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
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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Received on Thu Jul 11 2013 - 14:30:03 PDT
