From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Wed Nov 12 2014 - 21:07:16 CST
Thankyou Mitcheel for the reply, I have fixed this.
________________________________
From: Mitchell Gleed <aliigleed16_at_gmail.com>
Sent: Thursday, November 13, 2014 2:57 AM
To: NAMD list; Abhishek TYAGI
Subject: Re: namd-l: NAMD on SLURM
Hi Abhishek,
This question is better to ask your supercomputer administrator(s). I haven't really used GPU's with NAMD, but my university does use SLURM for job scheduling.
Here is a general submission script that has given me the best results for a 1-node multicore build on the clusters I run my simulations on (with a line added for gpu's, for your case):
\\\\\\\\\\\\\\
#!/bin/bash
#SBATCH --time=24:00:00 # walltime
#SBATCH --ntasks=16 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --gres=gpu:1
#SBATCH --mem-per-cpu=1024M # memory per CPU core
#SBATCH -J "jobname" # job name
# LOAD MODULES, INSERT CODE, AND RUN YOUR PROGRAMS HERE
module purge
module load icc/14.0.3
configfile=namd.config
logfile=namd.config.log
namdexec=/apps/namd2
${namdexec} +setcpuaffinity `numactl --show | awk '/^physcpubind/ {printf "+p%d +pemap %d",(NF-1),$2; for(i=3;i<=NF;++i){printf ",%d",$i}}'` $configfile > $logfile
//////////////
Request resources (processors, memory, etc.) according to the setup of the clusters you want to run on where the lines labeled #SBATCH are.
You may need to load up the specific compiler(s) you used to compile NAMD (in my case, icc/14.0.3). Set the variables for your namd configuration file (configfile), the file to store standard output (logfile), and the NAMD executable you are using (namdexec). I'm not sure if the particular launching scheme I use will work for you, so this is where testing different options will work and where a supercomputing administrator may be able to help, too.
My university has a handy SLURM submission script generator you could try out here: https://marylou.byu.edu/documentation/slurm/script-generator. The man page for slurm and sbatch can be helpful too.
Good luck
On Wed, Nov 5, 2014 at 10:30 PM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk<mailto:atyagiaa_at_connect.ust.hk>> wrote:
Hi,
Recently the server in my university is update to new configuration (http://itsc.ust.hk/services/academic-teaching-support/research-computing/high-performance-computing/gpu-cluster/hardware/) 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 (http://itsc.ust.hk/services/academic-teaching-support/research-computing/high-performance-computing/gpu-cluster/jobs/#slurm) i:
#!/bin/bash
#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 --mail-user=user_name_at_ust.hk<mailto:user_name_at_ust.hk> #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
./your_gpu_application
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
Abhishek
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