If netcdf configure failed, and it was not actually built, should we be
passing -DBINTRAJ flag to the preprocessors? If netcdf is going to fail,
why not specify -nobintraj in the configure command? If you do that, does
it work?
--Jason
On Mon, Dec 7, 2009 at 4:17 PM, Lachele Foley <lfoley.ccrc.uga.edu> wrote:
> I tried compiling it on an itanium system. The netcdf configure failed,
> which wasn't an issue for this location, and I did get a config.h file
> (yay!) from which I could delete compiler options as often required for
> ia64.
>
> But, I got the following. I'm guessing that if the netcdf config failed,
> then ptraj shouldn't be using netcdf stuff? I'm not asking for significant
> ia64 support here if that's what's required.
>
> ranlib f2c.a
> mv f2c.a /usr/local/programs/amber/amber11_AT_20091207/lib
> make[2]: Leaving directory
> `/usr/local/programs/amber/amber11_AT_20091207/src/f2c'
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o main.o
> main.c
> In file included from ptraj.h:69,
> from main.c:114:
> utility.h:47:38: error: ../netcdf/include/netcdf.h: No such file or
> directory
> make[1]: *** [main.o] Error 1
> make[1]: Leaving directory
> `/usr/local/programs/amber/amber11_AT_20091207/src/ptraj'
> make: *** [serial] Error 2
>
>
> For the curious:
>
> Linux glycam.ccrc.uga.edu 2.6.9-42.0.3.EL #1 SMP Mon Sep 25 17:14:34 EDT
> 2006 ia64 ia64 ia64 GNU/Linux
> GNU Fortran (GCC) 4.3.1
> gcc (GCC) 4.3.1
> >From netcdf_config.log:
> "
> checking for /usr/bin/nm... /usr/bin/nm -B
> checking nm flags...
> checking for C-equivalent to Fortran routine "SUB"... configure: error:
> Could not compile conftest.f
> "
>
> And, from the config.h file, the following changes were required to get
> that far:
>
> #OCFLAGS=-O3 -mtune=generic -msse -mfpmath=sse -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -DBINTRAJ $(AMBERBUILDFLAGS)
> OCFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
> $(AMBERBUILDFLAGS)
>
> #FOPTFLAGS= -O3 -mtune=generic -msse -mfpmath=sse $(LOCALFLAGS)
> $(AMBERBUILDFLAGS)
> FOPTFLAGS= -O3 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
>
>
>
> :-) Lachele
> --
> B. Lachele Foley, PhD '92,'02
> Assistant Research Scientist
> Complex Carbohydrate Research Center, UGA
> 706-542-0263
> lfoley.ccrc.uga.edu
>
>
> ----- Original Message -----
> From: case
> [mailto:case.biomaps.rutgers.edu]
> To: amber-developers.ambermd.org
> Sent:
> Mon, 07 Dec 2009 09:53:25 -0500
> Subject: [AMBER-Developers] latest release
> candidate for AmberTools 1.3
>
>
> > I have placed the current release candidate here:
> >
> > http://ambermd.org/downloads/AmberTools.04dec09.tar.bz2
> >
> > I think we are getting close! As usual, it is like pulling teeth to get
> > anyone to look at and update the documentation. I may have to just lock
> > all developers in a room at the January meeting and require a certain
> number
> > of updates before allowing them out. But please make changes now if you
> > can.
> > As I have mentioned before, this is an excellent opportunity for students
> > and post-docs to gain some recognition outside their own group by
> > contributing
> > to a common project.
> >
> > ...thx...dac
> >
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Mon Dec 07 2009 - 14:00:02 PST
