Hello,
I attach the file.
Thanks,
JIten
----- Original Message -----
From: "Guanglei Cui" <cuigl.csb.sunysb.edu>
To: <amber.scripps.edu>
Sent: Friday, September 24, 2004 2:49 AM
Subject: Re: AMBER: Amber job submission using PBS
> Can you send the PBS script as attachment, instead of copying and pasting
> to the email? Thanks.Hello,
>
> Guanglei
>
> Jiten wrote:
>> Hello,
>>
>> This is what I get in the PBS output file
>>
>> 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
>>
>> Where do I need to modify again ?
>>
>> Sincerely,
>>
>> JIten
>>
>> ----- Original Message ----- From: "Guanglei Cui" <cuigl.csb.sunysb.edu>
>> To: <amber.scripps.edu>
>> Sent: Friday, September 24, 2004 1:20 AM
>> Subject: Re: AMBER: Amber job submission using PBS
>>
>>
>>> You didn't specify topology file ... are you using the default name? You
>>> might want to check out the PBS output to be sure.
>>>
>>> Jiten wrote:
>>>
>>>> Thanks,
>>>>
>>>> I also tried to construct using the sample script from
>>>> http://amber.scripps.edu/cluster_info/pbs_script.html as follows. But
>>>> it is still not working. COuld anybody help me out ?
>>>>
>>>> #!/bin/bash
>>>> #PBS -l nodes=2, ppn=2
>>>> #PBS -l walltime=50:00:00
>>>> #PBS -j oe
>>>> #PBS -q normal
>>>> #PBS -N amber-jiten
>>>> #PBS -l pmem=2048MB
>>>> #PBS -l vmem=2048MB
>>>> cat $PBS_NODEFILE
>>>>
>>>> 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 `wc -l < $PBS_NODEFILE`
>>>> $sander \
>>>> -O -i gbin -c eq1.x -o mdout.test
>>>>
>>>>
>>>> Sincerely,
>>>>
>>>> Jiten
>>>>
>>>> ----- Original Message ----- From: "Guanglei Cui"
>>>> <cuigl.csb.sunysb.edu>
>>>> To: <amber.scripps.edu>
>>>> Sent: Friday, September 24, 2004 12:52 AM
>>>> Subject: Re: AMBER: Amber job submission using PBS
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> You can check out this page. The example is down almost at the bottom.
>>>>> http://gears.aset.psu.edu/hpc/systems/lionxm/userguide/
>>>>>
>>>>> Guanglei
>>>>>
>>>>> Jiten wrote:
>>>>>
>>>>>> Dear Amber users,
>>>>>> I am wondering if someone could provide me a template for the script
>>>>>> for the amber job submission using Portable Batch System (PBS).
>>>>>> Thanks in advance,
>>>>>> Sincerely,
>>>>>> N. Jiten Singh
>>>>>> C/O Prof. Kwang S. Kim
>>>>>> Department of Chemistry
>>>>>> Pohang University of Science and Technology
>>>>>> San 31, Hyojadong, Namgu
>>>>>> Pohang 790-784, Korea
>>>>>> Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
>>>>>> Fax : 82-54-279-8137 (or +82-54-279-3399)
>>>>>> Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e
>>>>>> Home Page : http://www.geocities.com/njs_19
>>>>>
>>>>>
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>>>>>
>>>>
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>>>
>>
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Received on Fri Sep 24 2004 - 05:53:00 PDT
