[CIG-SHORT] PETSc errors in PyLith

Brad Aagaard baagaard at usgs.gov
Wed Jul 5 08:33:19 PDT 2006


If you look closely you will see that the error is that PyLith cannot 
open "bm5_1.connect". This is an input file. It should have been 
created in the "Setting up symbolic links with prefix bm5_1..." part 
of the shell script, runbm5.sh.

> [0]PETSC ERROR: Unable to open file!
> [0]PETSC ERROR: Cannot open PetscViewer file: bm5_1.connect!

The shell script assumes you are using the bash shell. You can try 
using the attached Python script, runbm.py, as a replacement for the 
shell script, which should permit you to use any shell.

Note: Both the shell script and Python script assume you are running 
the simulation from a directory that contains all of the input files. 
If you are not following the tutorial in the PyLith User Guide, I 
recommend that you start with there.

Instructions on how to compile from source should be available later 
this week in the User Guide (if you want to build PyLith on a Solaris 


On Friday 30 June 2006 9:32 pm, Tabrez Ali wrote:
> 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: 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:
> /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: 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: 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
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