[CIG-SHORT] Pylith Running on cluster

Mon Dec 15 14:32:06 PST 2014

Hi Matt,
I have successfuly run the example problem /barshearwave/quad4 with 3 nodes
12 cores per each nodes. I am wondering about the "fork" wanning , is it
has something to do with this hanging for my large simulation?

Here's the stderr file :
*****************************************

----------------------------------------

Begin Torque Prologue (Mon Dec 15 16:24:20 2014)

Job ID:           1820108.cc-mgmt1.campuscluster.illinois.edu

Username:         xiaoma5

Group:            cee_elbanna

Job Name:         YOURJOBNAME

Limits:
      ncpus=1,neednodes=3:ppn=12,nodes=3:ppn=12,walltime=04:00:00

Job Queue:        secondary

Account:          cee_elbanna

Nodes:            taub335 taub339 taub349

End Torque Prologue

----------------------------------------

--------------------------------------------------------------------------

An MPI process has executed an operation involving a call to the

"fork()" system call to create a child process.  Open MPI is currently

operating in a condition that could result in memory corruption or

other system errors; your MPI job may hang, crash, or produce silent

data corruption.  The use of fork() (or system() or other calls that

create child processes) is strongly discouraged.

The process that invoked fork was:

  Local host:          taub339 (PID 8722)

  MPI_COMM_WORLD rank: 12

If you are *absolutely sure* that your application will successfully

and correctly survive a call to fork(), you may disable this warning

by setting the mpi_warn_on_fork MCA parameter to 0.

--------------------------------------------------------------------------

[12]PETSC ERROR:
------------------------------------------------------------------------

[12]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range

[12]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[12]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[12]PETSC
ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find
memory corruption errors

[12]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run

[12]PETSC ERROR: to get more information on the crash.

[12]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------

[12]PETSC ERROR: Signal received

[12]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
for trouble shooting.

[12]PETSC ERROR: Petsc Development GIT revision:
c754102742ddd04620cbeb83ad83e0546d180516  GIT Date: 2014-07-16 16:18:38
-0500

[12]PETSC ERROR: /home/xiaoma5/project-cse/pylith/bin/mpinemesis on a
arch-pylith named taub339 by xiaoma5 Mon Dec 15 16:24:24 2014

[12]PETSC ERROR: Configure options
--prefix=/home/xiaoma5/project-cse/pylith --with-c2html=0 --with-x=0
--with-clanguage=C --with-mpicompilers=1 --with-debugging=0
--with-shared-libraries=1 --download-chaco=1 --download-ml=1
--download-fblaslapack=1 --with-hdf5=1
--with-hdf5-include=/home/xiaoma5/project-cse/pylith/include
--with-hdf5-lib=/home/xiaoma5/project-cse/pylith/lib/libhdf5.dylib
--LIBS=-lz CPPFLAGS="-I/home/xiaoma5/project-cse/pylith/include "
LDFLAGS="-L/home/xiaoma5/project-cse/pylith/lib " CFLAGS="-g -O2"
CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS="-g -O2"
PETSC_DIR=/home/xiaoma5/project-cse/src/pylith/pylith-installer-2.0.3-0/petsc-pylith
PETSC_ARCH=arch-pylith

[12]PETSC ERROR: #1 User provided function() line 0 in  unknown file