AMBER Archive (2008)

Subject: Re: AMBER: mpd error in submitting parallel job

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Thu Feb 14 2008 - 13:45:47 CST

I'm not sure how it works for your machine, but in some configurations
you may need to start the mpd in your script, such as:
----------
mpdboot -v -f $PBS_NODEFILE

<<sander command>>

mpdallexit
----------

Gustavo.

On Thu, Feb 14, 2008 at 4:11 AM, Lili Peng <lpeng_at_ucsd.edu> wrote:
> Hi everyone,
>
> I've come across another mpd-related error (probably related to the same one
> in my previous inquiry) while submitting a parallel job. My input script is:
>
> #!/bin/csh
> #$ -cwd
> #
> #$ -m lpeng
> #$ -l h_rt=00:10:00
> #$ -e error_file
> #$ -o output_file
> #$ -pe mpi 16
> #
> #
> cd /nas/lpeng/test
> /nas/lpeng/opt/bin/mpirun -np 16\
> /nas/lpeng/src/amber9/exe/sander -O -i pgga10.in -p pgga10.top -c
> pgga10.crd -o pgga10.out -x pgga10.mdcrd -r pgga10.rst
>
> I checked the 'qstat' and the job ran to completion. However, the output
> files (pgga10.mdcrd, pgga10.out, and pgga10.rst) did not show up in my
> /test directory.
>
> I checked the error_file, but it has no data (0 kb). However, the
> output_file shows:
>
> /:xpt/gridengine/default/spool/compute-0-0/active_jobs/239954.1/pe_hostfile
> compute-1-20
> compute-1-20
> compute-3-0
> compute-3-0
> compute-2-25
> compute-2-25
> compute-0-0
> compute-2-2
> compute-2-2
> compute-0-17
> compute-0-17
> compute-0-19
> compute-0-19
> compute-0-20
> Warning: no access to tty (Bad file descriptor).
> Thus no job control in this shell.
> mpiexec_compute-1-20.local: cannot connect to local mpd
> (/tmp/mpd2.console_lpeng); possible causes:
> 1. no mpd is running on this host
> 2. an mpd is running but was started without a "console" (-n option)
>
> Then I go back and try "mpd &" but receive:
>
> An mpd is already running with console at /tmp/mpd2.console_lpeng at
> granite.ucsd.edu. Start mpd with the -n option for a second mpd on same
> host.
>
> This is where I get stuck. I Googled the problem, but nothing relevant came
> up. Does anyone have any leads on this issue? Your input would be
> appreciated. Please note that I already have "export PATH" to the mpd set.
>
> Sincerely,
> Lili
>
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