yes I can do that - what should I be looking for?
On Thu, Jul 11, 2013 at 5:46 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Jul 11, 2013 at 5:41 PM, Jorgen Simonsen <jorgen589.gmail.com
> >wrote:
>
> > yes it does exists.
> >
>
> Can you open it in a text editor?
>
>
> >
> >
> > On Thu, Jul 11, 2013 at 2:32 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > On Thu, Jul 11, 2013 at 5:05 PM, Jorgen Simonsen <jorgen589.gmail.com
> > > >wrote:
> > >
> > > > Dear Jason,
> > > >
> > > > Tha truely fixed the issue but a new one came up that it could find
> the
> > > > object file for the emap.o
> > > >
> > > > PGF90-F-0002-Unable to open source input file: emap.F90
> > > > PGF90/x86-64 Linux 12.4-0: compilation aborted
> > > >
> > > > I have changed to the directory src/ and made typed
> > > >
> > >
> > > Does that file exist? ($AMBERHOME/src/sander/emap.F90)
> > >
> > >
> > > >
> > > > make install
> > > >
> > > > Any suggestions?
> > > >
> > > >
> > > > On Thu, Jul 11, 2013 at 12:27 PM, Jason Swails <
> jason.swails.gmail.com
> > > > >wrote:
> > > >
> > > > > On Thu, Jul 11, 2013 at 3:07 PM, Jorgen Simonsen <
> > jorgen589.gmail.com
> > > > > >wrote:
> > > > >
> > > > > > Hi all,
> > > > > >
> > > > > > I am trying to compile amber12 on a cray-system. For the serial
> > > > > compilation
> > > > > > everything is fine and the make.test serial runs fine without any
> > > > issues.
> > > > > >
> > > > > > For the mpi-compilation I do have some problems getting it to
> work
> > > > fine.
> > > > > I
> > > > > > generate the config.h file using the following syntax:
> > > > >
> > > > >
> > > > > > ./configure -noX11 -nobintraj -crayxt5 -mpi pgi
> > > > > >
> > > > > > >From the test-run I get the following output:
> > > > > >
> > > > > > Obtaining the PGI suite version:
> > > > > > pgcc -V
> > > > > > The version is 12.4-0
> > > > > >
> > > > > > Testing the cc compiler:
> > > > > > cc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> > testp.c
> > > > > > OK
> > > > > >
> > > > > > Testing the ftn compiler:
> > > > > > ftn -O1 -o testp testp.f
> > > > > > OK
> > > > > >
> > > > > > Testing mixed C/Fortran compilation:
> > > > > > cc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o
> > testp.c.o
> > > > > > testp.c
> > > > > > ftn -O1 -c -o testp.f.o testp.f
> > > > > > cc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> > > testp.c.o
> > > > > > testp.f.o -pgf90libs
> > > > > > OK
> > > > > >
> > > > > > Testing pointer size:
> > > > > > cc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o
> > > > test_pointer_size
> > > > > > test_pointer_size.c
> > > > > > Detected 64 bit operating system.
> > > > > >
> > > > > > Testing flex: OK
> > > > > >
> > > > > > Checking for zlib: OK
> > > > > >
> > > > > > Checking for libbz2: OK
> > > > > >
> > > > > > Configuring fftw-3.3 for mdgx (may be time-consuming)...
> > > > > >
> > > > > > fftw-3.3 configure succeeded.
> > > > > >
> > > > > > The configuration file, config.h, was successfully created.
> > > > > >
> > > > > > The next step is to type 'make install'
> > > > > >
> > > > > > Cleaning the src directories. This may take a few moments.
> > > > > > Configure complete.
> > > > > >
> > > > > >
> > > > > > and the compilation ends with the following error
> > > > > >
> > > > > > AT12/amber12/bin/mpinab -c dna3.nab
> > > > > > nab2c failed!
> > > > > > make[2]: *** [dna3.o] Error 1
> > > > > >
> > > > > > I have seen it on the list but I did not find the solution to
> it. I
> > > > have
> > > > > > tried to compile directly like this
> > > > > >
> > > > > > mpinab -c dna3.nab
> > > > > >
> > > > > > and no new file is generated as asked for in the thread with the
> > same
> > > > > > issue. Any help much appreciated
> > > > > >
> > > > >
> > > > > My guess is that you will never need an MPI-enabled NAB (OpenMP
> would
> > > > > probably be better, anyway, if you really needed a threaded NAB
> > > > > application).
> > > > >
> > > > > In this case, you might as well just skip the parallel AmberTools
> > > > > installation (since MMPBSA.py.MPI has never worked for me on a Cray
> > > > machine
> > > > > before).
> > > > >
> > > > > You can go to $AMBERHOME/src/ and run "make install" there to skip
> > > > > AmberTools.
> > > > >
> > > > > HTH,
> > > > > Jason
> > > > >
> > > > > --
> > > > > Jason M. Swails
> > > > > Quantum Theory Project,
> > > > > University of Florida
> > > > > Ph.D. Candidate
> > > > > 352-392-4032
> > > > > _______________________________________________
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> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
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> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jul 11 2013 - 18:30:03 PDT
