Re: NAMD 2.7b1 on NCSA Abe

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Fri May 01 2009 - 12:18:05 CDT

It doesn't help. I have put the log file online if you want to have a look
at it:

http://artemide.bioeng.washington.edu/Files/dynamics_1.out

I had asked for 8 CPUs.

Could you please also paste jim's script into an e-mail or copy it
somewhere where I have access to?

Thanks,

      Gianluca

On Fri, 1 May 2009, Peter Freddolino wrote:

> Jim's run script has a couple of extra lines to start/stop mpd... you
> might want to try the following around your mpirun line:
>
> mvapich2-start-mpd
> setenv MV2_SRQ_SIZE 4000
> setenv VIADEV_SMP_EAGERSIZE 64
> setenv VIADEV_SMPI_LENGTH_QUEUE 256
> setenv VIADEV_ADAPTIVE_RDMA_LIMIT 0
> setenv VIADEV_RENDEZVOUS_THRESHOLD 50000
>
> mpirun -machinefile $PBS_NODEFILE -np $NPROCS
> ~jphillip/NAMD_2.7b1_Linux-x86_64/namd2 inputs/config_heat.namd >& logfile
>
> mpdallexit
>
> (the mpirun block should be one line but will probably be wrapped in
> this email).
>
> Jim, looks like the permissions on the 2.7b1 runbatch file are 750...
> any chance we can make this world readable?
>
> Best,
> Peter
>
>
> Gianluca Interlandi wrote:
>> Hi Peter,
>>
>> I cannot use ~jphillip/NAMD_scripts/runbatch_2.7b1 because it's not
>> readable or executable for the world:
>>
>> -rwxr-x--- 1 jphillip tvn 1488 Apr 1 20:08
>> /u/ac/jphillip/NAMD_scripts/runbatch_2.7b1
>>
>> /u/ac/jphillip/NAMD_scripts/runbatch_2.7b1: Permission denied.
>>
>> and I'm not in group "tvn".
>>
>> Sorry, I post here the full batchscript:
>>
>> #!/bin/csh
>> #PBS -l nodes=4:ppn=8
>> #PBS -l walltime=02:00:00
>> #PBS -l mem=4gb
>> #PBS -N T300_1auqe
>> #PBS -j oe
>> #PBS -q normal
>>
>> echo $PBS_NODEFILE
>> cat $PBS_NODEFILE
>>
>> cd $PBS_O_WORKDIR
>>
>> # Load necessary software
>> soft add +mpichvmi-intel
>>
>> # Determine the number of CPUs
>> set NPROCS = `wc -l $PBS_NODEFILE | awk '{print $1}'`
>>
>> mpirun -machinefile $PBS_NODEFILE -np $NPROCS
>> ~jphillip/NAMD_2.7b1_Linux-x86_64/namd2 inputs/config_heat.namd > logfile
>>
>>
>> Thanks for your help.
>>
>> Gianluca
>>
>>
>> On Thu, 30 Apr 2009, Peter Freddolino wrote:
>>
>>> Hi Gianluca,
>>> where is $NPROCS defined? I don't see it defined in your script before
>>> it is used. Any reason you're not just using the official 2.7b1 script
>>> (~jphillip/NAMD_scripts/runbatch_2.7b1)?
>>> Peter
>>>
>>> Gianluca Interlandi wrote:
>>>> Hi Peter,
>>>>
>>>> Sorry, I made a mistake when I copy-pasted the command line into the
>>>> e-mail. I am actually using the namd binary:
>>>>
>>>> mpirun -machinefile $PBS_NODEFILE -np $NPROCS \
>>>> ~jphillip/NAMD_2.7b1_Linux-x86_64/namd2 config.namd
>>>>
>>>> Gianluca
>>>>
>>>> On Thu, 30 Apr 2009, Peter Freddolino wrote:
>>>>
>>>>> Hi Gianluca,
>>>>> ~jphillip/NAMD_2.7b1_Linux-x86_64 is not the namd binary;
>>>>> ~jphillip/NAMD_2.7b1_Linux-x86_64/namd2 is the namd binary. You might
>>>>> want to start by making that the command that is being run by mpirun.
>>>>> Best,
>>>>> Peter
>>>>>
>>>>> Gianluca Interlandi wrote:
>>>>>> I have been trying to run NAMD2.7b1 on Abe but I have run into some
>>>>>> problems. I am using:
>>>>>>
>>>>>> #!/bin/csh
>>>>>> #PBS -l nodes=4:ppn=8
>>>>>> #PBS -l walltime=02:00:00
>>>>>>
>>>>>> mpirun -machinefile $PBS_NODEFILE -np $NPROCS \
>>>>>> ~jphillip/NAMD_2.7b1_Linux-x86_64 config.namd
>>>>>>
>>>>>> I found the executable thanks to the NAMD WIKI:
>>>>>> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdAtNCSA
>>>>>>
>>>>>> It seems that NAMD instead of running in parallel it starts 32
>>>>>> independent single CPU simulations:
>>>>>>
>>>>>> Charm++> cpu topology info is being gathered!
>>>>>> Charm++> 1 unique compute nodes detected!
>>>>>>
>>>>>> It repeats the above 32 times. Am I using it incorrectly?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Gianluca
>>>>>
>>>>>
>>>>
>>>> -----------------------------------------------------
>>>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>>>> +1 (206) 685 4435
>>>> +1 (206) 714 4303
>>>> http://artemide.bioeng.washington.edu/
>>>>
>>>> Postdoc at the Department of Bioengineering
>>>> at the University of Washington, Seattle WA U.S.A.
>>>> -----------------------------------------------------
>>>
>>
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>> +1 (206) 685 4435
>> +1 (206) 714 4303
>> http://artemide.bioeng.washington.edu/
>>
>> Postdoc at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     +1 (206) 714 4303
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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