cryos / avogadro-squared

Avogadro superbuild project, builds Avogadro dependencies and then Avogadro itself

I work at Voltron Data leading a lot of the build engineering and related work there. I was a Group Leader at NSLS-II (part of Brookhaven National Laboratory), and before that I was a Technical Leader at Kitware working on a number of open source scientific software projects including Avogadro, Open Chemistry, Tomviz, VTK, ParaView, CMake and others. I blog, have largely abandoned social media, and love living close to the beach.

I am passionate about writing portable, highly performant software that can run on Linux, macOS, Windows, and on the web. I have deep experience in C++, Qt, CMake and am pretty familiar with Python, TypeScript, React and related technologies. I was once a Gentoo developer, and I run Arch Linux as my preferred desktop/laptop and love keeping up with new developments in the technology world. I have contributed to a wide variety of open source projects over the years.

I am a physicist by training, completing a B.Sc. and Ph.D. in physics focusing on nanomaterial engineering. I used lots of materials characterization techniques including transmission electron microscopy, atomic force microscopy, X-ray and neutron techniques (mainly diffraction and reflectometry) as an experimentalist before making the leap to software. At the end of my Ph.D. I took part in Google Summer of Code as a student, then later a mentor and org admin.

I love science and software, trying to figure out where I might exist in the space the two occupy. I once gave a TEDx talk 'Open Up or Perish' shortly after my daughter was born that sums up my hopes for how we move science forward. I have given a few keynotes, many invited talks and many conference talks at software, open source and scientific conferences including OSCON, GTC, All Things Open, ACS, APS, ToScA, M&M, MRS and others.

Views are my own (obviously I would hope).

avogadro-squared's Issues

Avogadro-squared git clone fails

On Ubuntu 16.04, when I try
git clone --recursive git://github.com/cryos/avogadro-squared.git

I get the error:

Cloning into 'avogadro-squared'...
remote: Counting objects: 91, done.
remote: Total 91 (delta 0), reused 0 (delta 0), pack-reused 91
Receiving objects: 100% (91/91), 18.29 KiB | 0 bytes/s, done.
Resolving deltas: 100% (50/50), done.
Checking connectivity... done.
Submodule 'avogadro' (git://github.com/cryos/avogadro.git) registered for path 'avogadro'
Submodule 'avogadrovtk' (git://github.com/cryos/AvogadroVTK.git) registered for path 'avogadrovtk'
Submodule 'eigen' (git://github.com/cryos/eigen.git) registered for path 'eigen'
Submodule 'openbabel' (git://github.com/openbabel/openbabel.git) registered for path 'openbabel'
Submodule 'openqube' (git://github.com/cryos/openqube.git) registered for path 'openqube'
Cloning into 'avogadro'...
remote: Counting objects: 57465, done.
error: inflate: data stream error (incorrect data check) MiB/s   
fatal: pack has bad object at offset 57445900: inflate returned -3
fatal: index-pack failed
fatal: clone of 'git://github.com/cryos/avogadro.git' into submodule path 'avogadro' failed

I would appreciate any help in fixing this problem.

Cmake instructions missing build step

The instructions on the wiki for the linux/osx build get as far as

cmake ../avogadro-squared

but don't get all the way to actually building, which should be

cmake --build .

I don't have access to the wiki to make this change.

Great work on this repo by the way, makes the build process far less painful.

Avogadro-squared git clone fails

On Ubuntu 16.04, when I try
git clone --recursive git://github.com/cryos/avogadro-squared.git

I get the error:

Cloning into 'avogadro-squared'...
remote: Counting objects: 91, done.
remote: Total 91 (delta 0), reused 0 (delta 0), pack-reused 91
Receiving objects: 100% (91/91), 18.29 KiB | 0 bytes/s, done.
Resolving deltas: 100% (50/50), done.
Checking connectivity... done.
Submodule 'avogadro' (git://github.com/cryos/avogadro.git) registered for path 'avogadro'
Submodule 'avogadrovtk' (git://github.com/cryos/AvogadroVTK.git) registered for path 'avogadrovtk'
Submodule 'eigen' (git://github.com/cryos/eigen.git) registered for path 'eigen'
Submodule 'openbabel' (git://github.com/openbabel/openbabel.git) registered for path 'openbabel'
Submodule 'openqube' (git://github.com/cryos/openqube.git) registered for path 'openqube'
Cloning into 'avogadro'...
remote: Counting objects: 57465, done.
error: inflate: data stream error (incorrect data check) MiB/s   
fatal: pack has bad object at offset 57445900: inflate returned -3
fatal: index-pack failed
fatal: clone of 'git://github.com/cryos/avogadro.git' into submodule path 'avogadro' failed

I would appreciate any help in fixing this problem.

Build fails due to hash miss-match, Zlib 404s

Cmake fails to build owing to the following error:
-- verifying file...
file='/home/terminal/avogadro-build/zlib-1.2.8.tar.gz'
-- MD5 hash of
/home/terminal/avogadro-build/zlib-1.2.8.tar.gz
does not match expected value
expected: '44d667c142d7cda120332623eab69f40'
actual: 'd41d8cd98f00b204e9800998ecf8427e'
-- File already exists but hash mismatch. Removing...
-- Downloading...
dst='/home/terminal/avogadro-build/zlib-1.2.8.tar.gz'
timeout='none'
-- Using src='http://zlib.net/zlib-1.2.8.tar.gz'
-- Retrying...
-- Using src='http://zlib.net/zlib-1.2.8.tar.gz'
-- Retry after 5 seconds (attempt #2) ...
-- Using src='http://zlib.net/zlib-1.2.8.tar.gz'
-- Retry after 5 seconds (attempt #3) ...
^Cmake[2]: *** [CMakeFiles/zlib.dir/build.make:90: zlib-prefix/src/zlib-stamp/zlib-download] Interrupt
make[1]: *** [CMakeFiles/Makefile2:73: CMakeFiles/zlib.dir/all] Interrupt
make: *** [Makefile:84: all] Interrupt