Also, adding diagnostic output in your .pbs script can be very helpful.
Here are some useful variables that our active in one of our pbs
implementations here:
echo ------------------------------------------------------
echo PBS: qsub is running on $PBS_O_HOST
echo PBS: originating queue is $PBS_O_QUEUE
echo PBS: executing queue is $PBS_QUEUE
echo PBS: working directory is $PBS_O_WORKDIR
echo PBS: execution mode is $PBS_ENVIRONMENT
echo PBS: job identifier is $PBS_JOBID
echo PBS: job name is $PBS_JOBNAME
echo PBS: node file is $PBS_NODEFILE
echo PBS: current home directory is $PBS_O_HOME
echo PBS: PATH = $PBS_O_PATH
echo ------------------------------------------------------
echo "Running on these nodes:"
cat $PBS_NODEFILE
> Dear all,
>
> I tried to recompile amber8 and tried to narrow the problem down, I found
> out that if I use exactly same command:
>
> $AMBERHOME/exe/sander -O -i md.in -o md.out -c model_min.rst -p
> model.prmtop-r model_md.rst -x model_md.mdcrd
>
> after the installation of serial part (without parallel part), it is OK.
> And
> if i use it after finishing the parallel installation of amber, then I got
> error message:
>
> Unit 5 Error on OPEN: md.in
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_12655: p4_error: : 1
>
> Anyone can tell me what is wrong please? really appreciate your help.
>
> Regards,
> Rachel
>
> On 12/13/06, Rachel <comeonsos.googlemail.com> wrote:
>>
>> Dear all,
>>
>> I have compiled amber8 on a beowulf cluster using ifort, both serial and
>> parallel compilation were OK and all the tests passed without any
>> errors.
>>
>> However, when I tried to just run an interactive job using:
>> $AMBERHOME/exe/sander -O -i md.in -o md.out -p model.prmtop -c
>> model_min.rst -r model_md.rst -x model_md.mdcrd
>>
>> I got error message as:
>> Unit 5 Error on OPEN: md.in
>> [0] MPI Abort by user Aborting program !
>> [0] Aborting program!
>> p0_12655: p4_error: : 1
>>
>> The file md.in is in the directory where I ran this job.
>>
>> I know it is a problem caused by MPI, however, I don't quite know how to
>> get rid of this error. For your information, because the mpich under the
>> cluster root directory was not compiled by ifort, therefore when I tried
>> to
>> use that to compile parallel amber, I got some errors, and searched in
>> the
>> mailing list, found out that I need an mpich compiled using the same
>> compiler. Therefore I installed a new MPICH using ifort under my own
>> home
>> directory and set MPICH_HOME to the MPICH in my own directory when I
>> compiled amber8.
>>
>> Thanks in advance for your help.
>> Best regards,
>> Rachel
>>
>
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Received on Sun Dec 17 2006 - 06:07:32 PST
