Hi Lin,
I don't think Python is compiled in static, but I don't think this should be
an issue for a couple reasons.
Most of the PGI users, I think, will have GCC readily available (even many
systems using modules, like Kraken and Athena) with libraries in standard
locations so that you don't have to load a new module to compile python,
then have it break after you unload it.
Also, if this all fails, then you can use -nopython to force Amber to use
the system python instead of the one that came bundled with AmberTools. All
of this should be handled automatically at compile time, so the user doesn't
have to actually *see* any of this going on.
I think Ross has a system here with PGI compilers that I can test some stuff
out on, so I'll report back on my findings.
All the best,
Jason
On Wed, Mar 16, 2011 at 11:31 AM, Lin Fu <linfu3200.gmail.com> wrote:
> Hi Jason,
>
> You mean the python compiled here is static version, which will not be
> dynamically linked to any gnu stuff. If both python here in the amber and
> sander are static version, it will be fine since it is only system level
> call instead of source code level call. but If both are only dynamical link
> version, it might cause problem. since we might need to load both gnu and
> pgi stuff, which is usually excluded by module on the cluster. please
> correct me if it is not. Thanks.
>
> Best Regards,
> Lin
> 2011/3/16 Jason Swails <jason.swails.gmail.com>
>
> > It should make no difference. The python interpreter can be compiled
> with
> > GCC, and it can run any python script. MMPBSA.py calls sander via a
> system
> > call, so as long as it's *installed*, it'll work.
> >
> > Also keep in mind that MMPBSA.py is not compiled, since python is an
> > interpreted language. We can get away with this because Python doesn't
> > actually *link* to anything, it's just used to interpret python
> > programs/scripts.
> >
> > --Jason
> >
> > On Wed, Mar 16, 2011 at 10:39 AM, Lin Fu <linfu3200.gmail.com> wrote:
> >
> > > Hi Jason,
> > >
> > > >It doesn't seem like there's really any way around this. What do
> people
> > > think about letting Python just use GCC if it can find it in case
> someone
> > > chooses pgi at configure time?
> > > Not sure whether it will make the user confusing or not. Will the
> > MMPBSA.py
> > > be compatible with the MPI with different compilers if user runs in
> > > parallel. Another problem is that on most clusters Environment Module
> is
> > > used to manage the different enviroment of compiler, such as module
> load
> > > intel/pgi/gnu. some options are exclusive. Can gnu-compiled MMPBSA.py
> > > invoke
> > > the pgi-compiled serial version of sander, which is called by the
> > > MMPBSA.py.
> > > >if you can reconfigure using -nopython, and run it again to see if
> there
> > > are any errors elsewhere that would be great.
> > > It seems that mtkpp can also not pass the pgi compiler even after
> > excluding
> > > the python module due "-Wall" problem, but Ben said that he will give
> an
> > > solution about that.
> > >
> > > Best Regards,
> > > Lin
> > >
> > > 2011/3/15 Jason Swails <jason.swails.gmail.com>
> > >
> > > > Hi Lin,
> > > >
> > > > It doesn't seem like there's really any way around this. What do
> > people
> > > > think about letting Python just use GCC if it can find it in case
> > someone
> > > > chooses pgi at configure time?
> > > >
> > > > It won't cause any incompatibilities with anything else (as it's
> quite
> > > > isolated), and I think that getting it to compile correctly with PGI
> is
> > > > going to be difficult.
> > > >
> > > > We already have to force Python to use a different (xcode) compiler
> > when
> > > > building on Mac OS X, so I don't think this is really going to cause
> > any
> > > > issues.
> > > >
> > > > Thoughts?
> > > >
> > > > And Lin, if you can reconfigure using -nopython, and run it again to
> > see
> > > if
> > > > there are any errors elsewhere that would be great.
> > > >
> > > > Thanks!
> > > > Jason
> > > >
> > > > On Tue, Mar 15, 2011 at 4:42 PM, Lin Fu <linfu3200.gmail.com> wrote:
> > > >
> > > > > Hi Jason,
> > > > >
> > > > > I have tried to compile this version of ambertools with pgi, but it
> > > > failed
> > > > > to compile python module since "-Xlinker and -export-dynamic" can
> not
> > > be
> > > > > recognized by pgcc. Not sure whether you got similar error.
> > > > > pgcc -Xlinker -export-dynamic -o python \
> > > > > Modules/python.o \
> > > > > libpython2.6.a -lpthread -ldl -lpthread
> > -lutil
> > > > > -lm
> > > > > pgcc-Error-Unknown switch: -Xlinker
> > > > > pgcc-Error-Unknown switch: -export-dynamic
> > > > > make[1]: *** [python] Error 1
> > > > >
> > > > > Best Regards,
> > > > > Lin
> > > > >
> > > > > 2011/3/14 Jason Swails <jason.swails.gmail.com>
> > > > >
> > > > > > If anyone has access to the PGI compilers, bits of AmberTools
> > aren't
> > > > > > compiling for me out-of-the-box on athena, but there are enough
> > > > > > Cray-specific idiosyncrasies that I'm not confident enough to
> label
> > > > them
> > > > > > PGI
> > > > > > problems.
> > > > > >
> > > > > > Also, for those of you who will try building this alongside
> Amber11
> > > > > (dirty
> > > > > > or clean), don't forget to apply the script AT15_Amber11.py after
> > > > > configure
> > > > > > (from any directory, it just uses absolute paths based on
> > AMBERHOME).
> > > > > > Configure should print a warning message about this in any case.
> > > > > >
> > > > > > All the best,
> > > > > > Jason
> > > > > >
> > > > > > On Mon, Mar 14, 2011 at 12:03 PM, David A Case <
> > > > case.biomaps.rutgers.edu
> > > > > > >wrote:
> > > > > >
> > > > > > > Hi everyone:
> > > > > > >
> > > > > > > The second "release candidate" for AmberTools 1.5 is here:
> > > > > > >
> > > > > > > http://ambermd.org/downloads/AmberTools.14mar11.tar.bz2
> > > > > > >
> > > > > > > Please test this out:
> > > > > > >
> > > > > > > a. on its own
> > > > > > > b. in conjunction with Amber11 (either in a clean install,
> or
> > > > > untarred
> > > > > > > on top of a working, "dirty" directory already
> containing
> > AT
> > > > > 1.4.)
> > > > > > >
> > > > > > > It is better to test this than the at15-with-patches branch,
> > since
> > > > this
> > > > > > is
> > > > > > > what users would actually be getting. No GEM here yet, but
> other
> > > > > things
> > > > > > > should be getting close.
> > > > > > >
> > > > > > > ...thx...dac
> > > > > > >
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > AMBER-Developers mailing list
> > > > > > > AMBER-Developers.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Jason M. Swails
> > > > > > Quantum Theory Project,
> > > > > > University of Florida
> > > > > > Ph.D. Candidate
> > > > > > 352-392-4032
> > > > > > _______________________________________________
> > > > > > AMBER-Developers mailing list
> > > > > > AMBER-Developers.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > > > > >
> > > > > _______________________________________________
> > > > > AMBER-Developers mailing list
> > > > > AMBER-Developers.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Candidate
> > > > 352-392-4032
> > > > _______________________________________________
> > > > AMBER-Developers mailing list
> > > > AMBER-Developers.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > > >
> > > _______________________________________________
> > > AMBER-Developers mailing list
> > > AMBER-Developers.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Mar 16 2011 - 14:00:03 PDT
