From: Abhishek TYAGI (
Date: Wed Nov 05 2014 - 23:30:20 CST


Recently the server in my university is update to new configuration ( and we have to use SLURM to run our programs. I am using previously NAMD-multicore-Cuda version on this GPU cluster. But, as they have upgraded it and we need to execute our jobs using slurm I am not able to start NAMD as dont understand how to do it, the SLURM job script ( i:

#SBATCH -J slurm_job #Slurm job name
# Set the maximum runtime, uncomment if you need it
##SBATCH -t 72:00:00 #Maximum runtime of 72 hours
# Enable email notificaitons when job begins and ends, uncomment if you need it
##SBATCH #Update your email address
##SBATCH --mail-type=begin
##SBATCH --mail-type=end
# Choose partition (queue), for example, choose gpu-k
#SBATCH -p gpu-k
# To use 2 cpu cores in a node, uncomment the statement below
##SBATCH -N 1 -n 2
# To use 1 cpu core and 1 gpu device, uncomment the statement below
##SBATCH -N 1 -n 1 --gres=gpu:1
# Setup runtime environment if necessary
# Or you can source ~/.bashrc or ~/.bash_profile
source ~/.bash_profile
# Go to the job submission directory and run your application
cd $HOME/apps/slurm

1. I want to know which version of NAMD should I use for this cluster.
2. How to edit the script (above) to run NAMD job on slurm.
3. I have searched but not find suitable answer for this.

I know you people are experts to deal with this kind of problem, plese let me how to proceed.

Thanks in advance


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