[Debichem-devel] RFS: libchemps2/1.4-1 -- spin-adapted DMRG for ab initio quantum chemistry

Tue Jun 16 13:38:43 UTC 2015

Hi,

I also opened an issue about it on the CMake bug tracker [
http://public.kitware.com/Bug/view.php?id=15618] as they might want to
adjust FindHDF5.cmake in their newer versions.

Best,
Sebastian

2015-06-14 15:34 GMT-04:00 Sebastian Wouters <sebastianwouters at gmail.com>:

> Hi Michael,
>
> Thank you for your feedback!
>
> Regarding your questions:
>
> 1. I created a new repository and will delete the old one:
>
> http://anonscm.debian.org/cgit/debichem/packages/chemps2.git/
>
> This new repository has a tagged version upstream/1.5 without the debian
> folder, as requested. I've also changed the general package name from
> libchemps2 to chemps2 in the new repo.
>
> 2. In the new rules file, the option "-D html_theme=default" is passed to
> sphinx-build, which uses the default theme instead of the classic theme:
>
>
> http://anonscm.debian.org/cgit/debichem/packages/chemps2.git/tree/debian/rules#n19
>
> 3. libpython-dev was added to the control file:
>
>
> http://anonscm.debian.org/cgit/debichem/packages/chemps2.git/tree/debian/control#n20
>
> 4. I have currently used a work-around to make debuild work for sid:
>
> https://github.com/SebWouters/CheMPS2/blob/master/CheMPS2/CMakeLists.txt
>
> According to HDF5's specifications, one should include <hdf5.h>, see
> section 5 on
>
> http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL
>
> In sid's packaged hdf5 version, this file is installed in
> /usr/include/hdf5/serial/:
>
> https://packages.debian.org/sid/amd64/libhdf5-dev/filelist
>
> I think it is therefore CMake's task to correctly set the variable HDF5_INCLUDE_DIRS
> with FindHDF5.cmake. They will probably do so at one point in a new
> version. So maybe this needs to be patched to sid's cmake version, because
> else many programs will have this problem?
>
> 5. Already resolved:
>
>
> https://github.com/SebWouters/CheMPS2/commit/2468b307b9cabd91a558d83bd651dc27982dd522
>
> 6. The idea of the chemps2 library is that it should be a lightweight and
> efficient library providing core functionality. Additional features,
> outside of this core functionality, make use of the classes and
> functionality in the core library without touching them. After some debate
> with Sandeep Sharma (who rewrote the Block code for Garnet Chan) and
> Garnet himself, we agreed that this is most likely the optimal balance
> between speed and stability on the one hand, and ease-of-use and recycling
> code for future development on the other hand.
>
> From the tests, it seems that with ~ 30 functions, all API is provided.
> But for psi4 for example, all classes in DMRGSCF*.h are required as well,
> see https://github.com/psi4/psi4public/blob/master/src/bin/dmrg/dmrgscf.cc.
> And for generic purpose classes such as Davidson or DIIS, it might be
> useful for other programs to use them for a different purpose. The classes
> which initially seem least useful, the Tensor*.h will then again be used to
> construct intermediary contracted objects for dynamic correlation theories
> such as DMRG-NEVPT2.
>
> That being said, I'm well aware that any API change will break user space
> and will require a version number increase. The API in the version in this
> new repo is adjusted to MPI (although I don't officially support it yet --
> still need to do scaling tests and write a paper). The only major feature
> which will be added before the end of 2016 in the core package is the
> calculation of the 3-RDM. This will only require additional functionality
> and I will take care that it doesn't break the current API. All further
> developments of CheMPS2 will be split into a separate library making use of
> the core library, as said above.
>
> Due to the combination of all class functions in one header file (per
> class), currently the header files mutually call each other in a cascaded
> way. So either all or none are included (in practice). If you would like to
> have a minimal closed set of functions, I can make one specific header file
> with all relevant functions. As an alternative I could write C-wrappers
> around the CheMPS2 class, an option which I contemplated about for the
> python interface, but which I abandoned in favour of Cythonizing the
> C++-code.
>
> Let me know what you think, and if you want, I can make specific
> installation headers for debian.
>
> 7. I've adjusted all your comments regarding the library description.
>
> Best wishes,
> Sebastian
>
>
> 2015-06-13 13:24 GMT-04:00 Michael Banck <mbanck at debian.org>:
>
>> Hi Sebastian,
>>
>> On Thu, May 14, 2015 at 04:39:55PM -0400, Sebastian Wouters wrote:
>> > Hi Michael,
>> >
>> > I have now also added the python package: python-chemps2:
>> > http://anonscm.debian.org/cgit/debichem/packages/libchemps2.git/
>> >
>> > Is there anything else I can do?
>>
>> I had a further look, sorry for the delay.  My comments:
>>
>> 1. Is there a good reason the source package is called "libchemps2"
>> while the github project and release tarballs are called just "chemps2"
>> (modulo capitalization)?  I agree it would be awkward to switch the git
>> repo basename and all, but maybe better now than after the package is in
>> the archive?  In general, the source package name should be called
>> similar to the tarballs.
>>
>> 2. A build on Debian unstable fails when running sphinx, cause it cannot
>> find a 'classic' theme:
>>
>>
>> |PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html -c
>> obj-x86_64-linux-gnu/sphinx/ sphinx/ build/html
>> |Making output directory...
>> |Running Sphinx v1.2.3
>> |loading pickled environment... not yet created
>> |
>> |Theme error:
>> |no theme named 'classic' found (missing theme.conf?)
>> |make[1]: *** [override_dh_auto_build] Error 1
>>
>> That's a bit weird, but indeed I don't have a
>> /usr/share/sphinx/themes/classic/theme.conf
>>
>> Maybe it needs to be changed to "default"?  That one is available and
>> changing it to that makes the documentation build fine for me.
>>
>> 3. The following Build-Depends is missing:
>>
>>  - libpython-dev
>>
>> 4. The include for HDF5 in CheMPS2/include/chemps2/MyHDF5.h is not
>> working for me, there's no /usr/include/hdf5.h (anymore?). If I replace
>> that with '#include <hdf5/serial/hdf5.h>', it builds fine.
>>
>> 5. I was a bit surprised that there is only libchemps2.so.1 and not
>> libchemps2.so.1.x.y as is usual for libtool projects, but I guess that
>> is from CMake?
>>
>> 6. As a general (targetted at upstream) comment, it seems to me that
>> there are really a lot of files shipped in /usr/include/chemps2.  Be
>> aware that removing any function signature from any of those will
>> require you to bump the library version.  Is that really the external
>> API in there or are some/most meant to be internal and should not be
>> shipped?
>>
>> 7. About the description in debian/control, I would advise the following
>> changes.  But those are not required before upload:
>>
>>  - I would remove the first sentence of the 'design philosophy'
>>    paragraph, as implementation details or designs are usually
>>    discouraged in the description.  Maybe to make it more readable, you
>>    could break it down into a list of bullet-points as well, introduced
>>    with something like "Further Features include: [...]".
>>
>>  - remove the "In the future" paragraph - the description should be
>>    about the current state of affairs (though I agree we are sometimes
>>    bad at updating it when new upstream version implement new features).
>>
>>  - personally I would drop the last paragraph as well.  The homepage is
>>    already mentioned in the Homepage: field and in upstream-metadata,
>>    and the additional references are also mentioned in upstream-metadata
>>    (though I am not sure that information is exposed elsewhere yet).
>>    Finally, the documentation is shipped in the libchemps2-doc package,
>>    or is the documentation on your website different to it?  That said,
>>    if you prefer to leave that paragraph in, I'm fine with it.
>>
>>  - maybe expand 2-RDM as (I guess?) "second order reduced density
>>    matrix (2-RDM)" on first mention, though then again if users don't
>>    know what 2-RDM means they might not get a lot out of the package
>>    anyway.  You are expanding most of the other acronyms (like FCI,
>>    CASCI, CASSCF) already, though.
>>
>>  - Possibly add something like "CheMPS2 is parallelized via OpenMP." at
>>    the end, or am I mistaken about OpenMP?
>>
>>
>> Cheers,
>>
>> Michael
>>
>
>
>
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