Changes between Initial Version and Version 1 of computecanada

Timestamp:

10/13/21 08:47:18 (4 years ago)

Author:

Mathieu Morlighem

Comment:

--

computecanada

@@ +1 @@
+These directions should be good on any of the Canadian super computer systems using the common StdEnv/2020 Compute [https://docs.computecanada.ca/wiki/Standard_software_environments#StdEnv.2F2020 Canada module software stack]
+
+ == Download ISSM ==
+{{{
+#!sh
+svn --username XXX --password XXX  checkout http://issm.ess.uci.edu/svn/issm/issm/trunk-jpl
+}}}
+
+== ssh configuration ==
+
+You should first  create and upload an SSH key so you don't have to keep typing in your password. See directions: [https://docs.computecanada.ca/wiki/SSH_Keys]
+
+== Environment ==
+On Sherlock, add the following lines to `~/.bashrc`:
+{{{
+#!sh
+module load gcc/9.3.0 openmpi/4.0.3 matlab/2020a metis parmetis imkl petsc
+export ISSM_DIR=PATHTOTRUNK
+source $ISSM_DIR/etc/environment.sh
+}}}
+
+Change PATHTOTRUNK. Log out and log back in to apply this change.
+
+ == Installing ISSM on the cluster  ==
+You need to install the following packages in this exact sequence:
+ - m1qn3 (install.sh)
+
+Use the following configuration script (adapt to your needs):
+
+{{{
+#!sh
+./configure \
+        --prefix=$ISSM_DIR \
+        --with-numthreads=2 \
+       --with-mkl-libflags="-lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_openmpi_lp64 -lmkl_scalapack_lp64" \
+        --with-petsc-dir="$EBROOTPETSC" \
+       --with-mumps-dir="$EBROOTPETSC" \
+        --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
+        --with-mpi-include="/some/path/just/to/enable" \
+        --with-mpi-libflags="-lmpi_cxx -lmpi_mpifh -lmpi" \
+        --with-fortran-lib="-L$EBROOTGCC/lib64 -lgfortran"
+}}}
+
+== XXX_settings.m ==
+
+You have to add a file in `$ISSM_DIR/src/m` entitled `sherlock_settings.m` with your personal settings:
+
+{{{
+#!m
+cluster.login='XXX';
+cluster.port=0;
+cluster.codepath=XXX';
+cluster.executionpath='XXX';
+}}}
+
+Use your username for the `login` and enter your `codepath` and `executionpath`. These settings will be picked up automatically by MATLAB when you do `md.cluster=XXX()`