Table of Contents
- Download
1.1 Go to your scratch space
1.2 Download MESA
1.3 Download & untar the SDK - Edit your .bashrc
- Compile MESA
3.1 Compile the main program
3.2 Make your work directory - Run MESA
4.1 Make a batch file
4.2 Submit
1. Download
1.1 Go to your scratch space
cd /clusterfs/henyey/<username>
1.2 Download MESA
svn co -r 4631 http://mesa.svn.sourceforge.net/svnroot/mesa/trunk mesa
1.3 Download & untar the SDK
wget --user-agent="" http://www.astro.wisc.edu/~townsend/resource/download/mesasdk/mesasdk-x86_64-linux-20121106.tar.gz
tar xf mesasdk-x86_64-linux-20121106.tar.gz
2. Edit your .bashrc
export SCRATCH="/clusterfs/henyey/jwschwab/"
# for MESA
export MESA_DIR=$SCRATCH/mesa
export MESASDK_ROOT=$SCRATCH/mesasdk
source $MESASDK_ROOT/bin/mesasdk_init.sh
3. Compile MESA
3.1 Compile the main program
Make sure to either source your .bashrc or log out and back in. Now running the ./install
command should work.
3.2 Make your work directory
As usual, make a copy of the work directory. Since you may need a decent amount of space for the logs, this should probably live on your scratch space. Once you have that set up the way you normally would (run ./mk
, set up your inlist, etc).
4. Run MESA
4.1 Make a batch file
On one of these clusters, the way you run a job is by submitting one to the batch queue system. There’s specific info about this on the Henyey bSpace page. In general, you need a batch file that describes the job you want to run. My MESA ones look like this:
#!/bin/bash
#PBS -N MESA
#PBS -M <email_address>
#PBS -m abe
#PBS -l nodes=1:ppn=8,walltime=10:00:00
#PBS -q henyey_batch
#PBS -V
#
cd $PBS_O_WORKDIR
#
# this should be equal to the value of ppn
# there are 8 cores on each henyey node
#
export OMP_NUM_THREADS=8
./rn > rn.out
Things that you might want to adjust are the job name (-N
) and the job time limit (walltime
). The -m
& -M
flags have the system send you email when your jobs start/stop. And then of course, you may want to do something different with your ./rn
command, etc.
4.2 Submit
Supposing you named your batch file runmesa.sh
then:
qsub runmesa.sh
Then you can see where you are in the queue by typing:
qstat