Install and Running in Cluster

Asked by Surej Kumar

Hi

I would like check if we can install Esys-Escript in a HPC Cluster and able to run it.

1. Operation Systems = Red Hat Enterprise 6.4.
2. SUN Cluster & IBM Cluster : Operation Systems = Scientific Linux 5.11 (Boron)
3. SUN Oracle :Operation Systems = Scientific Linux 6.7 (Carbon)

Anyone has run Esys-EScript FEM in clusters? Any guideline will be great help on installation and running MPI .

Thanks and best regards

Surej

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Adam Ellery (aellery) said :
#1

Hi Surej,

It is possible to install and run esys escripts on a HPC cluster. Unfortunately, the default repository for scientific linux has several out-of-date packages and it may be necessary for you to upgrade these first before compiling esys-finley. Specifically, you will need either access to the intel compiler or the GNU c++ compiler (gcc-c++) version 4.8.0 or later as well as boost version 1.66 or later. If you are unsure how to do install these libraries, I can provide you with instructions on how to do so.

Once that is done, you should be able to get esys-finley up and running using the following steps:

1. Make sure you have the following dependencies installed: python-devel, numpy, scipy, scons, boost-devel, python-matplotlib, gcc-c++, boost-python

2. That should enable most features except for the ability to save and load files in netCDF format. Optionally, if you wish to enable netCDF you will need to also install the dependencies: netcdf-devel, gdal-python, gnome-python2-devel. These packages are available in the EPEL repository, located at http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm.

3. Download the esys-finley tarball and extract it. You should be able to do this using the commands:

wget https://launchpad.net/escript-finley/3.0+/5.2/+download/python-escript_5.2.tar.gz
tar zxf python-escript_5.2.tar.gz

4. Now you will need to create a new options file that tells the compiler where the libraries are located. Scientific linux is very similar to centOS so I recommend that you edit the existing centOS.py options file, that is located in the folder scons/templates. Specifically, you will need to change lines 26 and 27 to read:
26: pythonlibname = ['python2.6']
27: pythonincpath = ['/usr/include/python2.6']

5. Finally, navigate to the esys.finley source directory, and run:
scons -j1 options_file=scons/templates/centos7_0_options.py

Please tell me how that goes,

Adam

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