AMBER Archive (2004)

Subject: Re: AMBER: Amber job submission using PBS

From: Jiten (jiten_at_postech.ac.kr)
Date: Fri Sep 24 2004 - 01:21:27 CDT

Hello all,

Thanks for your comments. I am bit more through. This time it is different
kind of error.

$qsub AMBER.qsub ( I attach the new script)

I got the error massage as follows

node010
node017
node018
node071

     mdfil: Error unknown flag: =

     usage: sander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
                   [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip
rstdip -mdip mddip -inf mdinfo -radii radii]
Consult the manual for additional options.
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_17929: p4_error: : 1
Warning: Command line arguments for program should be given
after the program name. Assuming that /var/spool/PBS/aux/9465.sched is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming that -O is a
command line argument for the program.

Now I try to submit the job interactively as suggested by Thomas,

[e953kks_at_node115 4096wat]$ export
mpich_run="/opt/mpich/1.2.5..10/gm-2.0.12-2.4.20-28.7smp-i686/smp/gnu/ssh/bin/mpirun"

[e953kks_at_node115 4096wat]$ export sander="/home2/e953kks/amber8/exe/sander"

[e953kks_at_node115 4096wat]$ echo $sander
/home2/e953kks/amber8/exe/sander

[e953kks_at_node115 4096wat]$ $mpich_run -machinefile $PBS_NODEFILE -np 4
$sander -O -i gbin -c eq1.x -o mdout.test
p0_7774: p4_error: : 1

  Unit 5 Error on OPEN: gbin
[0] MPI Abort by user Aborting program !
[0] Aborting program!

  Unit 5 Error on OPEN: gbin
p0_7773: p4_error: : 1
[0] MPI Abort by user Aborting program !
[0] Aborting program!

  Unit 5 Error on OPEN: gbin
p0_14930: p4_error: OOPS: semop lock failed: -1
    p4_error: latest msg from perror: Identifier removed
p0_14929: p4_error: : 1
[0] MPI Abort by user Aborting program !
[0] Aborting program!

I created gbin file from Run.pure_wat

$cat > gbin <<EOF
 short md, nve ensemble
 &cntrl
   ntx=5, irest=1,
   ntc=2, ntf=2, tol=0.0000001,
   nstlim=10, ntt=0,
   ntpr=1, ntwr=10000,
   dt=0.001,
 /
 &ewald
   nfft1=50, nfft2=50, nfft3=50,
 /
EOF

It woks fine with the serial version of sander.

Then I tried running the another sander job using the mdin and crd/top files
which was running well in other machines. Again the same problem.

Any suggestions are highly appreciated,

Sincerely,

Jiten

----- Original Message -----
From: "Thomas E. Cheatham, III" <cheatham_at_chpc.utah.edu>
To: <amber_at_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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