Hi Sajeewa,
In that case I suspect that the mpirun program you are referring to in
your script is not the one that corresponds to the mpi installation that
was used to compiler sander.MPI.
All the best
Ross
On 2/8/13 1:04 PM, "Sajeewa Pemasinghe" <sajeewasp.gmail.com> wrote:
>Hi Ross,
>
>Nope. They are on the same line. Do you see them in different lines?. In
>my
>actual script I have written them on the same line.
>
>Thank you
>
>Sajeewa Dewage
>
>On Fri, Feb 8, 2013 at 3:46 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> Dear Sajeewa,
>>
>> This may just be a formatting issue in your email but is your sander.MPI
>> on a different line to the mpirun command? If yes then that is your
>> problem. Put them on the same line.
>>
>> All the best
>> Ross
>>
>>
>>
>> On 2/8/13 12:37 PM, "Sajeewa Pemasinghe" <sajeewasp.gmail.com> wrote:
>>
>> >Hi all,
>> >
>> >I have the following script to run TREMD.
>> >
>> >#!/bin/bash -f
>> >#PBS -q egacq
>> >#PBS -l nodes=12:ppn=7
>> >
>> >ulimit -s unlimited
>> >
>> >export
>>PATH=/wsu/arch/x86_64/mvapich-1.1/bin:/usr/local/amber10/bin:$PATH
>> >
>> >cd
>>
>>>/wsu/home/ej/ej02/ej0271/new_project_5_20_2012/REMD_gb/redtemps/temp_par
>>>al
>> >lel_with_pmemd/REMD_finally
>> >
>> >/wsu/arch/x86_64/mvapich-1.1/bin/mpirun -np 84
>> >/usr/local/amber10/bin/sander.MPI -ng 42 -groupfile remd.groupfile
>> >
>> >So I have allocated 84 cpus for 42 groups , so that 2 cpus get
>>allocated
>> >per group. But I get the following error message.
>> >
>> > Error: specified more groups ( 42 ) than the number of processors (1
>>) !
>> >
>> >and the program crashes. As I have already allocated 84 cores for 42
>> >groups
>> >I don't understand the meaning of the above error.
>> >
>> >Could anyone help me figure this out?
>> >
>> >Thank you
>> >
>> >Sajeewa Dewage
>> >_______________________________________________
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>> >http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
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Received on Fri Feb 08 2013 - 13:30:05 PST
