Parallel Group setup & mpi4py/OpenMDAO 2.2.X
I am trying to use the parallelization with mpi/openmdao.
I have tried on various ubuntu computers as well as ubuntu bash on windows (a windows 10 feature)
The dependencies work fine independently (i.e. import petsc4py and import mpi4py works fine and I can run the tests of these similar to the links: https://openmdao.readthedocs.io/en/1.7.3/getting-started/mpi_linux.html & http://mpi4py.scipy.org/docs/usrman/install.html)
But the Paralel Group code in the openmdao 2.2. manual does not work. For each attempt (varying computers) i seem to get another error most of them seemed like compatibility errors (i.e. I install petsc4py which breaks numpy or mpi4py installation causing proble in the existing openmdao core. )
On some computers I had my own openmpi and petsc installed but conda install command already installs those as far as I see.
Eventually I have tried these steps on a newly started amazon instance but had similar problems.
sudo apt-get install build-essential
wget http://repo.continuum.io/archive/Anaconda3-5.2.0-Linux-x86_64.sh
bash Anacond*
sudo apt-get install libibnetdisc-dev
sudo apt-get install libblas-dev libatlas-dev liblapack-dev
conda install mpi4py
conda install -c conda-forge petsc4py
if i check ''conda list'' onone of the computers the abbreviated output is ;
mpi 1.0 mpich conda-forge
mpi4py 3.0.0 py36_mpich_1 conda-forge
mpich 3.2.1 1 conda-forge
mpich2 1.4.1p1 0 anaconda
mpmath 1.0.0 py36hfeacd6b_2
msgpack-python 0.5.1 py36h6bb024c_0
multipledispatch 0.4.9 py36h41da3fb_0
mumps 5.0.2 blas_openblas_208 [blas_openblas]
conda-forge
numpy 1.14.3 py36_blas_openblas_200 [blas_openblas] conda-forge
numpydoc 0.7.0 py36h18f165f_0
openblas 0.2.20 8 conda-forge
openmdao 2.2.1 <pip>
openpyxl 2.4.10 py36_0
openssl 1.0.2o 0 conda-forge
petsc 3.9.1 blas_openblas_0 [blas_openblas]
conda-forge
petsc4py 3.9.1 py36_0 conda-forge
pexpect 4.3.1 py36_0
pickleshare 0.7.4 py36h63277f8_0
pillow 5.0.0 py36h3deb7b8_0
pip 10.0.1 <pip
On the same system if try to run mpirun -n 2 python my_par_model.py based on the manual code this is what i get
Does anyone have a suggestion where it could be failing or what steps i could follow for ubuntu implementation of anconda/openmdao/petsc/mpi4py and succesful run of paralel openmdao ?
I think MPI compatibility was the main issue. I was not aware that it had to be openmpi and indeed conda install command installs the mpich and possibly causing a problem with openmdao.
I will continue doing more tests but for a working system starting from a brand new installation of ubuntu-16.04.4-desktop-amd64.iso I followed these steps;
(Steps that take time are the openmpi installation and petsc4py pip instalattion.)
1 ) For some dependencies (taken from https://gist.github.com/mrosemeier/088115b2e34f319b913a)
sudo apt-get install libibnetdisc-dev
sudo apt-get install libblas-dev libatlas-dev liblapack-dev
2) Download/Install OpenMPI (mostly taken from http://lsi.ugr.es/jmantas/pdp/ayuda/datos/instalaciones/Install_OpenMPI_en.pdf)
wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.0.tar.gz
tar -xzf openmpi-3.1.0.tar.gz
cd openmpi-*
./configure --prefix="/home/$USER/.openmpi"
make
sudo make install
echo export PATH="$PATH:/home/$USER/.openmpi/bin" >> /home/$USER/.bashrc
echo export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/$USER/.openmpi/lib/" >> /home/$USER/.bashrc
3) MINICONDA & Rest (mostly taken from https://github.com/OpenMDAO/OpenMDAO/blob/master/.travis.yml)
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Minicond* # agree to add to the path etc.
conda install --yes python=3.6
conda install --yes numpy==1.14 scipy=0.19.1 nose sphinx mock swig pip;
pip install --upgrade pip;
pip install mpi4py
pip install petsc4py==3.9.1
#petsc4py Gives an error failed building wheel for petsc but then installs petsc itself, afterwards, petsc4py is also installed
sudo apt install git # in the cases git does not exist
# not sure why we need this part but i followed
pip install redbaron;
pip install git+https://github.com/OpenMDAO/testflo.git;
pip install coverage;
pip install git+https://github.com/swryan/coveralls-python@work;
# pyoptsparse and openmdao
git clone https://github.com/mdolab/pyoptsparse.git;
cd pyoptsparse;
python setup.py install;
cd ..;
conda install --yes matplotlib;
git clone http://github.com/OpenMDAO/OpenMDAO
cd OpenMDAO
pip install .
# optional
conda install spyder
4) Check the versions
mpirun --version : Open MPI 3.1.0
python --version : 3.6.5
pip --version :
pip 10.0.1 from /home/user/miniconda3/lib/python3.6/site-packages/pip (python 3.6)
conda list : (note that there is no mpich or similar in the conda list)
openmdao 2.2.1 <pip>
mpi4py 3.0.0 <pip>
petsc 3.9.2 <pip>
petsc4py 3.9.1 <pip>
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