From: Zumot, Elia Nabil (enz1_at_pitt.edu)
Date: Wed Feb 27 2013 - 14:15:51 CST
Hi Hanif,
First, load namd (module load namd), then use a script like the one below (I used it for a system of ~120,000 atoms).
#!/bin/bash
#SBATCH -J job_name # Job name
#SBATCH -o output.log # Name of stdout output file (%j expands to jobId)
#SBATCH -p large # Queue name
#SBATCH -N 8 # Total number of nodes requested (16 cores/node)
#SBATCH -n 128 # Total number of mpi tasks requested
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 1.5 hours
#SBATCH -A TG-grant-number # <-- Allocation name to charge job against
ibrun namd2 job_name.conf > job_name.log
Regards
Elia
Elia Zomot, PhD
Computational and Systems Biology Department
School of Medicine, University of Pittsburgh
3089 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
Voice: 412 624 8699 - Fax: 412 648 3163
enz1_at_pitt.edu
________________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of hanif mahboobi [hanifmahboobi_at_yahoo.com]
Sent: Wednesday, February 27, 2013 2:46 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: NAMD on Stampede
Hi Everyone,
Does anybody have any generic runbatch file for NAMD job submission on Stampede just like the ones worked on Ranger?
Best,
Hanif
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