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spack-ppd

This is the NRL Plasma Physics Division spack package repo.

Installation

Clone this repo somewhere (like $HOME/opt). Copy the .spack/repos.yaml file to $HOME/.spack/repos.yaml, and update it to point to spack-ppd:

repos:
  - $HOME/opt/spack-ppd # or wherever you put it
  - $spack/var/spack/repos/builtin

Building Molpro on Narwhal

Molpro is a commercial code, so you will need to obtain the tarball and update the Molpro package in spack-ppd to point to it. Do spack edit molpro and update the url line to point to the file.

We want to use a specific mpich module on the system and build a particular variant of Global Arrays (armci=openib and scalapack=True), which is all taken care of in the .spack/packages.yaml file. The lines you need to add to .spack/packages.yaml are in .spack/packages-narwhal.yaml in this repo. Be sure not to change any of the other contents of the file, and only copy in the mpich and globalarrays blocks (you only want one top-level packages: entry).

Install Molpro and keep the stage directory for tuning and testing:

$ spack install --keep-stage molpro %gcc@10.3.0 ^mpich@8.1.5

The package tuning and testing process will run molpro to establish some tuning parameters and perform some tests, requiring access to a compute node, so start an interactive job:

$ qsub -l ccm=1 -l select=1:ncpus=128:mpiprocs=128 -A NRLDC31794610 -q standard -l walltime=02:00:00 -I

Go to the staging directory and perform the tuning process which will likely take 20 minutes or more.

$ spack load /hmzfood
$ spack cd --stage-dir molpro
$ cd spack-src
$ make tuning

Once the tuning process is complete, you will have a file named tuning.rc in the spack-src/lib folder. You can either copy the file to ${MOLPRO_PREFIX}/molpro_2021.1/lib/tuning.rc or copy the contents to ${HOME}/.molprorc. The former is probably the best approach since the tuning is specific to a given build of Molpro. To determine ${MOLPRO_PREFIX} for the given build, run the following command and match the hash from the stage/build folder with the hash from the command's output:

spack find --paths molpro

Finally, you can/should run the tests provided with Molpro:

$ make MOLPRO_OPTIONS='-n2' test

Molpro-Narwhal Lessons Learned

TODO: So far, Molpro only runs on one node. This is probably an issue with mpich and global arrays. Possible remedy is to run tests in globalarrays to debug. Tried globalarrays variants armci=[mpi-ts, mpi-pr] with no luck.

Tried adding make tuning and make test steps to spack package, but molpro script looks for nodefile and expects to be run on compute nodes.

Tried running tuning on multiple MPI processes (make MOLPRO_OPTIONS='-n128 -m28g' tuning), but it seems it is meant for only one process. Or, maybe the number of processes is handled automatically and should just do make tuning like the instrucions say (not make MOLPRO_OPTIONS='-n1 -m28g' tuning).

Tried making the spack package as a CMakePackage, but couldn't figure out how to get the tests to build. The resulting executable seemed to run fine on one node, and the package file is package_CMake_package.py.

TODO: Latest build using cray-libsci + cray-mpich (from modules) has core dump at the end of successful job. Doesn't seem to happen when using mpich + openblas + netlib-lapack + netlib-scalapack, but mpich and libsci from modules seems more efficient. Should try getting a stack trace to see what is happening at job termination.

See the Molpro manual for info on allocating memory on a given machine. For narwhal standard nodes with 256GB RAM, perhaps these values work:

  • -n 40 -m 375m -G 5000m (40 CPUs on one node)
  • -n 30 -m 575m -G 5750m
  • -n 20 -m 975m -G 6500m
  • -n 2 -m 11775m -G 7850m

Setting ARMCI_DEFAULT_SHMMAX in spack load molpro but not sure it matters.