[[PageOutline]]

== Important note about storage ==

Totten has several drives. Your home directory is on a small drive (6 TB), so make sure to work on the big RAID system `/totten_1` that has 83 TB. You will probably need to create a directory:
{{{
#!sh
cd /totten_1
mkdir YOURUSERNAME
}}}

and replace `YOURUSERNAME` by your totten username. This is were you should install ISSM and create your "projects" directory.

== ssh configuration ==

You can add the following lines to `~/.ssh/config` on your local machine:
{{{
#!sh
Host totten totten.dartmouth.edu
   HostName totten.dartmouth.edu
   User YOURUSERNAME
}}}
and replace `YOURUSERNAME ` by your totten username.

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

{{{
#!sh
ssh totten
}}}

== 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 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 totten account:

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

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

{{{
#!sh
$your_remosthost%cat ~/id_rsa.pub >> ~/.ssh/authorized_keys
$your_remosthost%rm ~/id_rsa.pub
}}}

If Totten complains that about `/home/mmorligh/.ssh/authorized_keys: No such file or directory`, you may need to create an .ssh directory first.

== Environment ==

On totten, add the following lines to `~/.bashrc`:
{{{
#!sh
export ISSM_DIR=PATHTOTRUNK
source $ISSM_DIR/etc/environment.sh
#MATLAB alias
alias ma='LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6:/usr/lib/x86_64-linux-gnu/libgfortran.so.5:$ISSM_DIR/externalpackages/petsc/install/lib/libmpi.so:$ISSM_DIR/externalpackages/petsc/install/lib/libmpifort.so  /usr/local/MATLAB/R2023b/bin/matlab -nodesktop -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath;"'
}}}
Feel free to remove anything that you may have by default in this file.
''Log out and log back in'' to apply this change.

== Installing ISSM on totten ==

You can follow the instructions on the website [http://issm.jpl.nasa.gov/download/unix/]. You will need to install the following packages:
 * autotools
 * petsc (take the latest version 3.20 or later)
 * triangle
 * m1qn3

Use the following configuration script (adapt to your needs):
{{{
#!sh
./configure \
    --prefix=$ISSM_DIR \
    --without-kml \
    --with-matlab-dir="/usr/local/MATLAB/R2021b" \
    --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
    --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
    --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
    --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include" \
    --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib -lmpi -lmpifort"\
    --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
    --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
    --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \
    --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
    --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \
    --with-numthreads=32 \
    --enable-development \
    --enable-debugging
}}}

== Run Jupyter Notebook on totten ==
You can run Jupyter Notebook **on totten** (after `ssh` to the remote server) with the following command: 
{{{
#!sh
jupyter notebook --no-browser --port=8080
}}}
Keep this terminal alive, where you will need the token to access the Notebook.

To access your notebook via the **browser from your local machine**, you just need to link the totten's port `8080` to your `localhost:8080` by the command (on your local machine)
{{{
#!sh
ssh -L 8080:localhost:8080 yourname@totten.dartmouth.edu
}}}
After this, open a web browser on your local machine, and access the Jupyter Notebook from ` http://localhost:8080/`.
You might be asked to enter the token, which you can find in the terminal you kept alive for Jupyter Notebook. 

[wiki:kubeflow Install custom image on kubeflow]

== Installing ISSM with CoDiPack (AD) ==

You will need to install the following *additional* packages:
 * codipack 
 * medipack

Use the following configuration script (adapt to your needs, make sure to NOT include --with-petsc-dir):
{{{
#!sh
./configure \
   --prefix=$ISSM_DIR\
   --without-kriging \
   --without-kml \
   --without-Love \
   --without-Sealevelchange \
   --with-matlab-dir="/usr/local/MATLAB/R2021b" \
   --with-mpi-include=$ISSM_DIR/externalpackages/petsc/install/include  \
   --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib -lmpi -lmpifort"\
   --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
   --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
   --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
   --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
   --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
   --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
   --with-codipack-dir="$ISSM_DIR/externalpackages/codipack/install" \
   --with-medipack-dir="$ISSM_DIR/externalpackages/medipack/install" \
   --with-cxxoptflags="-g -O3 -fPIC -std=c++11 -DCODI_ForcedInlines" \
   --with-numthreads=32 \
   --enable-tape-alloc \
   --enable-development \
   --enable-debugging
}}}