Ok, thanks for the clarification!
Have a great day,
Dean
> From: Alan <alanwilter.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Sat, 1 May 2010 02:04:42 -0500
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] a possible typo bug while building pmemd with mpi
>
> 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<<
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon May 03 2010 - 11:00:05 PDT
