Re: [External] running NAMD with Slurm

From: Sharp, Kim (sharpk_at_pennmedicine.upenn.edu)
Date: Wed Jan 09 2019 - 12:41:20 CST

right, Brian's solution is easier if you have the right exec.
of course as Victor said you need a multinode build, but that alone
won't fix your issue.
Kim

On 1/9/19 12:57 PM, Bennion, Brian wrote:
> hello
>
> If you use the mpi aware namd executable all the searching for hostnames
> can be handled  by srun just using:
>
> srun -N 4 -n 96 namd2 blah.....
>
>
> Brian
>
>
> ------------------------------------------------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> Sharp, Kim <sharpk_at_pennmedicine.upenn.edu>
> *Sent:* Wednesday, January 9, 2019 9:15:19 AM
> *To:* namd-l_at_ks.uiuc.edu; Seibold, Steve Allan
> *Subject:* Re: [External] namd-l: running NAMD with Slurm
> Steve,
> details might differ as I am running a different version of namd, and
> hardware is obviously different.
>
> here is a slurm script we use on our cluster:
>
> -----------------------------------------------
> #!/bin/csh
> #SBATCH --mail-type=ALL
> #SBATCH --partition=namd
> #SBATCH --nodes=4
> #SBATCH --ntasks=96
> echo 'nodes: ' $SLURM_NNODES 'tasks/node: ' $SLURM_TASKS_PER_NODE 'total
> tasks: ' $SLURM_NTASKS
> set WORKDIR=/home/sharp/work/c166/
> cd $WORKDIR
> module load namd
> make_namd_nodelist
> charmrun ++nodelist nodelist.$SLURM_JOBID ++p $SLURM_NTASKS `which
> namd2`   +setcpuaffinity c166_s2000.conf > sharp_3Dec2018_.log
> ---------------------------------------------------------
>
> namd is launched via charmrun with the
>   ++nodelist hostnamefile
> option.
>
> this hostnamefile contains lines like:
>
> host node023 ++cpus 2
> host node024 ++cpus 2
>
> for however many nodes you requested. It is generated at the time slurm
> starts your job, because only at that time does slurm know the names of
> the nodes it is allocating to this job. you get this node list by
> executing the slurm command
>
> scontrol show hostnames
>
> in your job script and capturing/reformatting the output into the
> nodenamelist file. here we have a script make_namd_nodelist that does
> this, you can see it is executed right before the namd command
>
> best
> Kim
>
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> On 1/9/19 10:54 AM, Seibold, Steve Allan wrote:
>> Thanks Kim for your response. Here is my Slurm script as follows:
>>
>>
>> =====================================================
>>
>>
>> #!/bin/bash
>>
>> #SBATCH --job-name=Seibold           # Job name
>> #SBATCH --partition=mridata          # Partition Name (Required)
>> #SBATCH --mail-type=END,FAIL    # Mail events (NONE, BEGIN, END, FAIL, ALL)
>> #SBATCH --mail-user=stevesei_at_ku.edu   # Where to send mail
>> #SBATCH --nodes=2 --ntasks-per-node=15 --mem-per-cpu=250M --time=12:00:00
>> #SBATCH --output=md7_3BP_%j.log # Standard output and error log
>>
>> pwd; hostname; date
>>
>> #module load namd/2.12_multicore
>>
>> echo "Running on $SLURM_CPUS_ON_NODE cores"
>>
>>
>> ~/NAMD2/NAMD_2.13_Linux-x86_64/namd2 md7_3BP.namd
>>
>> ===========================================================
>>
>>
>> Thanks, Steve
>>
>
> --
> Kim Sharp, Ph.D,
> Dept. of Biochemistry & Biophysics
> Chair, Biochemistry & Molecular Biophysics Graduate Group
> Perelman School of Medicine at the University of Pennsylvania
> 805A Stellar Chance
> Philadelphia, PA 19104
> webpage: crystal.med.upenn.edu
> 215-573-3506
>

-- 
Kim Sharp, Ph.D,
Dept. of Biochemistry & Biophysics
Chair, Biochemistry & Molecular Biophysics Graduate Group
Perelman School of Medicine at the University of Pennsylvania
805A Stellar Chance
Philadelphia, PA 19104
webpage: crystal.med.upenn.edu
215-573-3506

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