Hi ,
it is named copper01.
On Thu, Jul 11, 2013 at 8:04 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> --
> Jason M. Swails
> Quantum Theory Project
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Jul 11, 2013, at 9:17 PM, Jorgen Simonsen <jorgen589.gmail.com> wrote:
>
> > Hi,
> >
> > No I do not think it is a XSEDE resource.
>
> What's the name of the machine?
>
> >
> > ls -ltr emap.F90
> >
> > -rw-r----- 1 jorgen dnnn 76412 2013-07-09 17:57 emap.F90
> >
> > it is a linux machine with ( cat /etc/*release )
> >
> > SUSE Linux Enterprise Server 11 (x86_64)
> > VERSION = 11
> > PATCHLEVEL = 1
> >
> >
> > On Thu, Jul 11, 2013 at 6:06 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >
> >> 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
> >>>>>>> _______________________________________________
> >>>>>>> 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
> >>>> _______________________________________________
> >>>> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jul 12 2013 - 09:30:02 PDT
