How to build the dependencies on Summit
- Our attempt to use spack on Summit to build all the dependencies so far failed and for now we are doing it manually.
- Load the following modules
module load gcc/7.4.0 module load zeromq/4.2.5 module load libfabric/1.7.0 module load python/3.7.0-anaconda3-5.3.0 - Create conda environment
conda create -n Test conda install conda pip numpy scipy pandas matplotlib source activae Test - Build mpi4py from source (using
conda installis not a good idea since we want to make sure that system MPI is used)wget https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-3.0.3.tar.gz tar xvf mpi4py-3.0.3.tar.gz cd mpi4py-3.0.3 python setup.py install - Install Cheetah/Savanna
git clone git@github.com:CODARcode/cheetah.git cd cheetah python setup.py install - Build simplest ADIOS installation with python support
git clone https://github.com/ornladios/ADIOS2.git ADIOS2 cd ADIOS2 mkdir build cd build cmake -DCMAKE_CXX_COMPILER=`which g++` -DCMAKE_C_COMPILER=`which gcc` -DCMAKE_Fortran_COMPILER:FILEPATH=`which gfortran` \ -DADIOS2_USE_MPI:STRING=True -DCMAKE_INSTALL_PREFIX=$HOME/SOFT_INSTALL/adios-2.5_simplest-gcc-7.4.0 -DADIOS2_USE_HDF5:STRING=False -DADIOS2_USE_SZ:STRING=False -DADIOS2_USE_ZFP:STRING=False -DADIOS2_USE_Blosc:STRING=False -DADIOS2_USE_BZip2:STRING=False -DADIOS2_USE_PNG:STRING=False -DADIOS2_USE_DataMan:STRING=True -DADIOS2_USE_Fortran:STRING=False .. make -j20 make install - Create a module (lua file) to use ADIOS, for example: ``` dir = os.getenv("HOME") .. '/SOFT_INSTALL/adios-2.5_simplest-gcc-7.4.0/' prepend_path('PATH', dir .. 'bin') prepend_path('LD_LIBRARY_PATH', dir .. 'lib64') prepend_path('CPATH', dir .. 'include') prepend_path('PYTHONPATH', dir .. 'lib64/python3.6/site-packages') setenv('ADIOS2_DIR', dir)
* Use `module use ...` to make the corresponding directory with modules visible and load ADIOS, for example, as follows:
module load Compiler/gcc/7.4.0/adios2/2.5_simplest-gcc-7.4.0
* Launch python interpreter and test that you can
import adios2
import cheetah
import mpi4py
import numpy
import pandas
```
* If it worked, you are ready to run tests