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-- Dr. Dean Cuebas, Associate Prof of Chemistry deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507 Dept. of Chemistry, Missouri State University Springfield, Missouri 65897 > > Does anyone know a good reliable, simple editor in Mac that simply assure me > that I am working with Unix LF files no matter was the input EOL format? > > Thanks, > > Alan > > On Thu, Apr 29, 2010 at 16:50, Jason Swails <jason.swails.gmail.com> wrote: > >> Hello, >> >> On Thu, Apr 29, 2010 at 11:18 AM, Alan <alanwilter.gmail.com> wrote: >> >>> Hi there, >>> >>> So compilation of Amber11 with mpi was going fine and the I got this: >>> >>> mpif90 -opmemd gbl_constants.o gbl_datatypes.o state_info.o >> file_io_dat.o >>> mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o >>> inpcrd_dat.o >>> dynamics_dat.o img.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o >>> pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o >>> pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o >>> nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o >> dihedrals.o >>> extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o >>> constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o >>> pmemd_lib.o runfiles.o file_io.o bintraj.o pmemd_clib.o pmemd.o random.o >>> degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o >>> pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o >>> nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o >>> charmm_gold.o ../../netcdf/lib/libnetcdf.a >>> ld: unknown option: -opmemd >>> collect2: ld returned 1 exit status >>> make: *** [pmemd] Error 1 >>> >>> Clearly is should be: >>> mpif90 -o pmemd gbl_constants.o ... >>> >> >> It's a little strange that you got this error (I haven't gotten it on any >> systems I tried building on), however, here is, in my opinion, the most >> logical explanation. >> >> This has to do with LDOUT defined at the bottom of your config.h file. >> Mine >> says: LDOUT= -o . For me, there is a space after the -o in my config.h >> file. If we then look at $AMBERHOME/src/pmemd/src/Makefile, we see the >> lines: >> >> pmemd$(SFX): $(NETCDF) $(OBJS) >> $(PMEMD_LD) $(PMEMD_OPTFLAGS) $(LDOUT)$. $(OBJS) $(PMEMD_NETCDFLIB) >> $(LDFLAGS) $(PMEMD_FLIBSF) >> >> Notice that there is no space between $(LDOUT) and $.. This is undoubtedly >> the error you ran into. I think it would be a better idea to simply put a >> space between those options in the Makefile, but perhaps there is a good >> reason why that's not done (i.e. for compatibility with other, non-GNU >> unices? I have no experience with those). My guess is that something >> removed that extra space at the end of -o in your config.h file... >> >> Ross and/or other developers, should we patch the Makefile to put a space >> there? (and the same for pmemd.MPI and pmemd.cuda as well) >> >> All the best, >> Jason >> >> >>> and when do this by hand all goes fine. But, trying to pinpoint the error >>> was very challenging for me so I could solve that. >>> >>> Cheers, >>> >>> Alan >>> -- >>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate >>> Department of Biochemistry, University of Cambridge. >>> 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>>>> http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><< >>> _______________________________________________ >>> 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 >> > > > > -- > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate > Department of Biochemistry, University of Cambridge. > 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>> http://www.bio.cam.ac.uk/~awd28<< > _______________________________________________ > 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 Fri Apr 30 2010 - 11:00:03 PDT