AMBER Archive (2008)

Subject: RE: AMBER: Restart MD Simulation

From: dpandit_at_brandeis.edu
Date: Sat May 24 2008 - 08:40:40 CDT

Hi Ross:
Yesterday, I also sent an email to our server admin and it seems my
job was just waiting in the que. As this is first restart job, I got
anxious and sent an email to amber list too. Now, my job is running.

Thank you.
Deepa

Quoting Ross Walker <ross_at_rosswalker.co.uk>:

> This message really doesn't contain any information for us to be able to
> help you. You could start by explaining what you mean by "unable to get it
> running". What error messages do you see? What is behavior you are referring
> to when you say "running"? Does it restart from the beginning? Does the
> queuing system refuse to accept it as a valid job? Does it start running and
> then crash with an error message? Is the server still broken?
>
> You need to be much more explicit here.
>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
>> Of dpandit_at_brandeis.edu
>> Sent: Friday, May 23, 2008 2:56 PM
>> To: amber_at_scripps.edu
>> Subject: AMBER: Restart MD Simulation
>>
>> Hi:
>> I am using following script to restart my job which was aborted due to
>> server failure but I am unable to get it running. I am using restart
>> file but I am not sure what am I doing wrong?
>>
>> Thank you.
>> Deepa
>>
>>
>> #!/bin/bash
>> #$ -S /bin/bash
>> #$ -N pro_hGH_May23
>> #$ -pe mpich 8
>> #$ -M dpandit_at_brandeis.edu
>> #$ -m bes
>> mpirun -np 8 /share/apps/amber9/exe/sander.MPI -O -i pro_hGH_apr21.in
>> -p hgh_sol_apr7.prmtop -c pro_hGH_5.rst -r pro_hGH_5_rst.rst -o
>> pro_hGH_5_rst.out -x pro_hGH_5_rst.mdcrd
>> gzip -9 pro_hGH_5_rst.mdcrd
>> echo "DONE"
>>
>>
>>
>>
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>
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