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[ESPResSo-users] mpi and compressed block files

From: Martin Lindén
Subject: [ESPResSo-users] mpi and compressed block files
Date: Thu, 06 Sep 2012 14:50:39 +0200
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:15.0) Gecko/20120827 Thunderbird/15.0


I am fairly new to Espresso, and have some trouble with reading
checkpoints, as described at the end of Sec. 10.1.7 in the users guide
for 3.1.0.

To reproduce the problem:

1. Run blockread3.tcl in serial mode. This reads a uncompressed and a
compressed version of a blockfile (idential content), and works as expected.
> Espresso blockread3.tcl

2. Run in mpi mode with one processor. Somewhat artificial, but works:
> mpirun -n 1 Espresso blockread3.tcl

3. The problem is mpi on multiple processors:
> mpirun -n 4 Espresso blockread3.tcl


WARNING: node_grid incompatible with current n_nodes, ignoring
error waiting for process to exit: child process lost (is SIGCHLD
ignored or trapped?)
    while executing
"close $innnn"
    (file "blockread3.tcl" line 14)
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.

Two processors (mpirun -n 2 ...) sometimes go through, and sometimes
crashes, but more than two always crashes on my system.

A temporary fix is of course to stay away from compressing the block
files. But it would be nice to be able to work with compressed files
when I go to larger systems.

System info:

{ Compilation status { FFTW } { BOND_ANGLE_HARMONIC } { LENNARD_JONES }

mpirun (Open MPI) 1.5.4

gzip 1.4

ubuntu 12.04 64 bit.


Martin Lindén, PhD
Dept. of Biochemistry and Biophysics, Stockholm University

Attachment: sm_checkpoint.block
Description: Text document

Attachment: sm_compr_checkpoint.block.gz
Description: GNU Zip compressed data

Attachment: blockread3.tcl
Description: Text Data

Attachment: signature.asc
Description: OpenPGP digital signature

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