NAMD

NAMD on GPU

1. SSH into GPU cluster using the following command: ssh This email address is being protected from spambots. You need JavaScript enabled to view it. .

2. The default setting of NAMD has been set to use rsh to distribute tasks to the compute node. In the GPU cluster; rsh is disabled. User need to change his/her environment from rsh to ssh connection by typing the following command: export CONV_RSH=/usr/bin/ssh (For NAMD authentication) and export PVM_RSH=/usr/bin/ssh (For Torque authentication).

3. From then, create a directory named: namdtest in the following directory: /GPU/home/username.

4. To run NAMD jobs through Ethernet network, do the following:

4.1 cd to /GPU/home/username/namdtest and create the following example script file named: namd.moab.
-----------------------------------------------------------------------
###These lines are for Moab
#MSUB -l nodes=2:ppn=16:gpus=4 partition=c2070
#MSUB -l walltime=168:00:00
#MSUB -m be
#MSUB -V
#MSUB -o /GPU/home/username/namdtest/out
#MSUB -e /GPU/home/username/namdtest/err
#MSUB -d /GPU/opt/namd/NAMD_2.8_Source/Linux-x86_64
#MSUB -mb

##### Running commands
echo "++++++++++"
echo "host files is:"
echo " "
cat $PBS_NODEFILE
cp $PBS_NODEFILE $PBS_STEP_OUT.hostfile
echo " "
echo "++++++++++"

nproc=`cat $PBS_NODEFILE | wc -l`
cd /GPU/opt/namd/NAMD_2.8_Source/Linux-x86_64/
charmrun +p$nproc namd2 /GPU/opt/namd/NAMD_2.8_Source/apoa1/apoa1.namd > /GPU/home/username/namdtest/OUTPUT

-----------------------------------------------------------------------
5. To run NAMD jobs through Infiniband network, do the following:

5.1 cd to /GPU/home/username/namdtest and create the following example script file named: namd.moab.
-----------------------------------------------------------------------
###These lines are for Moab
#MSUB -l nodes=2:ppn=16:gpus=4 partition=c2070
#MSUB -l walltime=168:00:00
#MSUB -m be
#MSUB -V
#MSUB -o /GPU/home/username/namdtest/out
#MSUB -e /GPU/home/username/namdtest/err
#MSUB -d /GPU/opt/namd/NAMD_2.8_Source/Linux-x86_64
#MSUB -mb

##### Running commands
echo "original machine file is:"
echo "++++++++++"
cat $PBS_NODEFILE
echo "++++++++++"
cat $PBS_NODEFILE|sed -e 's/.*/&-ib/'>$PBS_STEP_OUT.hostfile
echo "modified machine file is:"
echo "++++++++++"
cat $PBS_STEP_OUT.hostfile

nproc=`cat $PBS_NODEFILE | wc -l`
cd /GPU/opt/namd/NAMD_2.8_Source/Linux-x86_64/
charmrun +p$nproc namd2 /GPU/opt/namd/NAMD_2.8_Source/apoa1/apoa1.namd > /GPU/home/username/namdtest/OUTPUT
-----------------------------------------------------------------------
6. Save the file and run the command: msub namd.moab. NOTE: In the script file, user can either use partition=c2070 or partition=c1060.
7. To check the status of the job, type the command: showq.
8. To check the status of the nodes, type the command: pbsnodes. Note: This command will display available nodes and gpus within the nodes.

Documentation for users:

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