Hello,
Thanks for your reply. Upon following the instructions for submitting
interactively, I come acrross the follwing massges,
[e953kks.node022 e953kks]$ qsub -I -l nodes=2:ppn=2,walltime=1:00:00 -q
normal
qsub: waiting for job 9435.sched to start
qsub: job 9435.sched ready
[e953kks.node025 e953kks]$ $PBS_NODEFILE list.
bash: /var/spool/PBS/aux/9435.sched: Permission denied
[e953kks.node025 e953kks]$ cd /home2/e953kks/amber8/test/4096wat
[e953kks.node025 4096wat]$ set mpich_run =
"/opt/mpich/1.2.5..10/gm-2.0.12-2.4.20-28.7smp-i686/smp/gnu/ssh/bin//mpirun"
[e953kks.node025 4096wat]$ set sander = "/home2/e953kks/amber8/exe/sander"
[e953kks.node025 4096wat]$ $mpich_run -machinefile $PBS_NODEFILE -np 4
$sander -O -i gbin -c eq1.x -o mdout.test
bash: -machinefile: command not found
[e953kks.node025 4096wat]$ $mpich_run $PBS_NODEFILE -np 4 $sander -O -i
gbin -c eq1.x -o mdout.test
bash: /var/spool/PBS/aux/9435.sched: Permission denied
[e953kks.node025 4096wat]$ cp /home2/e953kks/amber8/exe/sander .
[e953kks.node025 4096wat]$ $mpich_run -machinefile $PBS_NODEFILE -np 4
.../sander -O -i gbin -c eq1.x -o mdout.test
bash: -machinefile: command not found
[e953kks.node025 4096wat]$ $mpich_run $PBS_NODEFILE -np 4 ./sander -O -i
gbin -c eq1.x -o mdout.test
bash: /var/spool/PBS/aux/9435.sched: Permission denied
[e953kks.node025 4096wat]$
Now when checking /var/spool/PBS/aux
[e953kks.node025 aux]$ ls -l
total 4
-rw-r--r-- 1 root root 32 Sep 24 12:54 9435.sched
Any further suggestions will be appreciated.
Sincerely,
Jiten
----- Original Message -----
From: "Thomas E. Cheatham, III" <cheatham.chpc.utah.edu>
To: <amber.scripps.edu>
Sent: Friday, September 24, 2004 2:59 AM
Subject: Re: AMBER: Amber job submission using PBS
>
>> > node001
>> > node002
>> > node004
>> > node007
>> > /var/spool/PBS/mom_priv/jobs/9355.sched.SC: -machinefile: command not
>> > found
>> > /var/spool/PBS/mom_priv/jobs/9355.sched.SC: -O: command not found
>
> Regarding the PBS problems, a very good way to debug these is to attempt
> to run the job interatively in the queue.
>
> qsub -I -l nodes=2:ppn=2,walltime=1:00:00 -q normal
>
> Then if this starts up, you will be on the first node of the assigned
> $PBS_NODEFILE list.
>
> Then you can try doing each of the commands by hand.
>
> cd /home2/e953kks/amber8/test/4096wat
> set mpich_run =
> "/opt/mpich/1.2.5..10/gm-2.0.12-2.4.20-28.7smp-i686/smp/gnu/ssh/bin//mpirun"
> set sander = "/home2/e953kks/amber8/exe/sander"
>
> $mpich_run -machinefile $PBS_NODEFILE -np 4 $sander -O -i gbin -c eq1.x -o
> mdout.test
>
>
> Sometimes with mpich versions I've had trouble in the past if the
> executable to run is not in/out of the current directory, i.e. the paths
> get messed up so it thinks your job is running out of the path where your
> exe is.
>
> So, try
>
> cp -p /home2/e953kks/amber8/exe/sander .
>
> $mpich_run -machinefile $PBS_NODEFILE -np 4 ./sander -O -i gbin -c
> eq1.x -o mdout.test
>
> The interactive testing in the queue is a very nice way to go...
>
> Good luck,
>
>
> -----------------------------------------------------------------------
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>
>
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Received on Fri Sep 24 2004 - 05:53:00 PDT
