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Bug #131

segmentation fault in mdrun on linux cluster (opteron architecture)

Added by Dorin Preda almost 13 years ago. Updated over 12 years ago.

Status:
Closed
Priority:
High
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

Context: =========
- gromacs application used in parallel on a cluster( linux Opteron
architecture, PME problem).

Environment: ============
- RedHat 3 Update 4 / Red Hat 4 Update 4
- architecture x86_64 Opteron
- Interconnect : gigabit ethernet
- Compilers : gcc, Pathscale, PGI
- MPI : mpich2, mpich-1.2.7, lam-7.1.2
- gromacs : 3.3.1
- fftw : 3.1.2 (but also used the gromacs-built in FFT)

Input data: ===========
- see the archive attached containing :
- the input file for the problem
- the run script
- some outputs of the segmentation fault runs
- the scripts used to compile gromacs and fftw

Symtomes: =========

- one of the processes makes a segmentation fault (see the file
output.txt in the attached archive)
- after debugging the segfault seems to come inside a fft function
- changing the fftw with gromacs buil-in fftw doesn't solve the problem
- changing debugging options (disabling optimization, adding boundary
check and stack checks) doesn't solve the problem
- using fftw assertion points to a failed assertion (see outputs)
rapport-bug.tar.bz2 (2.6 MB) rapport-bug.tar.bz2 archive with outputs, compile and run files Dorin Preda, 02/11/2007 08:16 PM

History

#1 Updated by Dorin Preda almost 13 years ago

Created an attachment (id=107)
archive with outputs, compile and run files

#2 Updated by David van der Spoel over 12 years ago

Your system has a pressure of 1e7 bar. That probably means the system is not
well equilibrated. You can try to search the mailing list for clues as to what
to do.

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