Custom Search
-- Jason Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 On May 31, 2010, at 10:52 AM, George Tzotzos <gtzotzos.me.com> wrote: > Hi Jason > > Thanks for the latest instructions to compile MPICH2. > > However, I encountered yet another problem. Hopefully it's the last one. > > ./configure -mpi gnu in $AMBERHOME/AmberTools/src works fine > > The configuration file, config.h, was successfully created. > > If you have amber11, the most common next step is to > 'cd ../../src; make clean; make parallel'. See the Users' Manual > for information on building a parallel version of AmberTools > > > Trying to do a "make parallel" in amber11/src gives the error below > > _schlegel_dg_ in schlegel_dg.o > _schlegel_dg_ in schlegel_dg.o > _evb_ntrfc_ in evb_ntrfc.o > _evb_ntrfc_ in evb_ntrfc.o > _evb_ntrfc_ in evb_ntrfc.o > _evb_ntrfc_ in evb_ntrfc.o > _evb_ntrfc_ in evb_ntrfc.o > ___ncsu_abmd_hooks_MOD_on_force in ncsu-abmd-hooks.o > ___ncsu_abmd_hooks_MOD_on_sander_init in ncsu-abmd-hooks.o > ___ncsu_abmd_hooks_MOD_on_sander_init in ncsu-abmd-hooks.o > ___ncsu_abmd_hooks_MOD_on_sander_init in ncsu-abmd-hooks.o > ___ncsu_sander_hooks_MOD_rem_preinit in ncsu-sander-hooks.o > ___ncsu_sander_hooks_MOD_rem_preinit in ncsu-sander-hooks.o > _qm2_load_params_and_allocate_ in libsqm.a(qm2_load_params_and_allocate.o) > ld: symbol(s) not found > collect2: ld returned 1 exit status > make[1]: *** [sander.MPI] Error 1 > make: *** [parallel] Error 2 > > Any ideas? > > Thanks in advance > > George > > > > On May 31, 2010, at 4:01 PM, Jason Swails wrote: > >> Ah, it appears as though you have g77 installed on your machine? I think >> that the configure script is trying to use g77 as the Fortran 77 compiler, >> when it should be using gfortran. Change the configure line to this: >> >> ./configure FC=gfortran F77=gfortran F90=gfortran CC=gcc CXX=g++ >> --prefix=/usr >> make >> sudo make install >> >> This should make sure that gfortran and gcc are used as the compilers for >> all fortran and c code (and g++ for c++ code). >> >> Good luck! >> Jason >> >> On Mon, May 31, 2010 at 9:47 AM, George Tzotzos <gtzotzos.me.com> wrote: >> >>> Hi Jason, >>> >>> Many thanks for the prompt reply. >>> >>> I downloaded MPICH2 as you suggested and tried to install. However, I'm >>> unable to proceed with the installation. >>> >>> See the error message below >>> >>> Any suggestions? >>> >>> Many thanks in advance >>> >>> George >>> >>> checking whether g77 accepts the FLIBS found by autoconf... yes >>> checking whether C can link with >>> -L/usr/local/lib/gcc/i686-apple-darwin8.8.1/3.4.0 >>> -L/usr/local/lib/gcc/i686-apple-darwin8.8.1/3.4.0/../../.. -lfrtbegin >>> -lg2c... yes >>> checking for linker for Fortran main programs... Use Fortran to link >>> programs >>> checking whether Fortran 77 and C objects are compatible... no >>> checking for file... file >>> configure: error: **** Incompatible Fortran and C Object File Types! **** >>> F77 Object File Type produced by "g77 -O2" is : : Mach-O object i386. >>> C Object File Type produced by "gcc -O2" is : : Mach-O 64-bit object >>> x86_64. >>> make: *** No targets specified and no makefile found. Stop. >>> make: *** No rule to make target `install'. Stop. >>> >>> On May 31, 2010, at 3:18 PM, Jason Swails wrote: >>> >>>> Hi George, >>>> >>>> Once you have the compilers built for Mac OS X 10.6, installing Amber >>> itself >>>> is quite simple (all you need is a simple ./configure gnu, make serial, >>> and >>>> make serial in the amber11/AmberTools/src and amber11/src directories). >>>> Luckily, building the compilers from macports or fink is a one-time >>>> necessity, so from now on Amber11 should be quite easy to build. >>>> >>>> Amber11 in parallel requires, once your system is properly set up, only >>> for >>>> you to type "./configure -mpi gnu" in the amber11/AmberTools/src >>> directory >>>> and then make parallel instead of make serial as described above. The >>> only >>>> additional thing you need is an MPI installation. You can either use >>>> macports or fink to build the MPI, or you can build your own from source. >>> I >>>> would suggest building your own, since it's quite easy. >>>> >>>> First thing to do is pick an MPI and download the source code. As has >>> been >>>> suggested many times before, I would suggest MPICH2 (you can download the >>>> source code from >>>> >>> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.2.1p1/mpich2-1.2.1p1.tar.gz >>>> Untar the archive in a directory, then cd into that directory and type >>>> "./configure --prefix=/usr; make; make install". >>>> >>>> This will configure it to be put in /usr/bin and /usr/lib and >>> /usr/include >>>> for the binaries, libraries, and include files, respectively. This >>> should >>>> successfully overwrite the fortran-deficient MPI installation that comes >>>> with xcode tools. >>>> >>>> After you've done this, the 3 simple commands described above (and in the >>>> Amber11 manual) should be sufficient to build a parallel version. >>> However, >>>> you have to make clean before you do this, since you don't want to use >>> the >>>> serial installation as a starting point. >>>> >>>> Mengjuei has also set up a very helpful "amber on mac" weblog that you >>> can >>>> find here http://amberonmac.blogspot.com/. >>>> >>>> Good luck! >>>> Jason >>>> >>>> On Mon, May 31, 2010 at 5:09 AM, George Tzotzos <gtzotzos.me.com> wrote: >>>> >>>>> Hi folks, >>>>> >>>>> I've made a successful serial installation of AMBER11 on a quad core MAC >>>>> (Intel Core i7). My installation was done pretty much on the lines >>> suggested >>>>> in the message of Erik Zuiderweg dated May 24. >>>>> >>>>> My question is whether there's a way to take this as a starting point >>> for a >>>>> parallel installation or does one need to recompile the program from >>>>> scratch? If the former option is possible any suggestions on how to >>> proceed >>>>> from there would be most useful. I went through the mail archive but >>> somehow >>>>> I'm getting lost in the detail. >>>>> >>>>> Your help would be greatly appreciated >>>>> >>>>> George >>>>> >>>>> >>>>> _______________________________________________ >>>>> AMBER mailing list >>>>> AMBER.ambermd.org >>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>> >>>> >>>> >>>> >>>> -- >>>> Jason M. Swails >>>> Quantum Theory Project, >>>> University of Florida >>>> Ph.D. Graduate Student >>>> 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. Graduate Student >> 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 Mon May 31 2010 - 11:31:19 PDT