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Re: [ESPResSo-users] mpi and compressed block files

From: Axel Arnold
Subject: Re: [ESPResSo-users] mpi and compressed block files
Date: Fri, 07 Sep 2012 15:38:02 +0200
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:15.0) Gecko/20120827 Thunderbird/15.0

Hi Martin!

On 09/07/2012 01:43 PM, Martin Lindén wrote:
Instead, I think the problem occurs when trying to close the channel
associated with the gzipped file:
error waiting for process to exit: child process lost (is SIGCHLD
ignored or trapped?)
      while executing
"close $innnn"
      (file "blockread3.tcl" line 14)
Ok, that error is something else, caused by OpenMPI that abuses signals to communicate between the nodes. With up to three nodes, everything is ok, as it uses SIGUSR1 and SIGUSR2, but for the 4th node, it uses SIGPIPE/SIGCHLD. This makes it impossible for the program to decide whether a spawned child process has terminated, and therefore you get the error above. To avoid the error, you can put a catch around the close statement. You will just not be able to figure out whether gzip had problems, but otherwise, this works.

Now, as a warning, there are also MPI implementations, e.g. on BlueGene, which just return close any tasks immediately. On platforms like this, reading gzipped files through the Tcl popen is currently impossible. From tcl8.6b1 on, there seems to be a native zlib command (, but that is fairly new stuff and you would have to compile your own Tcl.


JP Dr. Axel Arnold           Tel: +49 711 685 67609
ICP, Universität Stuttgart   Email: address@hidden foun
Pfaffenwaldring 27
70569 Stuttgart, Germany

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