Re: AMBER: mpd error in submitting parallel job
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 $PBS_NODEFILE
<<sander command>>
mpdallexit
----------
Gustavo.
On Thu, Feb 14, 2008 at 4:11 AM, Lili Peng <lpeng.ucsd.edu> wrote:
> Hi everyone,
>
> I've come across another mpd-related error (probably related to the same one
> in my previous inquiry) while submitting a parallel job. My input script is:
>
> #!/bin/csh
> #$ -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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Received on Sun Feb 17 2008 - 06:07:26 PST
