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Setup python 3 (including mpi4py) without admin rights
The following guide shows how to get a complete python installation without administrator rights:
Step 1: We move to the folder where we want to place our installation:
/afs/cern.ch/work/g/giadarol/sim_workspace_mpi_py3
Step 2: We download, compile and install the latest version of python 3 from the python website:
mkdir python_src
cd python_src
wget https://www.python.org/ftp/python/3.8.0/Python-3.8.0.tar.xz
tar xvf Python-3.8.0.tar.xz
cd Python-3.8.0
./configure --prefix=/afs/cern.ch/work/g/giadarol/sim_workspace_mpi_py3/python3
make
make install
Possible issues with ssl: In order to be able to use pip at a later stage, python needs to be compiled with ssl support. Please check that this is the case:
/afs/cern.ch/work/g/giadarol/sim_workspace_mpi_py3/python3/bin/python3
import ssl
In case this gives an exception, please install ssl library and recompile python (in Ubuntu this can be done by sudo apt install libssl-dev).
Possible issues with sqlite3: In order to be able to use jupyter notebooks at a later stage, python needs to be compiled with sqlite3 support. Please check that this is the case:
/afs/cern.ch/work/g/giadarol/sim_workspace_mpi_py3/python3/bin/python3
import sqlite3
In case this gives an exception, please install sqlite library and recompile python (in Ubuntu this can be done by sudo apt install libsqlite3-dev).
Possible issues with tk: In order to be able to use ipython --pylab at a later stage, python needs to be compiled with tk support. Please check that this is the case:
/afs/cern.ch/work/g/giadarol/sim_workspace_mpi_p3/python3/bin/python3
import _tkinter
In case this gives an exception, please install tk library and recompile python (in Ubuntu this can be done by sudo apt install tklib; sudo apt install tk-dev ).
Step 4: We create our virtual environment
cd /afs/cern.ch/work/g/giadarol/sim_workspace_mpi_py3
mkdir venvs
cd venvs
/afs/cern.ch/work/g/giadarol/sim_workspace_mpi_py3/python3/bin/python3 -m venv py3
Step 5: We activate our brand new virtual environment
source /afs/cern.ch/work/g/giadarol/sim_workspace_mpi_py3/venvs/py3/bin/activate
If we type:
which python
we get:
/afs/cern.ch/work/g/giadarol/sim_workspace_mpi_py3/venvs/py3/bin/python
Step 6: We use pip to install the python modules that we need
pip install numpy scipy cython h5py ipython matplotlib
Step 7 (optional): Installing mpi4py
We do not have an MPI installation we need to get one (for CERN users: skip this for CNAF cluster):
cd /afs/cern.ch/work/g/giadarol/sim_workspace_mpi/python_src
wget https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.2.tar.bz2
tar jxf openmpi-1.10.2.tar.bz2
cd openmpi-1.10.2
./configure --prefix=/afs/cern.ch/work/g/giadarol/sim_workspace_mpi/openmpi
make all install
We set the environment variable for the MPI compiler:
export MPICC=/afs/cern.ch/work/g/giadarol/sim_workspace_mpi/openmpi/bin/mpicc
At this point be careful not to have other MPI paths in your environment (for example set in your .bashrc)
pip will use the compiler pointed by your MPICC variable to compile mpi4py:
pip install mpi4py
Important: Python jobs using mpi4py must be run with the mpiexec corresponding to the MPI compiler that has been used. In our case:
/afs/cern.ch/work/g/giadarol/sim_workspace_mpi/openmpi/bin/mpiexec
Of course we can add the folder to our PATH or create a shortcut.
Step 8: Install h5py: If you don't need parallel hdf5 I/O you can just:
pip install h5py
Instead in case you need parallel hdf5 I/O and you want to compile your own hdf5 library:
wget https://support.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.10.5.tar.bz2
tar jxf hdf5-1.10.5.tar.bz2
cd hdf5-1.10.5/
./configure --prefix=/afs/cern.ch/work/g/giadarol/sim_workspace_mpi/hdf5lib --enable-parallel --enable-shared
make
make install
CC=/usr/bin/mpicc HDF5_MPI="ON" HDF5_DIR=/afs/cern.ch/work/g/giadarol/sim_workspace_mpi/hdf5lib pip install --no-binary=h5py h5py
Step 9: At this point we are able to download and install the PyECLOUD-PyHEADTAIL environment:
git clone https://github.com/PyCOMPLETE/PyECLOUD
git clone https://github.com/PyCOMPLETE/PyKLU
git clone https://github.com/PyCOMPLETE/PyHEADTAIL
git clone https://github.com/PyCOMPLETE/PyPIC
git clone https://github.com/PyCOMPLETE/NAFFlib
git clone https://github.com/PyCOMPLETE/PyPARIS
cd PyPIC
make
cd ../PyHEADTAIL
make
cd ..
mv PyHEADTAIL PyHEADTAIL_inst
mv PyHEADTAIL_inst/PyHEADTAIL .
cd PyECLOUD
./setup_pyecloud
cd ../PyKLU
./install
cd ../NAFFlib/NAFFlib
make py2
cd ../..
mv NAFFlib NAFFlib_inst
mv NAFFlib_inst/NAFFlib .
A couple of references that helped with this task:
[1] https://www.open-mpi.org/faq/?category=building#easy-build