Running NAMD on Linux Cluster

From: 김민재 (kjh950429_at_gmail.com)
Date: Tue Feb 26 2019 - 09:22:37 CST

Hi
I have been facing several problems while trying to run a MD simulation
through a supercomputer. I have read through the namd user guide and
followed their instructions. So, I have been writing bash scripts to run
namd. Following the userguide I wrote script called 'mympiexec':
 #!/bin/csh
shift; shift; exec ibrun $*

Then, I wrote a script called 'runme': (NAMD is the directory that holds
namd2 and mympiexec)

cd NAMD
./charmrun +p8 ++mpiexec ++remote-shell ./mympiexec ./namd2 ./1ca2_eq.conf

However, I got the following error message(testy):
Warning: Permanently added '[c12]:22554,[192.168.0.112]:22554' (ECDSA) to
the list of known hosts.
ibrun: Command not found.
ibrun: Command not found.
Charmrun> error attaching to node '127.0.0.1':
Timeout waiting for node-program to connect
(I attached the other message to this email)

I also tried another method advised in a html guide to NAMD. I wrote
'runscript':
#!/bin/csh
setenv LD_LIBRARY_PATH "${1:h}:$LD_LIBRARY_PATH"
$*

 And then, I wrote and ran the following script 'runCUDA':
#!/bin/csh
cd NAMD
./charmrun ++runscript ./runscript +p8 ./namd2 +idlepoll ++ppn 1 ./1ca2_eq

In this case I got the following error message (testx):
Warning: Permanently added '[c38]:22554,[192.168.0.138]:22554' (ECDSA) to
the list of known hosts.
ssh_exchange_identification: read: Connection reset by peer
Charmrun> Error 255 returned from remote shell (localhost:0)
Charmrun> Reconnection attempt 1 of 3
ssh_exchange_identification: read: Connection reset by peer
Charmrun> Error 255 returned from remote shell (localhost:0)
Charmrun> Reconnection attempt 1 of 3
ssh_exchange_identification: read: Connection reset by peer
Charmrun> Error 255 returned from remote shell (localhost:0)
Charmrun> Reconnection attempt 2 of 3
ssh_exchange_identification: read: Connection reset by peer
Charmrun> Error 255 returned from remote shell (localhost:0)
Charmrun> Reconnection attempt 2 of 3
ssh_exchange_identification: read: Connection reset by peer
Charmrun> Error 255 returned from remote shell (localhost:0)
Charmrun> Reconnection attempt 3 of 3
ssh_exchange_identification: read: Connection reset by peer
Charmrun> Error 255 returned from remote shell (localhost:0)
Charmrun> Reconnection attempt 3 of 3
ssh_exchange_identification: read: Connection reset by peer
Charmrun> Error 255 returned from remote shell (localhost:0)
Charmrun> Too many reconnection attempts; bailing out
ssh_exchange_identification: read: Connection reset by peer
Charmrun> Error 255 returned from remote shell (localhost:0)
Charmrun> Too many reconnection attempts; bailing out

I am new to namd and I would really appreciate help. Thanks


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