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README.md

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easybuild

EasyBuild is a software build and installation framework that allows you to manage software in an efficient way: (http://easybuild.readthedocs.io/en/latest/Introduction.html). This repo provides additional easyconfigs for ELIC ecosystem

Install

Go to /opt/easybuild and:

rmdir easyconfigs; git clone ssh://egit/pbarriat/easyconfigs.git

Requirements

  • openSUSE : gcc-c++ patch libopenssl-devel gperf
  • CentOS : openssl-devel libibverbs-devel autoconf automake binutils bison flex gcc gcc-c++ gettext libtool make patch pkgconfig bzip2 unzip
  • ubuntu :
sudo apt install gcc-4.8 g++-4.8 gfortran-4.8 libibverbs-dev

sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 10
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 20
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 10
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-7 20
sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-4.8 10
sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-7 20

sudo update-alternatives --set cc /usr/bin/gcc
sudo update-alternatives --set c++ /usr/bin/g++
sudo update-alternatives --set f77 /usr/bin/gfortran

sudo update-alternatives --config gcc
sudo update-alternatives --config g++
sudo update-alternatives --config gfortran

Getting started

Check if you have the lastest easybuild version:

sudo pip install easybuild --upgrade
cd /opt/easybuild/easyconfigs/foss-2017b

Then call screen and :

  • eb --tmpdir=/tmp --parallel=12 ./R-3.4.3-foss-2017b-X11-20171023.eb
  • eb --tmpdir=/tmp --parallel=12 netCDF-Fortran-4.4.4-foss-2017b.eb -r
  • eb --tmpdir=/tmp --parallel=12 ./netCDF-4.4.1.1-foss-2017b-HDF5-1.8.19.eb -r
  • eb --tmpdir=/tmp --parallel=12 ./CDO-1.9.2-foss-2017b.eb -r
  • eb --tmpdir=/tmp --parallel=12 ./NCO-4.7.1-foss-2017b.eb -r
  • eb --tmpdir=/tmp --parallel=12 GEOS-3.6.2-foss-2017b-Python-3.6.3.eb -r
  • eb --tmpdir=/tmp --parallel=12 Tkinter-2.7.14-foss-2017b-Python-2.7.14.eb
  • eb --tmpdir=/tmp --parallel=12 MATLAB-UCL-2017a.eb
cd /opt/easybuild/easyconfigs/intel-2016.02
  • eb --tmpdir=/tmp --parallel=12 iccifort-2016.2.181-GCC-4.9.3-2.25.eb -r
  • eb --tmpdir=/tmp --parallel=12 ./icc-2016.2.181-GCC-4.9.3-2.25.eb
  • eb --tmpdir=/tmp --parallel=12 ./ifort-2016.2.181-GCC-4.9.3-2.25.eb
  • eb --tmpdir=/tmp --parallel=12 iccifort-2016.2.181-GCC-4.9.3-2.25.eb
  • eb --tmpdir=/tmp --parallel=12 ./netCDF-Fortran-4.4.4-intel-2016.02-GCC-4.9.eb
  • eb NCL-6.4.0-intel-2018.eb -r
  • eb GDAL-2.2.0-intel-2018-Python-3.6.1.eb -r

Finally, run ./utils/install_modulerc_new.sh

Python2 packages

Fix /opt/modules/all/GEOS/3.6.2-foss-2017b-Python-2.7.14.lua by adding setenv("GEOS_DIR", root)

module load GDAL/2.2.3-foss-2017b-Python-2.7.14 GEOS/3.6.2-foss-2017b-Python-2.7.14
pip install --upgrade pip

pip install cffi vsc-base vsc-install

pip install geos netcdf4 cdo geoval cartopy iris matplotlib ipython pyproj scikit-image pillow pandas xarray joblib six gdal shapely rasterio geopandas pytest boto3 salem motionless progressbar2 fiona geopandas configobj https://github.com/matplotlib/basemap/archive/v1.1.0.tar.gz

pip install spyder python_qt_binding python-qt Qt.py ecmwf-api-client pybufr-ecmwf 

module purge

Fix /opt/modules/all/Python/2.7.14-foss-2017b.lua by adding:

if not isloaded("GDAL/2.2.3-foss-2017b-Python-2.7.14") then load("GDAL/2.2.3-foss-2017b-Python-2.7.14") end

if not isloaded("GEOS/3.6.2-foss-2017b-Python-2.7.14") then load("GEOS/3.6.2-foss-2017b-Python-2.7.14") end

Python3 issue

Check if you have an issue with Python3:

module load Python/3.6.1-intel-2018
pip

If yes:

pip install -Iv pysha3==0.3
pip
vimdiff /opt/software/Python/3.6.1-intel-2018/lib/python3.6/hashlib.py utils/hashlib.py

Python3 packages

Fix /opt/modules/all/GEOS/3.6.1-intel-2018-Python-3.6.1.lua by adding setenv("GEOS_DIR", root)

module load GDAL/2.2.0-intel-2018-Python-3.6.1 PROJ

pip install geos netcdf4 cdo geoval cartopy matplotlib ipython pyproj scikit-image pillow pandas xarray joblib six gdal shapely rasterio geopandas pytest boto3 salem motionless progressbar2 fiona geopandas configobj https://github.com/matplotlib/basemap/archive/v1.1.0.tar.gz

module purge

R packages

module purge
module load R
cd /opt/easybuild/easyconfigs/utils
Rscript ipak.R

Matlab 2013a

rsync -av 10.90.90.50:/opt/software/MATLAB/2013a /opt/software/MATLAB
scp 10.90.90.50:/opt/modules/all/MATLAB/2013a.lua /opt/modules/all/MATLAB