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
>
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Received on Wed Mar 16 2011 - 12:00:03 PDT
