[Debichem-devel] OpenMM package for Debian/Ubuntu

[Andreas Tille]

Hi,

On Thu, Jan 23, 2014 at 10:35:48AM +0100, Andreas Tille wrote:
> > Andreas meant some subset of your group to register on alioth.debian.org
> > (caveat, your account name will have a suffix "-guest" auto-added and you
> > need to add this manually for login) and then join Debian Med 
> > on https://alioth.debian.org/projects/debian-med
> 
> s/debian-med/debichem/
> 
> > via that conate hyperlink. In a separate email (already deleted, sorry) I 
> > recall to have read that he moved the OpenMM bits to the Debichem project,
> > i.e. away from Debian Med, but I did not find it there, yet.
> 
> I'm in the middle of moving it to
> 
>    git://anonscm.debian.org/debichem/packages/openmm.git
> 
> I'll come back either today evening or tomorrow with results and comments.

Well, it is not really evening ... but here are my remarks:
 
I have commited the packaging to DebiChem Git.  It is advisable if those
(upstream ?) developers who are interested in working on this package

  a) become a member of 
       https://alioth.debian.org/projects/debichem
  b) subscribe this mailing list for communication
       https://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debichem-devel
     (we could spare longish CC lists - please confirm if you subscribed)

For the package I detected two sources of trouble where I need your
input.  I tweaked your file debian/README.md to document these problems.
Once they might be solved this file can go anyway because the
instructions are redundant if the package is in official Debian.

The first and probably major problem is that the build depends on
packages in non-free: nvidia-cuda-toolkit.  That means the package can
only go to contrib.  In case there might be some options to drop the
non-free accellerator code and provide some general package we might
consider whether it makes sense to provide a free package without the
nvidia dependency in main and one linked against nvidia libs in contrib.
I personally do not have any experience with things like this.

Moreover currently the package does not even build and this is alsoe
connected to the nvidia libraries.  I get:


cd /tmp/buildd/openmm-5.2+dfsg/obj-x86_64-linux-gnu/platforms/cuda/sharedTarget && /usr/bin/c++   -DOPENMM_AUTHORS=\"Peter.Eastman\" -DOPENMM_BUILD_VERSION=0 -DOPENMM_COPYRIGHT_YEARS=\"2008\" -DOPENMM_LIBRARY_NAME=OpenMM -DOPENMM_MAJOR_VERSION=5 -DOPENMM_MINOR_VERSION=2 -DOpenMMCUDA_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/buildd/openmm-5.2+dfsg/obj-x86_64-linux-gnu/platforms/cuda/src -I/tmp/buildd/openmm-5.2+dfsg/platforms/cuda/src -I/tmp/buildd/openmm-5.2+dfsg/platforms/cuda/./include -I/tmp/buildd/openmm-5.2+dfsg/src -I/tmp/buildd/openmm-5.2+dfsg/libraries/validate/include -I/tmp/buildd/openmm-5.2+dfsg/platforms/reference/include -I/tmp/buildd/openmm-5.2+dfsg/libraries/csha1/include -I/tmp/buildd/openmm-5.2+dfsg/libraries/hilbert/include -I/tmp/buildd/openmm-5.2+dfsg/libraries/lbfgs/include -I/tmp/buildd/openmm-5.2+dfsg/libraries/sfmt/include -I/tmp/buildd/openmm-5.2+dfsg/libraries/lepton/include -I/tmp/buildd/openmm-5.2+dfsg/libraries/quern/include -I/tmp/buildd/openmm-5.2+dfsg/libraries/jama/include -I/tmp/buildd/openmm-5.2+dfsg/olla/include -I/tmp/buildd/openmm-5.2+dfsg/openmmapi/include -I/tmp/buildd/openmm-5.2+dfsg/./include    -DOPENMM_CUDA_BUILDING_SHARED_LIBRARY -o CMakeFiles/OpenMMCUDA.dir/__/src/CudaKernelSources.cpp.o -c /tmp/buildd/openmm-5.2+dfsg/obj-x86_64-linux-gnu/platforms/cuda/src/CudaKernelSources.cpp
make[3]: *** No rule to make target `/libcuda.so', needed by `libOpenMMCUDA.so'.  Stop.
make[3]: Leaving directory `/tmp/buildd/openmm-5.2+dfsg/obj-x86_64-linux-gnu'
make[2]: *** [platforms/cuda/sharedTarget/CMakeFiles/OpenMMCUDA.dir/all] Error 2
make[2]: Leaving directory `/tmp/buildd/openmm-5.2+dfsg/obj-x86_64-linux-gnu'
make[1]: *** [all] Error 2


Any idea how to fix this?


Finally I dropped some remark about the binary code copy of saxon jars
inside the code.  I think we can deal with this since saxon is packaged
for Debian and we just might need to tweak the build system to use the
Debian packaged library.


The repository is ready to be used with git-buildpackage.  If you have
trouble with this you might either consult the Debian Med policy
document which should sufficiently describe its usage - or for sure
come back here on this list with your question where I'd be happy to
patiently guide you through the usage of the needed tools.

Kind regards

      Andreas.

-- 
http://fam-tille.de