== Getting an account ==

New users have to ask Byron

== ssh configuration ==

You can add the following lines to `~/.ssh/config` on your local machine:
{{{
#!sh
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:

{{{
#!sh
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):
{{{
#!sh
$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:

{{{
#!sh
$your_localhost%scp ~/.ssh/id_rsa.pub username@your_remotehost:~
}}}

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

{{{
#!sh
$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`:
{{{
#!sh
#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):

{{{
#!sh
./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:

{{{
#!m
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:

 {{{
#!m
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:

 {{{
#!sh
qstat -u USERNAME
}}}

You can delete your job manually by typing:

{{{
#!sh
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:

{{{
#!sh
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:

{{{
#!m
md=loadresultsfromcluster(md,'SOMETHING');
}}}