Installation on HPC - Geodels/eSCAPE GitHub Wiki

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Content

• compilers
• Dependencies
• Custom packages
• eSCAPE
• Testing installation
• Example of installation on HPC

The HPC installation has been tested with both GNU fortran compiler (5.4.0) and Intel-mkl ifort (18.0.1) compiler.

eSCAPE is compatible with Python version (2.7.x, 3.5.x and above). Python version 2.7.15 has been tested on HPC.

Before you begin compiling eSCAPE and its dependencies, make sure you have set up your computer environment to include Python (2.7 and above), MPI implementation and a supported fortran compiler (gfortran and ifort have been tested).

eSCAPE requires the PETSc library and petsc4py package. On HPC platforms, the PETSc library is often a default module. If this is not the case you can follow the guide provided in the local installation page.

You will then need to have several other dependencies installed as pip packages. You can check which of them will need to be installed by opening a Python kernel and performing the following set of commands:

import numpy
import pandas
import scipy
from mpi4py import MPI
from petsc4py import PETSc
import ruamel.yaml as yaml
import meshio

If some of these packages are not installed you can install them via pip:

pip install XXX [--user]

where XXX is the missing package.

For petsc4py it is necessary to set the environment variables PETSC_DIR and PETSC_ARCH to their appropriate values (which will depend on your HPC installation):

export PETSC_DIR=\path\to\petsc\location
export PETSC_ARCH=petsc-arch-values
pip install [--user] petsc4py

Two additional packages are required prior to eSCAPE installation:

• meshplex
• fillit

meshplex package could be installed with pip:

pip install [--user] meshplex

In case you encounter some difficulties during installation related to fastfunc dependency, one can used the following forked version:

git clone https://github.com/Geodels/meshplex.git
cd meshplex
python setup.py install [--user] 
cd ..

fillit is installed using the following set of commands:

export F90=fortran-compiler
git clone https://github.com/Geodels/fillit.git
cd fillit
python setup.py install [--user] 

where fortran-compiler needs to be replaced with the fortran compiler used to build PETSC (this will depend of the HPC installation but will likely be gfortran or ifort)

OK, now that all dependencies are installed we can finally proceed with eSCAPE:

git clone https://github.com/Geodels/eSCAPE.git
cd eSCAPE
python setup.py install [--user]

You can then do a simple test to check that all packages have been successfully installed by starting a python kernel and importing each module individually:

import numpy
import pandas
import scipy
from mpi4py import MPI
from petsc4py import PETSc
import ruamel.yaml as yaml
import meshio
import meshplex
import fillit
import eSCAPE

If you found a bug, have questions, or are just having trouble with eSCAPE, you can:

1. join the eSCAPE User Group on Slack by sending an email request to: Join eSCAPE User Group
2. open an issue in our issue tracker and we'll try to help resolve the concern.

• USyD Artemis HPC

module purge
module load python/2.7.15-intel petsc-intel-mpi hdf5
export F90=ifort
git clone https://github.com/Geodels/fillit.git
cd fillit
python setup.py install --user

git clone https://github.com/Geodels/eSCAPE.git
cd eSCAPE
python setup.py install --user