Raad2: MDynaMix

Sample Job File ("mdmx.job")

#!/bin/bash
#SBATCH --job-name=mdp
#SBATCH --time=01:00:00
#SBATCH --output=slurm.out
#SBATCH --error=slurm.err
#SBATCH --partition=l_long
#SBATCH --qos=ll
#SBATCH --hint=nomultithread
#SBATCH --ntasks=48
 
srun ~/bin/mdp > file.out

How to run this sample job file

sbatch mdmx.job

Compiling your own instance of MDynaMix

1) Create your own bin directory and an mdynamix build directory. Download and un-tar the software:

 
mkdir bin
mkdir mdynamix
cd mdynamix
wget http://www.fos.su.se/~sasha/mdynamix/versions/md528.tar.gz
tar xzf md528.tar.gz
cd md528

2) Copy one of the existing make files to create your own, customized for the Cray system:

cp Makefile.mpi Makefile.cray_mpi

3) Edit the file Makefile.cray_mpi and replace the string "mpif77" with "ftn".

4) Edit the file Makefile and add the following two lines immediately before the line reading "clean:".

 
cray_mpi:
        make -f Makefile.cray_mpi

The 2nd line above must begin with a tab character, and NOT with eight spaces.

5) Type "module list" and ensure that both the "PrgEnv-cray" and "cray-mpich" modules are loaded...

fachaud74@raad2a:~/mdynamix/md528> module list
Currently Loaded Modulefiles:
  1) modules/3.2.10.6                                8) ugni/6.0.14-6.0.6.0_18.12__g777707d.ari        15) alps/6.6.0-6.0.6.0_35.25__gd0a1ab9.ari
  2) eproxy/2.0.22-6.0.6.0_5.1__g1ebe45c.ari         9) pmi/5.0.13                                     16) rca/2.2.18-6.0.6.0_19.14__g2aa4f39.ari
  3) cce/8.7.0                                      10) dmapp/7.1.1-6.0.6.0_51.37__g5a674e0.ari        17) atp/2.1.1
  4) craype-network-aries                           11) gni-headers/5.0.12-6.0.6.0_3.26__g527b6e1.ari  18) perftools-base/7.0.1
  5) craype/2.5.14                                  12) xpmem/2.2.14-6.0.6.0_10.1__g34333c9.ari        19) PrgEnv-cray/6.0.4
  6) cray-libsci/18.04.1                            13) job/2.2.3-6.0.6.0_9.47__g6c4e934.ari           20) cray-mpich/7.7.0
  7) udreg/2.3.2-6.0.6.0_15.18__g5196236.ari        14) dvs/2.7_2.2.94-6.0.6.1_8.1__g3b7aea4

6) Proceed to compile the code with:

make cray_mpi

7) Copy the resulting "mdp" file to your bin directory.

cp mdp ~/bin

8) Change to one of the mdynamix benchmarks directories:

cd ~/mdynamics/md528/bench_suite/test1