Re: Running NAMD on Linux Cluster

From: Aravinda Munasinghe (aravinda1879_at_gmail.com)
Date: Wed Feb 27 2019 - 12:03:35 CST

Hi,
Since you are running this in a cluster (assuming there is a workload
manager), if you only need to run namd using gpus in a single node, try
without charmrun.

  ./namd2 +p<what ever you request> +setcpuaffinity <configfile>

And also make sure you have intel and cuda libraries loaded properly.
Best,
Aravinda Munasinghe

On Wed, Feb 27, 2019 at 8:12 AM 김민재 <kjh950429_at_gmail.com> wrote:

>
>
> ---------- 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,
>>
>>

-- 
Aravinda Munasinghe,

This archive was generated by hypermail 2.1.6 : Sun Sep 15 2019 - 23:20:21 CDT