Getting an account

more to come...

ssh configuration

You can add the following lines to ~/.ssh/config on your local machine:

Host frontera.tacc.utexas.edu frontera
     HostName frontera.tacc.utexas.edu
     User YOURUSERNAME

and replace YOURUSERNAME by your TACC username.

Once this is done, you can ssh frontera by simply doing:

ssh frontera

Environment

On frontera, add the following lines to ~/.bash_login:

export ISSM_DIR=PATHTOTRUNK
source $ISSM_DIR/etc/environment.sh
module load petsc/3.15

Log out and log back in to apply this change.

Installing ISSM on frontera

frontera will only be used to run the code, you will use your local machine for pre and post processing, you will never use frontera's matlab. You can check out ISSM and install the following packages:

• m1qn3

Use the following configuration script (adapt to your needs):

./configure \
   --prefix=$ISSM_DIR \
   --with-wrappers=no \
   --with-mpi-include="$TACC_IMPI_INC" \
   --with-mpi-libflags="-L$TACC_IMPI_LIB/release_mt -lmpi" \
   --with-petsc-dir="$TACC_PETSC_DIR" \
   --with-petsc-arch=$ISSM_ARCH \
   --with-metis-dir="$TACC_PETSC_DIR/$PETSC_ARCH" \
   --with-mkl-libflags="-L$TACC_MKL_LIB -mkl=parallel" \
   --with-mumps-dir="$TACC_PETSC_DIR/$PETSC_ARCH" \
   --with-scalapack-dir="$TACC_PETSC_DIR/$PETSC_ARCH" \
   --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
   --enable-debugging \
   --enable-development

frontera_settings.m

You have to add a file in $ISSM_DIR/src/m entitled frontera_settings.m with your personal settings on your local issm install:

cluster.login='seroussi';
cluster.codepath='/home1/03729/seroussi/trunk-jpl/bin/';
cluster.executionpath='/work/03729/seroussi/trunk-jpl/execution/';

use your username for the login and enter your code path and execution path. These settings will be picked up automatically by matlab when you do md.cluster=frontera()

Note that the `executionpath' creates temporary binary files that can be removed once the job is complete. For this reason, you can set the path to be somewhere on the $SCRATCH filesystem, which is unlimited temporary storage on frontera.

Running jobs on frontera

On frontera, each node has 24 cores and you can use any multiple of 24 for the total number of processors. The more nodes and the longer the requested time, the more you will have to wait in the queue. So choose your settings wisely:

md.cluster=frontera('numnodes',2);

Before you run your job, make sure to open a port first and enter the port number in md.cluster. Here is a handy alias:

alias ls5tunnel='ssh -L 1099:localhost:22 ls5'

That will open port number 1099 that you can then use in ISSM so that you don't need to enter your password.

to have a job of 2 nodes, 12 cpus for nodes, so a total of 24 cores.

To submit a job on frontera, do:

sbatch job.queue

Now if you want to check the status of your job and the queue you are using, type in the bash with the frontera session:

showq -u USERNAME

You can delete your job manually by typing:

scancel JOBID

where JOBID is the ID of your job (indicated in the Matlab session). Matlab indicates too the directory of your job where you can find the files JOBNAME.outlog and JOBNAME.errlog. The outlog file contains the informations that would appear if you were running your job on your local machine and the errlog file contains the error information in case the job encounters an error.