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
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Received on Wed Mar 16 2011 - 11:30:03 PDT
