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coeus-ngsolve

Instructions / scripts for setting up serial and parallel installations of Netgen/Ngsolve on the PSU Coeus or Gaia cluster

Overview

Following this installation procedure, you should end up with directories in your home directory something like this:

.
├── coeus-ngsolve
├── common
│   ├── install
│   │   ├── bin
│   │   ├── include
│   │   ├── lib
│   │   └── share
│   └── src
│       ├── cmake-3.15.7
│       └── Python-3.6.12
├── NGparallel
│   ├── bin
│   ├── include
│   ├── lib
│   ├── ngsolve
│   └── share
├── NGserial
│   ├── bin
│   ├── include
│   ├── lib
│   ├── ngsolve
│   └── share
└── local
    ├── pyeigfeast
    ├── fiberamp
    └── my_python_project

Step 0

  • Fill out the form to request access to the clusters. You should get an email with instructions within a few days.
  • Install the Cisco VPN client on your local machine.
  • Create accounts at Github and Bitbucket (if you don't already have them), generate SSH keys for your local machine(s) and copy/paste the contents of the public key file id_rsa.pub to your Github account. There are good instructions for this here. (personallly I'd recommend either no passphrase or a short one that you can remember). Add the public key to your Bitbucket account as well.
  • Once you have been granted access to the cluster, Follow the Getting Started steps.

Step 1 (after you've logged in to the cluster and logged out)

On your local machine, copy the contents of ~/.ssh/id_rsa.pub, your SSH public key, to your clipboard. Then on the cluster node, do nano ~/.ssh/authorized_keys, and paste this key text at the bottom of the file. This will allow you to access the cluster via ssh and sftp without having to enter a password each time.

Also, while you're at it, locate the public key file on the cluster: ~/.ssh/id_rsa_pub and copy/paste its contents to your GitHub and Bitbucket accounts so you can work with your repositories from the cluster without having to enter passwords.

Step 2

Clone this repository to your home directory on the login node.

cd ~ && git clone [email protected]:ddrake/coeus-ngsolve.git

Step 3

Modules are an easy way for ensuring that environment variables such as $PATH and $LD_LIBRARY_PATH are set correctly for the process you want to perform. Usually you will want to have the modules gcc-9.2.0, and intel (for coeus) or intel-18.0 (for gaia) loaded before you start running a job. So-called 'private modules' are just a way of extending this functionality for software (such as the latest NGSolve) that is not installed on the Coeus. For more info on modules see here

Add private modules for NGSolve, depending on which cluster you are on:

cp -r ~/coeus-ngsolve/privatemodules_coeus ~/ && mv ~/privatemodules_coeus ~/privatemodules

or

cp -r ~/coeus-ngsolve/privatemodules_gaia ~/ && mv ~/privatemodules_coeus ~/privatemodules

It's a good idea to check the last line of each of the module files to ensure that the Python minor version (e.g. 3.8) associated with NGSolve matches the version you installed in Step 4.

Step 4

Edit the file ~/.bashrc on the cluster node using nano, vim or emacs, pasting in the following lines. If you don't know any of these editors, use nano ~/.bashrc. Uncomment the line for the cluster you are setting up. The $CLUSTER variable is used by several scripts.

# export CLUSTER="GAIA"
# export CLUSTER="COEUS"

export COMMON_INSTALL_DIR=~/common/install

export PATH=$COMMON_INSTALL_DIR/bin:$PATH

export LD_LIBRARY_PATH=$COMMON_INSTALL_DIR/lib:$LD_LIBRARY_PATH

export PYTHONPATH=$HOME/local:$PYTHONPATH

module use --append $HOME/privatemodules

Source these changes by source ~/.bashrc

The modules ngsolve/serial, ngsolve/parallel and ngsolve/phi_serial should now appear if you type module avail.

Step 5

Run ./install_cmake3 3.1.3 to install cmake3 in a 'common' directory in your $HOME folder (see the tree above).

Note: Cmake 3.1.3 is not a recent version, but we need to install it first because recent versions of Cmake won't boostrap from the very old CMake on the Coeus or Gaia.

Now if you do which cmake, you should see ~/common/install/bin/cmake

and if you do cmake --version, you should see cmake version 3.1.3

Now you're ready to install a higher CMake version by running the install script again.

On Coeus or Gaia, you should be able to do:

./install_cmake3 3.15.7

You may not be able to get a higher version like 3.16 or 3.17 because the openssl is pretty old on both clusters

CMake versions available for download are listed here: [https://cmake.org/download/]

Step 6

Install Python3

On Coeus, you should be able to do:

./install_python3 3.8.6

On Gaia, because of the really old openssl, the highest you can go is:

./install_python3 3.6.12

Python versions for download are listed here: [https://www.python.org/downloads/].

Step 7

pip3 install --upgrade pip
pip3 install ipython numpy scipy sympy matplotlib pytest cxroots

Step 8

Create a local directory where you will put Python projects so (if they have an __init__.py file), they will be in the PYTHON_PATH with our .bashrc setup

mkdir ~/local
cd ~/local
git clone https://bitbucket.org/jayggg/pyeigfeast.git

Step 9

Open install_ngsolve_serial in an editor to make sure the cmake command is to your liking. The Intel MKL Pardiso sparse solver is recommended, but does not appear to be available on Gaia. On Gaia, UMFPack should be enabled instead.

run install_ngsolve_serial to install Netgen/Ngsolve for most purposes.

To test the install, first do module load ngsolve/serial module load gcc-9.2.0 module load intel if on coeus or module load intel-18.0 if on gaia

Then open a python or ipython console and try import ngsolve

Step 10

Make sure the module load commands above are present in your slurm batch script. Having these in your script means that no matter what your local environment settings are when your scheduled job is started, the job's environmment will be correct.

Sample 'slurm_coeus' and 'slurm_gaia' scripts are provided here. Create a working directory and copy one of these into it and edit as needed. Then submit your job like this: sbatch slurm_gaia

It's a good idea to read the (short) Slurm documentation

Updating

To update NGSolve, simply re-run ./install_ngsolve_serial. The NGserial directory will be deleted and recreated. If you're using ngs_special_functions, you'll need to re-install it.

You can re-run the install_python and install_cmake scripts at any time to update those pre-requisites to any desired version. It's not necessary to delete previous versions of these.

Optional items

If you need NGSolve special functions, such as Bessel functions (fiberamp does), you can install that package using the provided scripts.

If you need to use NGSolve's capabilities for splitting the mesh among multiple MPI processes, run ./install_ngsolve_parallel. This will create a directory ~/NGparallel. You can use module load ngsolve/parallel to set the environment for your scripts.

Private modules make it easy to switch between the serial and parallel NGSolve installations or schedule jobs simultaneously in each context.

Additional scripts

There are some additional scripts provided here for installing Petsc, ngs-petsc, and an NGSolve install for the Xeon Phi nodes. Some additional steps may be required for these. Improved scripts and documentation are a work in progress as the clusters evolve.