Hello Every One,
I am using NAMD for the last couple of years. Now I got a chance to use NAMD on cluster. To ask very simply, can any one provide me a kind of script.sh or tell me how to make such script to execute NAMD on cluster.
I am trying to run NAMD with a previous commands like charmrun ++local namd2 +p8 abc.conf > abc.log. When ever I use charmrun here, I am receiving some MPI related errors. Now after one day of browsing, I just realized that my way is not ok, i need to make and then simply run that .sh script.
I am not really good in linux, just can do basics.
Thanks
If this does not work . . .
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node81.html
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node82.html
. . . post the error message.
The execution of the actual command (namd2) is same whether you run it on one node or on multiple nodes, the rest of the job script matters. Can you attach the rest of the job script and the type of scheduler you are running the job on?
actually i worked on NAMD simulation on singlle CPU machine. but now i have to transfer on different cluster. can anyone help me for 2questions:
1) how to connect to different primary login node which have definite log in IP ?
2) what should be script for running the NAMD.conf file on Cluster super computer?
please help me anyone. Thanks in advance.
Regards.
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