[AMBER] running simulation using increased number of cores

From: onetwo <twoone21.rediffmail.com>
Date: 14 Sep 2013 04:13:50 -0000

Dear All,

We have just installed RACK server in our lab, in which we have installed AMBER software in

parallel. Server shows that it has 160 cores. When I run simulation job, I give np 160,

equilibration job crashed. Then I tried using np 8, then it worked, then again I increased np to

32, it is running fine, but for 4ns production run for 321 amino acid, it is taking 72 hours to

finish. When I used to run it on 8 cores on our previous workstation, it used to take same time.

I tried on server np 80 also, still it shows more than 70 hours to finish.

Please suggest, if I am missing something. and how to utilize all the cores for faster simulation


Thanks in advance.

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Received on Fri Sep 13 2013 - 21:30:03 PDT
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