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-- 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/amberReceived on Thu Jul 11 2013 - 20:30:03 PDT