On Fri, Apr 30, 2010 at 1:52 PM, Dean Cuebas
<deancuebas.missouristate.edu>wrote:
>
> > Reply-To: AMBER Mailing List <amber.ambermd.org>
> > Date: Thu, 29 Apr 2010 11:13:03 -0500
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] a possible typo bug while building pmemd with mpi
> >
> > The problem is not space...
> >
> > I am having a hell with TextWrangler as I find out that this application
> > simply doesn't convert to Unix LF, so when I copied a file in terminal
> and
> > open it with twedit is Mac CR EOL and it causes problems with
> compilations
> > and makes.
>
> I've never had a problem with TextWrangler... could you send me the file
> you
> are having problems with?
>
It was the config.h created by configure. There is a problem with any text
editor that removes whitespace, since the space after -o in LDOUT in
config.h is important as I explained in my last reply in this thread. This
problem is enough to make the link step look like gfortran -opmemd (since
the space after -o has been removed by textwrangler). Perhaps this is an
option that can be toggled? Perhaps it's the default, but in any case, that
was ultimately concluded as the source of the issue.
All the best,
Jason
> Dean
> --
> 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><
> 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 <http://www.bio.cam.ac.uk/%7Eawd28><<
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Apr 30 2010 - 20:30:03 PDT
