[ESPResSo-users] mpi and compressed block files

[Martin Lindén]

Hi!

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:

ESPResSo-3.1.0
{ Compilation status { FFTW } { BOND_ANGLE_HARMONIC } { LENNARD_JONES }
{ LJCOS } { LJCOS2 } { MPI_CORE } { EXCLUSIONS } }

mpirun (Open MPI) 1.5.4

gzip 1.4

ubuntu 12.04 64 bit.

Sincerely,

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

sm_checkpoint.block
Description: Text document

sm_compr_checkpoint.block.gz
Description: GNU Zip compressed data

blockread3.tcl
Description: Text Data

signature.asc
Description: OpenPGP digital signature