \ PetscOptionsObject->options = ((PetscObject)obj)->options; \ for (PetscOptionsObject->count=(PetscOptionsPublish?-1:1); PetscOptionsObject->count<2; PetscOptionsObject->count++) {\ PetscErrorCode _5_ierr = PetscObjectOptionsBegin_Private(PetscOptionsObject,obj);CHKERRQ(_5_ierr); The ((PetscObject)obj)->options requires the definition of PetscObject which is not in user facing headers, so this bombs. Matt -- 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

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