Slurm Run on supercomputer

From: Marisol Oswald (marisoloswald1988_at_gmail.com)
Date: Sun Jan 22 2017 - 18:21:01 CST

Hello All,

I am using Slurm Commands to run NAMD on a supercomputer where I have
access to

234 64GB, 2 x 8-core 2.0GHz CPUs
    90 K20m GPU
    16 Xeon phi
    base OS - RHEL/Centos 6.4

I have the following questions.

1) Which version of NAMD 2.12 (see below the list), I must use?

2) Here is my batch file: What srun command I must use?

*********************

#!/bin/bash

#SBATCH -o testtiny_namdslurm.%j.out
#SBATCH -J testnamdmpp
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=16
#SBATCH --time=12:00:00
#SBATCH --partition=sched_xyz

cd $HOME/NAMD_2.12_Linux-x86_64-verbs-smp

module add e/openmpi/1.8.8

# Now I am confused what command to use. I tried the following (none
worked):

#Try 1

srun -N5 -n5 ./namd2 ++ppn 15 Production_Run_12_23_16.conf

#Try 2

/home/x/NAMD_2.12_Linux-x86_64-ibverbs-smp/charmrun +p32 ++mpiexec-no-n
++remote-shell ibrun namd2 ++verbose Production_Run_x12_23_16.conf

*********************************
Version 2.12 (2016-12-22) Platforms:
- Linux-x86_64-multicore
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1501>
(64-bit
Intel/AMD single node)
- Linux-x86_64
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1495>
(64-bit
Intel/AMD with ethernet)
- Linux-x86_64-TCP
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1496>
(TCP
may be better on gigabit)
- Linux-x86_64-ibverbs
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1497>
(InfiniBand
via OpenFabrics OFED, not for Omni-Path, no MPI needed)
- Linux-x86_64-ibverbs-smp
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1500>
(InfiniBand
plus shared memory, no MPI needed)
- Linux-x86_64-multicore-CUDA
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1499>
(NVIDIA
CUDA acceleration)
- Linux-x86_64-ibverbs-smp-CUDA
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1498>
(NVIDIA
CUDA with InfiniBand)
- Linux-x86_64-netlrts
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1505>
(Multi-copy
algorithms)
- Linux-x86_64-verbs
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1508>
(Multi-copy
algorithms on InfiniBand)
- Linux-x86_64-verbs-smp
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1510>
(Multi-copy
algorithms on InfiniBand)
- Linux-x86_64-verbs-smp-CUDA
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1509>
(Multi-copy
algorithms on InfiniBand)
- Linux-KNL-multicore
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1514>
(Intel
Xeon Phi KNL processor single node)
Thank you!
Marisol

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