Update the README with submit and compiler/mpi

utils/matrix/README.md

@@ -16,8 +16,22 @@ Instructions
    ./conda/configure_compass_env.py --env_name compass_matrix \
        --compiler all --mpi all --conda ~/miniconda3/
    ```
-   This will save some info in `conda/logs/matrix.log` that is needed for the
-   remainder of the build.
+   See the next section for more details.  This will save some info in 
+   `conda/logs/matrix.log` that is needed for the remainder of the build.  If
+   you want to set up load scripts for more environments than you actually
+   want to run your matrix on, you can edit `matrix.log`.  The syntax is:
+   ```
+   <machine>
+   <compiler>, <mpi>
+   <compiler>, <mpi>
+   <compiler>, <mpi>
+   ...
+   ```
+   It is also safe to rerun `./conda/configure_compass_env.py` with just the
+   subset of compilers and MPI libraries you want for the matrix.  Any
+   load scripts created in previous calls will not be deleted and the conda
+   environment will just be updated, not recreated unless you explicitly ask
+   for it to be recreated.
 
 2. Copy `example.cfg` to the base of the branch:
    ```shell
@@ -41,6 +55,44 @@ Instructions
    ```shell
    ./utils/matrix/setup_matrix.py -f matrix.cfg
    ```
+   Optionally use the `--submit` flag to submit jobs once each configuration
+   has been built and set up.
 
 8. The matrix build doesn't take care of running the jobs on a compute node.
    You will need to do that yourself.
+
+Matrix of compilers and MPI libraries
+-------------------------------------
+
+You control the matrix of compilers and MPI libraries by how you call
+```shell
+./conda/configure_compass_env.py ...
+```
+This is because the configure script knows about which compilers and MPI 
+libraries are  available for a given machine, something tricky to figure out in 
+`./util/matrix/setup_matrix.py` directly.
+
+You can do:
+```shell
+./conda/configure_compass_env.py --compiler all --mpi all ...
+```
+to get all supported compilers and MPI libraries.  You can do:
+```shell
+./conda/configure_compass_env.py --compiler intel --mpi all ...
+```
+to get just the `intel` configurations.  You can do:
+```shell
+./conda/configure_compass_env.py --compiler all --mpi openmpi ...
+```
+to get just the `openmpi` configurations or:
+```shell
+./conda/configure_compass_env.py --compiler intel ...
+```
+(omitting the `--mpi`) to get the default MPI library for intel.  Finally, you
+can give a list of compilers and a list of the same length of MPI libraries,
+such as:
+```shell
+./conda/configure_compass_env.py --compiler intel intel intel gnu \
+    --mpi impi openmpi mvapich mvapich ...
+```
+This will give you 3 intel variants and a gnu variant.