Changes between Version 4 and Version 5 of pleiadesbash

Timestamp:

03/19/18 10:13:45 (7 years ago)

Author:

Mathieu Morlighem

Comment:

--

pleiadesbash

@@ -33 +33 @@
 == 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:
+'''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:
  - cmake
- - PETSc (use the pleiades script and ``follow`` the instructions, you will need to submit a job and compile PETSc manually, do not make test, it will not work on the cluster)
  - 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
+make
+}}}
+and
+{{{
+#!sh
+make install
+}}}
+and that's it!
 
 For documentation of pleiades, see here: http://www.nas.nasa.gov/hecc/support/kb/
 
-Use the following configuration script (adapt to your needs):
+Use the following configuration script for ISSM (adapt to your needs):
 
 {{{