Fwd: Running NAMD on Linux Cluster

From: 김민재 (kjh950429_at_gmail.com)
Date: Wed Feb 27 2019 - 07:10:34 CST

---------- 전달된 메일 ----------
보낸사람: 김민재 <kjh950429_at_gmail.com>
날짜: 2019년 2월 27일 (수) 오전 10:18
제목: Re: namd-l: Running NAMD on Linux Cluster
받는사람: Aravinda Munasinghe <aravinda1879_at_gmail.com>

Hi

I’m new to namd, so I am using a precompiled namd binary that I downloaded
from the namd website. To be more specific, I used the
“Linux-x86_64-ibverbs-smp-CUDA” package (I’m trying to make use NVIDIA GPU
acceleration.)

Thanks

2019년 2월 27일 (수) 오전 5:06, Aravinda Munasinghe <aravinda1879_at_gmail.com>님이 작성:

> Hi,
> If you compiled charm from scratch as well, I recommend you to see if it
> was compiled properly. (Try charm hello world). If it didn't work, most
> probably from the error I see, your charm did not execute properly. What
> flags did you use when compiling charm?
> Best,
> Aravinda Munasinghe
> On Tue, Feb 26, 2019 at 10:24 AM 김민재 <kjh950429_at_gmail.com> 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
>>
>>
>>
>>
>>
>>
>
> --
> Aravinda Munasinghe,
>
>

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