== Getting an account ==

New users have to ask the PIs (Eric Larour or Mathieu Morlighem) to request a NASA account for them if they don't have one already:
 - go to [https://www.nas.nasa.gov/hecc/portal/accounts] select option 3 ("I want to request a NASA identity for one of my new users")
 - provide the information requested

Then, a NAS account has to be created by the new user:
 - go to [https://www.nas.nasa.gov/hecc/portal/accounts] select option 2 ("I want to request and account for myself")
 - provide the information requested using either GID = s1690 for Eric's group or GID = s1507 for Mathieu's group
 - the PI will receive an email to approve the request
 - All users must complete NASA-mandatory Basic IT Security Training (This year's training is called "FY2016 CYBERSECURITY AND SENSITIVE UNCLASSIFIED INFORMATION AWARENESS TRAINING"). 
 - UCI IT Security officer: Josh Drummond jdrummon@uci.edu
 - JPL IT Security officer: Tomas Soderstrom Tomas.J.Soderstrom@jpl.nasa.gov

== Password-less ssh ==

Follow the steps outlined here [http://www.nas.nasa.gov/hecc/support/kb/Setting-Up-SSH-Passthrough_232.html]

== Environment ==

Since you will be using `bash`, add the following to your `~/.bashrc`:
{{{
#ISSM
export ISSM_DIR="/u/jbondzio/ISSM/trunk-jpl"
source $ISSM_DIR/etc/environment.sh

#Packages
module load pkgsrc
module load comp-intel/2016.2.181
module load mpi-sgi/mpt
}}}

And replace `ISSM_DIR` with your actual trunk. ''Log out and log back in'' to apply this change.

== Installing ISSM on Pleiades ==

'''Do NOT install mpich'''. We have to use the one provided by NAS. Pleiades 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:
 - m1qn3
 - PETSc (see instructions below)

Installing PETSc on a cluster is challenging because PETSc cannot call `mpiexec` without formally submitting a job. You first need to run the installation script `install-3.8-pleiades.sh`. You will then be stopped by PETSc with the following message:
{{{
#!sh
=================================================================================
    Since your compute nodes require use of a batch system or mpiexec you must:

 1) cd /home3/mmorligh/issm/trunk-jpl/externalpackages/petsc/src

 2) Submit ./conftest-arch-linux2-c-opt to 1 processor of your batch system or system you are
    cross-compiling for; this will generate the file reconfigure-arch-linux2-c-opt.py

 3) Run ./reconfigure-arch-linux2-c-opt.py (to complete the configure process).
=================================================================================
}}}

To make your life easy, you have a script ready to go. Go to the `src` folder, where PETSc is being installed, open `script.queue` and change `group_list` to `s1507` if you are in Mathieu's group. Then submit the job using `qsub`:
{{{
#!sh
qsub script.queue
}}}

A job ID (similar to `3513616.pbspl1.nas.nasa.gov`) will appear to the screen. Once the job is done, you should see a new file in the current directory: `./reconfigure-arch-linux2-c-opt.py`. Once you see it, you can run:
{{{
#!sh
./reconfigure-arch-linux2-c-opt.py
}}}
PETSc is going to compile its packages, and at the end, you will need to copy and paste the `make` commands:
{{{
#!sh
xxx=========================================================================xxx
 Configure stage complete. Now build PETSc libraries with (gnumake build):
   make PETSC_DIR=/home1/mmorligh/issm/trunk-jpl//externalpackages/petsc/src PETSC_ARCH=arch-linux2-c-opt all
xxx=========================================================================xxx
}}}
Copy and execute `make PETSC_DIR=....`. Then:
{{{
#!sh
=========================================
gmake[1]: Leaving directory '/home3/mmorligh/issm/trunk-jpl/externalpackages/petsc/src'
Now to install the libraries do:
make PETSC_DIR=/home1/mmorligh/issm/trunk-jpl//externalpackages/petsc/src PETSC_ARCH=arch-linux2-c-opt install
=========================================
}}}
Copy and execute `make PETSC_DIR=.... PETSC_ARCH=arch-linux2-c-opt install`. And that's it!

For documentation of pleiades, see here: http://www.nas.nasa.gov/hecc/support/kb/

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

{{{
#!sh
./configure \
 --prefix=$ISSM_DIR \
 --with-wrappers=no \
 --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
 --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
 --with-mpi-include=" " \
 --with-mpi-libflags=" -lmpi" \
 --with-mkl-libflags="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm " \
 --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
 --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \
 --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
 --with-cxxoptflags="-O3 -axAVX" \
 --with-fortran-lib="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/ -lifcore -lifport" \
 --with-vendor="intel-pleiades" \
 --enable-development
}}}

== Installing ISSM on Pleiades with Dakota ==

For Dakota to run, you you will still need to make autotools, cmake PETSc, and m1qn3.

In addition, will need to build the external package:
 - boost, install-1.55-pleiades.sh
 - dakota, install-6.2-pleiades.sh

Finally, add the following to your configuration script:

{{{
 --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
 --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
}}}

== Installing ISSM on Pleiades with CoDiPack ==

For CoDiPack, you you will still need to make autotools, cmake PETSc, and m1qn3.

In addition, will need to build the external package:
 - medipack, install.sh
 - codipack, install.sh

Your configuration script should look like that:

{{{
#!sh
./configure \
   --prefix=$ISSM_DIR \
   --with-wrappers=no \
   --without-Love \
   --without-GiaIvins \
   --without-kriging \
   --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
   --with-mpi-include=" " \
   --with-mpi-libflags=" -lmpi" \
   --with-mkl-libflags="-L/nasa/intel/Compiler/2016.2.181/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm " \
   --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
   --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \
   --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
   --with-cxxoptflags="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" \
   --with-fortran-lib="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/ -lifcore -lifport" \
   --with-gsl-dir="$ISSM_DIR/externalpackages/gsl/install" \
   --with-vendor="intel-pleiades" \
   --with-codipack-dir="$ISSM_DIR/externalpackages/codipack/install" \
   --with-medipack-dir="$ISSM_DIR/externalpackages/medipack/install" \
   --enable-tape-alloc \
   --enable-development 
}}}

You will get a lot of warnings while compiling (like ''warning #2196: routine is both "inline" and "noinline"''), just ignore them.
== pfe_settings.m ==

You have to add a file in `$ISSM_DIR/src/m` entitled `pfe_settings.m` (on the machine you wish to access Pleiades) with your personal settings:

{{{
#!m
cluster.login='mmorligh';
cluster.queue='devel';
cluster.codepath='/u/mmorligh/issm/trunk/bin';
cluster.executionpath='/nobackup/mmorligh/execution/';
cluster.grouplist='s1690';
cluster.port=1099;
}}}

use your username for the `login` and enter your code path and execution path. Be sure to create the final execution directory (mkdir) within the nobackup folder. These settings will be picked up automatically by matlab when you do `md.cluster=pfe()`. To determine your `grouplist`, on Pleiades run: 

{{{
%groups USERNAME
}}}

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

== Running jobs on Pleiades ==

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=pfe('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. 

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,'runtimename','SOMETHING');
}}}