This is the second time in less than a year I’ve face the problem of configuring parallel hdf5 on a server. I don’t even know why I bother! Oh, yeah, that’s right, I thought hdf5 was cool when I was first introduced to it, and I wanted to make it even more complicated by introducing concurrent i/o. Anyway, what follows is my catalogue of errors when trying to install on an ubuntu server. If you’ve got any suggestions on what I’m doing wrong, please comment :().

What do?

Attempting to .configure, make, make install, OpenMpi & parallel-HDf5 (using the CC=mpicc option) Attempting to .configure, make, make install zlib Attempting to pip install mpi4py & h5py (with links to the pHDf5 library using specific options for pip)

See below for details on steps already taken and specific bugs:


Status: No bugs

> curl -O
> tar xf openmpi-2.0.4.tar.gz
> cd openmpi-2.0.4
> ./configure --prefix=$HOME/.local
> make all
> make install
> mpirun --version

This compiles perfectly. All the executables are located in my .local path.

The last commands prints,

> mpirun (Open MPI) 2.0.4

ZLIB (shared object)

Status: Bugs

> curl -O ...
> tar xf ...
> cd zlib-x.x.x
> ./configure --prefix=$HOME/.local
> make test

Everything works. The C header file is in the .local/include dir and the shared object is in the .local/lib directory.

ZLIB (Python)

Status: bugs

However, installation of the zlib Python module with pip fails:

> pip install zlib

This prints,

> Collecting zlib
>    Could not find a version that satisfies the requirement zlib (from versions: )
>    No matching distribution found for zlib

I tried to fix this by explicitly telling the C compiler where to find the zlib stuff.

> zlib_lib="$HOME/.local/lib"
> zlib_inc="$HOME/.local/include"
> export CPPFLAGS="-I${zlib_inc} ${CPPFLAGS}"
> export LD_LIBRARY_PATH="${zlib_lib}:${LD_LIBRARY_PATH}"
> export LDFLAGS="-L${zlib_lib} -Wl,-rpath=${zlib_lib} ${LDFLAGS}"
> pip install zlib

But, this also fails and produces the same message as above from pip.

So, it seems I have zlib properly installed, but I do not have a working Python module called, zlib.

Oh, I’m running the default ubuntu Python 3.6 (not anaconda or anything.)

pHDf5 (C)

Status: bugs

Downloaded from

> cd hdf5-1.10.4
> CC=$HOME/.local/bin/mpicc ./configure --prefix=$HOME/.local --enable-shared --enable-parallel

This seems to give me the output I want. But doing

> make
> make check

fails to return a positive result. Namely, the MPI_ABORT seems to be called during the parallel tests.

Also, I have tried to install the regular hdf5 library (with no parallel support) by doing,

> CC=$HOME/.local/bin/mpicc ./configure --prefix=$HOME/.local --enable-shared

But, this also fails on the > make check stage.

Note that I have gotten this setup running before with my macbook pro 8.1 back in May 2018:

The above link might be helpful in future attempts to get this constellations of software up and running on the master-node.

End pain and suffering, please help.

A common coin is a “distributed object that is expected to deliver, with some probability, the same sequence of random bits b1, b2, …,bn …to each process”