Raad2: MDynaMix
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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