Hi Dean,
It is precisely what Jason said. My twedit was stripping whitespaces at the
end of line and making "LDOUT = -o " --> "LDOUT = -o"
It was doing so because I needed to edit config.h because of gcc-4 and Fink
mpicc, which is wrongly calling apple gcc instead of Fink gcc-4, remember a
related tip I gave other day?.
Fink guys are aware now about this issue the coming Fink ompi 1.4.1 package
should solve this problem.
Cheers,
Alan
On Sat, May 1, 2010 at 04:12, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> >
> >
> >
> > _______________________________________________
> > 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<<
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Received on Sat May 01 2010 - 00:30:04 PDT
