Re: Running NAMD on Linux Cluster

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Feb 27 2019 - 13:57:49 CST

As the error message says, there does not appear to be a command called
"ibrun" on your cluster. This is not surprising, since the standard
command is mpiexec. You would only need to write a "mympiexec" script if
you needed to call a different program to launch parallel jobs. The
"ibrun" command is the job launch command at TACC used as an example.

Jim

On Wed, 27 Feb 2019, ~@민~^ wrote:

> 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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