AMBER Archive (2007)

Subject: Re: AMBER: MPI script

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jul 13 2007 - 17:15:36 CDT

try using sander.MPI as the binary.
also let us know which Amber version you are using.

On 7/13/07, Taryn Hartley <taryn_hartley_at_hotmail.com> wrote:
>
>
> In submitting a job to run on AMBER, this is the script I used:
>
> #!/bin/csh
> #
> # Maximum wallclock time (hh:mm:ss)
> #PBS -l walltime=18:00:00
>
> # Memory limit
> #PBS -l mem=4gb
>
> # Number of processors requested
> #PBS -l ncpus=4
>
> # Queue name
> #PBS -q standard
> #
> # Export all my environment variables to the job
> #PBS -V
> #
> # Charge job to project ktr
> #PBS -A ktr
> #
> # Job name (default = name of script file)
> #PBS -N bundlewat
> #
> # Filename for standard output (default = <job_name>.o<job_id>)
> #PBS -o bundlewat.out
> #
> # Filename for standard error (default = <job_name>.e<job_id>)
> #PBS -e bundlewat.err
> #
> # Determine the working directory where the input script is located
> # and the output files are to be placed
> cd /u/ac/thartley/test/
> #
> # Run the MPI program on all nodes/processors requested by the job
> # In this case, MD run with 4 processors
> mpirun -np 4 $AMBERHOME/exe/sander -O -i bundlewat.in -p bundlewat.prmtop -c
> bundlewat.rst -r bundlewat.rst -o bundlewat.out -x bundlewat.mdcrd
>
> And below is the contents of the error file that was returned:
>
>
> set_SCR: using existing PBS job directory /scratch/batch/193665
> MPI: co-compute2: 0x3cf0000045a321a0: forrtl: severe (19): invalid reference
> to varia
> ble in NAMELIST input, unit 5, file
> /u/ac/thartley/test/bundlewat.in, line 6, poMPI:
> co-compute2: 0x3cf0000045a321a0: sition 32
> MPI: co-compute2: 0x3cf0000045a321a0: Image PC
> Routine
> Line Source
> MPI: co-compute2: 0x3cf0000045a321a0: sander 4000000000C91390
> Unknown
> Unknown Unknown
> MPI: co-compute2: 0x3cf0000045a321a0: sander 4000000000C8C560
> Unknown
> Unknown Unknown
> MPI: co-compute2: 0x3cf0000045a321a0: sander 4000000000C34250
> Unknown
> Unknown Unknown
> MPI: co-compute2: 0x3cf0000045a321a0: sander 4000000000B882E0
> Unknown
> Unknown Unknown
> MPI: co-compute2: 0x3cf0000045a321a0: sander 4000000000B87810
> Unknown
> Unknown Unknown
> MPI: co-compute2: 0x3cf0000045a321a0: sander 4000000000BD5930
> Unknown
> Unknown Unknown
> MPI: co-compute2: 0x3cf0000045a321a0: sander 40000000001BD7A0
> Unknown
> Unknown Unknown
> MPI: co-compute2: 0x3cf0000045a321a0: sander 400000000018B7D0
> Unknown
> Unknown Unknown
> MPI: co-compute2: 0x3cf0000045a321a0: sander 40000000001874F0
> Unknown
> Unknown Unknown
> MPI: co-compute2: 0x3cf0000045a321a0: sander 4000000000003D40
> Unknown
> Unknown Unknown
> MPI: co-compute2: 0x3cf0000045a321a0: libc.so.6.1 2000000001D0DC50
> Unknown
> Unknown Unknown
> MPI: co-compute2: 0x3cf0000045a321a0: sander 4000000000003A80
> Unknown
> Unknown Unknown
> MPI: could not run executable (case #4)
>
> If anyone could help me figure out what is wrong (with the script, I
> presume) I would greatly appreciate it! - Taryn
>
> ________________________________
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