On Fri, Jul 12, 2013 at 12:03 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> Hi ,
>
> it is named copper01.
>
OK. Unfortunately I don't have access to the machine and I've never seen
the problem you're reporting. It seems unrelated to Amber... The admin
of your system may have a better idea of what's happening.
Good luck,
Jason
>
> 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
> >
> _______________________________________________
> 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 Fri Jul 12 2013 - 10:00:03 PDT
