[CIG-SHORT] PETSc errors in PyLith

Fri Jun 30 21:32:44 PDT 2006

Hello 

I am a graduate student at Purdue and I am trying to use PyLith on a Linux
cluster [intel-xeon/mpich 1.2.6/gcc 3.3.5] (The printenv output is attached)

When I run the scecbm5 example I get some PETSc errors which are listed below
(looks like the library is linked from the wrong location).

Any ideas as to what could be wrong. Also are there any plans to port PyLith to
Solaris?

Thanks in advance

Regards,
Tabrez

Setting up symbolic links with prefix bm5_1...
Running PyLith...
mpirun -np 1 /tmp/stali/pylith-0.8-linux-x86/bin/pylith3dapp.py --typos=relaxed
--scanner.fileRoot=bm5_1 --scanner.asciiOutput=full --scanner.
ucdOutput=ascii -log_summary -pc_type bjacobi -sub_pc_type ilu -ksp_monitor
-ksp_view -ksp_rtol 1e-09

Hello from pl3dsetup.__init__!

Hello from pl3drun.__init__!

Hello from pl3dscan.__init__ (begin)!
Setting default keyword values:

Hello from pl3dscan.__init__ (end)!
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Unable to open file!
[0]PETSC ERROR: Cannot open PetscViewer file: bm5_1.connect!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development Version 2.3.1, Patch 14, unknown HG revision:
unknown
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: /tmp/stali/pylith-0.8-linux-x86/bin/pylith3dapp.py on a
linux-gnu named re-034.rcac.purdue.edu by stali Fri Jun 30 23:56:00 20
06
[0]PETSC ERROR: Libraries linked from
/home/leif/monolith/install/petsc-dev/lib/linux-gnu-cxx-real-debug
[0]PETSC ERROR: Configure run at Fri Jun 23 13:51:07 2006
[0]PETSC ERROR: Configure options --with-sieve=true --with-clanguage=C++
--with-boost-dir=/home/leif/monolith/gcc-4.0.2/include --with-x=0 --w
ith-cxx=apg++ --with-cc=apgcc --with-fc=g95
--with-mpi-dir=/home/leif/monolith/mpich --with-shared=0
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: PetscViewerFileSetName_ASCII() line 579 in
src/sys/viewer/impls/ascii/filev.c
[0]PETSC ERROR: PetscViewerFileSetName() line 461 in
src/sys/viewer/impls/ascii/filev.c
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or try http://valgrind.org on linux to find memory corruption errors
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: ---------------------  Stack Frames
------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR:       INSTEAD the line number of the start of the function
[0]PETSC ERROR:       is given.
[0]PETSC ERROR: [0] PetscViewerFileSetName_ASCII line 523
src/sys/viewer/impls/ascii/filev.c
[0]PETSC ERROR: [0] PetscViewerFileSetName line 456
src/sys/viewer/impls/ascii/filev.c

-------------- next part --------------
PATH=/opt/mpich-1.2.6/p4-gcc-3.3.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/usr/pbs/bin:/usr/maui/bin:/opt/c3-3:/autohome/u76/stali/codes:/tmp/stali/pylith-0.8-linux-x86/bin
PBS_O_HOME=/home/clerk/u76/stali
PBS_O_LANG=C
PBS_O_LOGNAME=stali
PBS_O_PATH=/opt/mpich-1.2.6/p4-gcc-3.3.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/usr/pbs/bin:/usr/maui/bin:/opt/c3-3:/autohome/u76/stali/codes:/tmp/stali/pylith-0.8-linux-x86/bin
PBS_O_MAIL=/var/mail/stali
PBS_O_SHELL=/bin/tcsh
PBS_O_HOST=radon.rcac.purdue.edu
PBS_O_WORKDIR=/tmp/stali/pylith/tutorials/scecbm5/workarea
PBS_O_SYSTEM=Linux
PBS_O_QUEUE=workq
HOME=/home/clerk/u76/stali
LOGNAME=stali
PBS_JOBNAME=STDIN
PBS_JOBID=368651.xenon.rcac.purdue.edu
PBS_QUEUE=workq
SHELL=/bin/tcsh
USER=stali
PBS_JOBCOOKIE=772F8BA940F68E352AEE8DBB71CCF782
PBS_NODENUM=0
PBS_TASKNUM=1
PBS_MOMPORT=15003
PBS_NODEFILE=/var/spool/PBS/aux/368651.xenon.rcac.purdue.edu
OMP_NUM_THREADS=1
NCPUS=1
TMPDIR=/tmp/pbs.368651.xenon.rcac.purdue.edu
PBS_ENVIRONMENT=PBS_INTERACTIVE
TERM=vt100
HOSTTYPE=i386-linux
VENDOR=intel
OSTYPE=linux
MACHTYPE=i386
SHLVL=1
PWD=/tmp/stali/tutorials/scecbm5/workarea
GROUP=eas
HOST=re-034.rcac.purdue.edu
MODULE_VERSION=3.1.6
MODULE_VERSION_STACK=3.1.6
MODULESHOME=/opt/modules-3.1.6/3.1.6
MODULEPATH=/opt/modules-3.1.6/versions:/opt/modules-3.1.6/$MODULE_VERSION/modulefiles:/opt/modules-3.1.6/modulefiles:
LOADEDMODULES=mpich/gcc/335
LD_LIBRARY_PATH=/opt/mpich-1.2.6/p4-gcc-3.3.5/lib:/tmp/stali/pylith-0.8-linux-x86/lib/
FC=mpif77
_MODULESBEGINENV_=/home/clerk/u76/stali/.modulesbeginenv
_LMFILES_=/opt/modules-3.1.6/modulefiles/mpich/gcc/335
CC=mpicc
MPI_HOME=/opt/mpich-1.2.6/p4-gcc-3.3.5
CXX=mpiCC