Changes between Initial Version and Version 1 of totten

Timestamp:

10/22/21 06:59:12 (3 years ago)

Author:

Mathieu Morlighem

Comment:

--

totten

@@ +1 @@
+== Getting an account ==
+
+First, you need to send an email to Mathieu and request an account.
+
+== 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 YOURRONNEUSERNAME
+}}}
+and replace `YOURRONNEUSERNAME ` 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
+}}}
+
+== Environment ==
+
+On totten, add the following lines to `~/.bashrc`:
+{{{
+#!sh
+export ISSM_DIR=PATHTOTRUNK
+source $ISSM_DIR/etc/environment.sh
+#MATLAB alias
+export LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6" #Bug with MATLAB, issmversion gets a bunch of undefined symbols
+alias ma='matlab -nodesktop -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath;"'
+}}}
+
+In order to source `~/.bashrc` on startup, create `~/.bash_profile`, and add the following lines:
+{{{
+if [ -f ~/.bashrc ]; then
+  . ~/.bashrc
+fi
+}}}
+
+''Log out and log back in'' to apply this change.
+
+== Installing ISSM on totten ==
+
+You can follow the instructions on the website [http://issm.jpl.nasa.gov/download/unix/]. Choose Petsc v3.12 or later. You should not need Python.
+
+Use the following configuration script (adapt to your needs):
+
+{{{
+#!sh
+./configure \
+    --prefix=$ISSM_DIR \
+    --without-kml \
+    --with-matlab-dir="/usr/local/matlab/" \
+    --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$ISSM_DIR/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort"\
+    --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+    --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+    --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+    --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
+    --with-numthreads=32 \
+    --enable-development \
+    --enable-debugging
+}}}
+
+
+== Python and Openssh ==
+In order to install gdal, you need to install the python from the externalpackages.
+Once that is done, unset the PYTHON-related variables in etc/environment.sh, because this python installation causes future issues with other packages, e.g. PETSC.
+
+== Installing ISSM with CoDiPack (AD) ==
+
+You will need to install the following additional packages:
+ - codipack 
+ - medipack
+ - gsl
+
+Use the following configuration script (adapt to your needs, make sure to NOT include --with-petsc-dir):
+{{{
+#!sh
+./configure \
+   --prefix=$ISSM_DIR\
+   --without-kriging \
+   --without-kml \
+   --without-Love \
+   --without-Sealevelchange \
+   --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \
+   --with-matlab-dir="/usr/local/matlab/" \
+   --with-mpi-include=$ISSM_DIR/externalpackages/petsc/install/include  \
+   --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib -lmpifort -lmpi" \
+   --with-metis-dir=$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-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \
+   --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-numthreads=20  \
+   --enable-tape-alloc \
+   --enable-development \
+   --enable-debugging
+
+}}}