hdf5.h missing h5py fails to install about pbcore

[dalupus]

On ubuntu 16.0.4
sudo apt-get install libhdf5-serial-dev hdf5-tools
pip install h5py

[adeslatt]

update 3/1/2015 (wow -- exactly one year later-- kind of freaky!)

had to do the same thing again but versions change in a year.
wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.14.tar
and
export HDF5_DIR=/mnt/hdf5-1.8.14/hdf5
pip install tables
and again... this worked.

[yzhao062]

@dalupus Thanks! This fixes my problem on Ubuntu 14.04.

[marcocamma]

on Debian stable (8.1)

export HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/serial/
pip install h5py
hope it helps,
marco

[adeslatt]

Because I am doing a new install on an ubuntu instance that I am using in a starcluster -- I need also to install the HDF5 software from here:
http://www.hdfgroup.org/HDF5/release/obtainsrc.html
./configure the makefile
make the makefile
and likely install
This should fix the issue

[adeslatt]

Not pretty -- but I downloaded then the python libraries to go with the hdf5 libraries.

wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.12.tar.gz

and

wget https://pypi.python.org/packages/source/h/h5py/h5py-2.2.1.tar.gz

I had to do the following:

export HDF5_DIR=/mnt/hdf5-1.8.12/hdf5/

pip install tables --force

and that worked.

[mjhsieh]

take a look at https://github.com/mjhsieh/buildablesrc/ and see if .travis.yml and Makefile files can help you the next time you do this.

[pengchy]

Thank you adeslatt, this information is very useful!

[dfz2019]

@dalupus Thanks a lot! It really saved me, I'm stuck in this problem for several hours without having any clues. This fixes my problem on Raspberry Pi with Raspian system.

[auranprost]

Same issue here. Here's information on what I am running and how I solved it

OS: CentOS 7
Python Version: 2.7.5 && 2.7.15 && 3.6.0 in a virtualenv

yum update
yum install -y hdf5*
pip install six
pip install numpy
pip install Cython
pip install h5py