Re: NAMD 2.7b1 on NCSA Abe

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Apr 30 2009 - 22:58:09 CDT

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.
-----------------------------------------------------

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