Getting an account

New users have to ask Byron

ssh configuration

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

Host aci aci-b.aci.ics.psu.edu
  HostName aci-b.aci.ics.psu.edu
  User eps5217
  HostbasedAuthentication no

and replace eps5217 by your aci username.

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

ssh aci

Password-less ssh

Once you have the account, you can setup a public key authentification in order to avoid having to input your password for each run. You need to have a SSH public/private key pair. If you already have one, you can skip their creation described below. If you do not, you can create a SSH public/private key pair by typing the following command and following the prompts (no passphrase necessary):

$your_localhost% ssh-keygen -t rsa
Generating public/private rsa key pair.
Enter file in which to save the key (/Users/username/.ssh/id_rsa):RETURN
Enter passphrase (empty for no passphrase):RETURN
Enter same passphrase again:RETURN
Your identification has been saved in /Users/username/.ssh/id_rsa.
Your public key has been saved in /Users/username/.ssh/id_rsa.pub.

Two files were created: your private key /Users/username/.ssh/id_rsa, and the public key /Users/username/.ssh/id_rsa.pub. The private key is read-only and only for you, it is used to decrypt all correspondence encrypted with the public key. The contents of the public key need to be copied to ~/.ssh/authorized_keys on your aci account:

$your_localhost%scp ~/.ssh/id_rsa.pub username@your_remotehost:~

Now on ACI, copy the content of id_rsa.pub:

$your_remotehost%cat ~/id_rsa.pub >> ~/.ssh/authorized_keys
$your_remotehost%rm ~/id_rsa.pub

If you don't have the required permission to change authorized_keys, change it to 777 (using chmod) and once the public key is added to it, change it back to 440.

Environment

Add the following to your ~/.bashrc:

#ISSM vairables
export ISSM_DIR="/gpfs/group/brp106/default/USERNAME/trunk-jpl"
source $ISSM_DIR/etc/environment.sh
alias cdi="cd $ISSM_DIR"

#ISSM modules
module load intel/16.0.3
module load mkl/11.3.3
module load impi/5.1.3

And replace ISSM_DIR with your actual trunk. Log out and log back in to apply this change. Make sure to download ISSM on gpfs, i.e., not in your home directory (much faster i/o).

Installing ISSM on ACI

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

• autotools
• PETSc (use the pleiades script and follow the instructions, you will need to submit a job and compile PETSc manually, do not make test, it will not work on the cluster)
• m1qn3

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

./configure \
   --prefix=$ISSM_DIR \
   --with-wrappers=no \
   --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
   --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
   --with-mpi-include="/opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/include/" \
   --with-mpi-libflags="-L/opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/lib/ -lmpicxx -lmpifort -lmpi -lmpigi -lifcore -lifport" \
   --with-mkl-libflags="-L/opt/intel/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core"\
   --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
   --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \
   --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
   --enable-development

aci_settings.m

You have to add a file in $ISSM_DIR/src/m entitled aci_settings.m with your personal settings:

cluster.name='aci';
cluster.login='eps5217';
cluster.queue='brp106_a_g_sc_default';
cluster.codepath='/gpfs/group/brp106/default/eps5217/trunk-jpl/bin';
cluster.executionpath='/gpfs/scratch/eps5217/';
cluster.nodes=1;
cluster.ppn=20;
cluster.time=3*60;

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=pfe()

Make sure your module list includes pkgsrc, comp-intel/2016.2.181, and mpi-sgi/mpt .

Running jobs on ACI

On Pleiades, 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=aci('numnodes',8,'time',30,'processor','wes','queue','devel');
md.cluster.time=10;

to have a maximum job time of 10 minutes and 8 westmere nodes. If the run lasts longer than 10 minutes, it will be killed and you will not be able to retrieve your results.

Now if you want to check the status of your job and the queue you are using, use this command:

qstat -u USERNAME

You can delete your job manually by typing:

qdel 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.

To watch your current jobs:

watch qstat  -a

If you want to load results from the cluster manually (for example if you have an error due to an internet interruption), you find in the informations Matlab gave you /home/srebuffi/trunk-jpl/execution//SOMETHING/JOBNAME.lock , you copy the SOMETHING and you type in MATLAB:

md=loadresultsfromcluster(md,'SOMETHING');