Re: run namd cuda with srun.

From: Fırat Yılmaz (firat.yilmaz_at_eduline.com.tr)
Date: Wed Jun 21 2017 - 03:36:09 CDT

Hi Patrick,

Now i am able to run namd over slurm. Now just had a "Stale File Handle"
error but its related to nfs over rdma.

Thank you very much Patrick.

Best Regards.

Fırat Yılmaz
Systems Engineer

Eduline Bilişim Sanayi ve Ticaret Ltd. Şti. www.eduline.com.tr

Nisbetiye Mah. Gümüş Sok Kır Apt. Sitesi B Blok No:5/4 34340 Beşiktaş / İSTANBUL

Tel : +90 212 324 60 61 Faks : +90 212 324 65 70

On 21-06-2017 10:42, Patrick BOUSQUET-MELOU wrote:
> Hi Firat,
>
> Yes.
> NAMD 2.12 MPI+SMP+CUDA version, compiled from sources with Intel MPI, is used with Slurm and its srun command in my computing center.
>
> With Intel MPI :
>
> # Enable Intel MPI / srun coupling
> export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so
>
> Then we launch with sbatch the following script :
>
> ###
> #!/bin/bash
>
> #SBATCH —nodes 2
> #SBATCH —ntasks-per-node 14
> #SBATCH --gres gpu:2
>
> PPN=`echo $SLURM_CPUS_PER_TASK - 1 | bc`
>
> srun namd2 +ppn $PPN input.namd > namd2.log
> ###
>
> If you use Open MPI, set « export SLURM_MPI_TYPE=pmi2 » and use the same script.
>
>
>
> Très cordialement,
>
> Patrick BOUSQUET-MELOU
> Responsable support scientifique
> CRIANN
> 745, avenue de l'Université
> 76800 Saint Etienne du Rouvray
> Tél. : (+33) 2 32 91 42 91
> Mail : support_at_criann.fr
> Web : http://www.criann.fr
>
>> Le 20 juin 2017 à 23:03, Fırat Yılmaz <firat.yilmaz_at_eduline.com.tr> a écrit :
>>
>> Hi There,
>>
>> Is it possible to run namd cuda version on multinodes with slurm? I insatalled the cuda60 and able to run on charmrun but i want slurm avare of node status.
>>
>>
>> --
>> Fırat Yılmaz
>> Systems Engineer
>>
>> Eduline Bilişim Sanayi ve Ticaret Ltd. Şti. www.eduline.com.tr
>>
>> Nisbetiye Mah. Gümüş Sok Kır Apt. Sitesi B Blok No:5/4 34340 Beşiktaş / İSTANBUL
>>
>> Tel : +90 212 324 60 61 Faks : +90 212 324 65 70
>>

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