[petsc-dev] Error running on Titan with GPUs & GNU

Mon Oct 29 17:13:16 CDT 2018

Still getting this error with downloaded lapack. I sent the logs on the
other thread.

18:02 master= /lustre/atlas/proj-shared/geo127/petsc$ make
PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda
PETSC_ARCH="" test
Running test examples to verify correct installation
Using
PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda
and PETSC_ARCH=
*******************Error detected during compile or link!*******************
See http://www.mcs.anl.gov/petsc/documentation/faq.html
/lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials ex19
*********************************************************************************
cc -o ex19.o -c -O
 -I/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/include
  `pwd`/ex19.c
cc -O  -o ex19 ex19.o
-L/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/lib
-Wl,-rpath,/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/lib
-L/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/lib
-lpetsc -lHYPRE -lflapack -lfblas -lparmetis -lmetis -ldl
/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/lib/libpetsc.a(dlimpl.o):
In function `PetscDLOpen':
dlimpl.c:(.text+0x3b): warning: Using 'dlopen' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/lib/libpetsc.a(send.o):
In function `PetscOpenSocket':
send.c:(.text+0x3be): warning: Using 'gethostbyname' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
true ex19
rm ex19.o
Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI
process
See http://www.mcs.anl.gov/petsc/documentation/faq.html
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
Number of SNES iterations = 2
Application 19080270 resources: utime ~0s, stime ~1s, Rss ~72056, inblocks
~19397, outblocks ~51049
Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 MPI
processes
See http://www.mcs.anl.gov/petsc/documentation/faq.html
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
[1]PETSC ERROR: [0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
--------------------- Error Message
--------------------------------------------------------------
[1]PETSC ERROR: [0]PETSC ERROR: Error in external library
Error in external library
[1]PETSC ERROR: [0]PETSC ERROR: Error in LAPACK routine 0
Error in LAPACK routine 0
[1]PETSC ERROR: [0]PETSC ERROR: See
http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
shooting.
[1]PETSC ERROR: [0]PETSC ERROR: Petsc Development GIT revision:
v3.10.2-461-g0ed19bb123  GIT Date: 2018-10-29 13:43:53 +0100
Petsc Development GIT revision: v3.10.2-461-g0ed19bb123  GIT Date:
2018-10-29 13:43:53 +0100
[1]PETSC ERROR: [0]PETSC ERROR: ./ex19 on a  named nid08331 by adams Mon
Oct 29 18:07:59 2018
./ex19 on a  named nid08331 by adams Mon Oct 29 18:07:59 2018
[1]PETSC ERROR: [0]PETSC ERROR: Configure options --with-cudac=1
--with-batch=0
--prefix=/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda
--download-hypre --download-metis --download-parmetis
--download-fblaslapack --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC
--with-cxxlib-autodetect=0 --with-fc=ftn --with-fortranlib-autodetect=0
--with-shared-libraries=0 --known-mpi-shared-libraries=1
--with-mpiexec=aprun --with-x=0 --with-64-bit-indices --with-debugging=0
PETSC_ARCH=arch-titan-opt64idx-gnu-cuda
PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc
Configure options --with-cudac=1 --with-batch=0
--prefix=/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda
--download-hypre --download-metis --download-parmetis
--download-fblaslapack --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC
--with-cxxlib-autodetect=0 --with-fc=ftn --with-fortranlib-autodetect=0
--with-shared-libraries=0 --known-mpi-shared-libraries=1
--with-mpiexec=aprun --with-x=0 --with-64-bit-indices --with-debugging=0
PETSC_ARCH=arch-titan-opt64idx-gnu-cuda
PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc
[1]PETSC ERROR: [0]PETSC ERROR: #1 KSPComputeEigenvalues_GMRES() line 144
in /lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/impls/gmres/gmreig.c
#1 KSPComputeEigenvalues_GMRES() line 144 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/impls/gmres/gmreig.c
[1]PETSC ERROR: #2 KSPComputeEigenvalues() line 132 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: [1]PETSC ERROR: #2 KSPComputeEigenvalues() line 132 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/interface/itfunc.c
#3 KSPChebyshevComputeExtremeEigenvalues_Private() line 288 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/impls/cheby/cheby.c
[0]PETSC ERROR: [1]PETSC ERROR: #3
KSPChebyshevComputeExtremeEigenvalues_Private() line 288 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/impls/cheby/cheby.c
#4 KSPSolve_Chebyshev() line 390 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/impls/cheby/cheby.c
[0]PETSC ERROR: [1]PETSC ERROR: #4 KSPSolve_Chebyshev() line 390 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/impls/cheby/cheby.c
#5 KSPSolve() line 780 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: [1]PETSC ERROR: #5 KSPSolve() line 780 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/interface/itfunc.c
#6 PCMGMCycle_Private() line 20 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: [1]PETSC ERROR: #6 PCMGMCycle_Private() line 20 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/pc/impls/mg/mg.c
#7 PCApply_MG() line 377 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: [1]PETSC ERROR: #7 PCApply_MG() line 377 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/pc/impls/mg/mg.c
#8 PCApply() line 462 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: [1]PETSC ERROR: #8 PCApply() line 462 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/pc/interface/precon.c
#9 KSP_PCApply() line 281 in
/lustre/atlas/proj-shared/geo127/petsc/include/petsc/private/kspimpl.h
[0]PETSC ERROR: [1]PETSC ERROR: #9 KSP_PCApply() line 281 in
/lustre/atlas/proj-shared/geo127/petsc/include/petsc/private/kspimpl.h
#10 KSPFGMRESCycle() line 166 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/impls/gmres/fgmres/fgmres.c
[0]PETSC ERROR: [1]PETSC ERROR: #10 KSPFGMRESCycle() line 166 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/impls/gmres/fgmres/fgmres.c
#11 KSPSolve_FGMRES() line 291 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/impls/gmres/fgmres/fgmres.c
[0]PETSC ERROR: [1]PETSC ERROR: #11 KSPSolve_FGMRES() line 291 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/impls/gmres/fgmres/fgmres.c
#12 KSPSolve() line 780 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: [1]PETSC ERROR: #12 KSPSolve() line 780 in
/lustre/atlas1/geo127/proj-shared/petsc/src/ksp/ksp/interface/itfunc.c
#13 SNESSolve_NEWTONLS() line 224 in
/lustre/atlas1/geo127/proj-shared/petsc/src/snes/impls/ls/ls.c
[0]PETSC ERROR: [1]PETSC ERROR: #13 SNESSolve_NEWTONLS() line 224 in
/lustre/atlas1/geo127/proj-shared/petsc/src/snes/impls/ls/ls.c
#14 SNESSolve() line 4396 in
/lustre/atlas1/geo127/proj-shared/petsc/src/snes/interface/snes.c
[0]PETSC ERROR: [1]PETSC ERROR: #14 SNESSolve() line 4396 in
/lustre/atlas1/geo127/proj-shared/petsc/src/snes/interface/snes.c
#15 main() line 161 in
/lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials/ex19.c
[0]PETSC ERROR: [1]PETSC ERROR: #15 main() line 161 in
/lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials/ex19.c
PETSc Option Table entries:
[0]PETSC ERROR: [1]PETSC ERROR: PETSc Option Table entries:
-da_refine 3
[0]PETSC ERROR: [1]PETSC ERROR: -da_refine 3
-ksp_type fgmres
[0]PETSC ERROR: [1]PETSC ERROR: -ksp_type fgmres
-pc_type mg
[0]PETSC ERROR: -pc_type mg
[1]PETSC ERROR: ----------------End of Error Message -------send entire
error message to petsc-maint at mcs.anl.gov----------
[0]PETSC ERROR: ----------------End of Error Message -------send entire
error message to petsc-maint at mcs.anl.gov----------
Rank 0 [Mon Oct 29 18:07:59 2018] [c20-3c1s5n3] application called
MPI_Abort(MPI_COMM_WORLD, 76) - process 0
Rank 1 [Mon Oct 29 18:07:59 2018] [c20-3c1s5n3] application called
MPI_Abort(MPI_COMM_WORLD, 76) - process 1
_pmiu_daemon(SIGCHLD): [NID 08331] [c20-3c1s5n3] [Mon Oct 29 18:07:59 2018]
PE RANK 1 exit signal Aborted
Application 19080271 exit codes: 134
Application 19080271 resources: utime ~0s, stime ~1s, Rss ~72056, inblocks
~19405, outblocks ~51055
5a6
> Application 19080272 resources: utime ~1s, stime ~1s, Rss ~72056,
inblocks ~19420, outblocks ~51049
/lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials
Possible problem with ex19_hypre, diffs above
=========================================
*******************Error detected during compile or link!*******************
See http://www.mcs.anl.gov/petsc/documentation/faq.html
/lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials ex5f
*********************************************************
ftn -c -O
-I/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/include
-o ex5f.o ex5f.F90
ftn -O   -o ex5f ex5f.o
-L/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/lib
-Wl,-rpath,/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/lib
-L/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/lib
-lpetsc -lHYPRE -lflapack -lfblas -lparmetis -lmetis -ldl
/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/lib/libpetsc.a(dlimpl.o):
In function `PetscDLOpen':
dlimpl.c:(.text+0x3b): warning: Using 'dlopen' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/lustre/atlas/proj-shared/geo127/petsc_titan_opt64idx_gnu_cuda/lib/libpetsc.a(send.o):
In function `PetscOpenSocket':
send.c:(.text+0x3be): warning: Using 'gethostbyname' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
rm ex5f.o
Possible error running Fortran example src/snes/examples/tutorials/ex5f
with 1 MPI process
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