Changes between Version 15 and Version 16 of totten

Timestamp:

04/09/24 05:34:43 (10 months ago)

Author:

Mathieu Morlighem

Comment:

--

totten

@@ -10 +10 @@
 }}}
 
-and replace `YOURUSERNAME` by your totten username. This is were you should checkout ISSM and create your "projects" directory.
-
-== Getting an account ==
-
-First, you need to send an email to Mathieu and Ed and request an account.
+and replace `YOURUSERNAME` by your totten username. This is were you should install ISSM and create your "projects" directory.
 
 == ssh configuration ==
@@ -74 +70 @@
 source $ISSM_DIR/etc/environment.sh
 #MATLAB alias
-export LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" #Bug with MATLAB, issmversion gets a bunch of undefined symbols
-alias ma='matlab -nodesktop -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath;"'
+alias ma='LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6:/usr/lib/x86_64-linux-gnu/libgfortran.so.5:$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 removing anything that you may have by default in this file.
+Feel free to remove anything that you may have by default in this file.
 ''Log out and log back in'' to apply this change.
 
@@ -84 +79 @@
 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 3.16 or later)
+ * petsc (take the latest version 3.20 or later)
  * triangle
  * m1qn3
@@ -95 +90 @@
     --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$ISSM_DIR/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort"\
-    --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
-    --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
-    --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
-    --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
+    --with-triangle-dir="$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
 }}}
-
-
-== 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.
 
 == Run Jupyter Notebook on totten ==
@@ -147 +138 @@
    --without-Love \
    --without-Sealevelchange \
-   --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \
    --with-matlab-dir="/usr/local/MATLAB/R2021b" \
    --with-mpi-include=$ISSM_DIR/externalpackages/petsc/install/include  \
-   --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort"\
+   --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib -lmpi -lmpifort"\
    --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
    --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \