On Thu, Jul 11, 2013 at 9:00 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> yes I can do that - what should I be looking for?
>
The error message made me wonder if there were strange permissions on that
file that prevented the compiler from being able to open it. Clearly not...
Is this an XSEDE resource? What machine are you trying to compile on?
>
> 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
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
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> > > > > 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
> > > >
> > > _______________________________________________
> > > 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
> >
> _______________________________________________
> 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
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Received on Thu Jul 11 2013 - 18:30:03 PDT
