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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 |
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
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