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Jordi Camps Puchades
jcamps.lsi.upc.edu
Supercomputing research, support and development
Barcelona Supercomputing Center | Instituto Nacional de Bioinformática
| GNHC-2 UPC-CIRI
(http://inb.lsi.upc.edu)
http://www.bsc.es | http://www.inab.org
Tel. : 934 137 602 | Tel. : 934 037 155
Fax : 934 137 721 | Fax : 934 037 157
c/ Jordi Girona, 29 | c/ Josep Samitier, 1-5
Edifici Nexus II, despatx 1B | PCB, Edifici Modular, PBC32
E-08034 Barcelona | E-08028 Barcelona
Catalunya (Spain) | Catalunya (Spain)
> -----Mensaje original-----
> De: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu]
> En nombre de Luis Gracia
> Enviado el: miércoles, 15 de noviembre de 2006 19:35
> Para: amber.scripps.edu
> Asunto: Re: AMBER: gfortran/gcc versus ifort/icc
>
> We had a lot of problems with netcdf on x86_64 using
> gfortran. What I ended up doing is:
> - getting a binary distribution of netcdf from the homepage
> - deleting the netcdf directory provided by amber and
> creating a symbolic link to the binary distribution directory
> - changing the amber Makefiles to not compile netcdf
>
> The following should do it.
> cd $AMBERHOME/src
> mv netcdf netcdf-dist
> ln -s /path/to/netcdf netcdf
> patch -p0 -N -r patch_netcdf_rejects < netcdf.patch
>
>
> This is the patch:
> ---------------------- start ---------------
> --- configure.dist 2006-10-09 18:50:57.000000000 -0400
> +++ configure 2006-10-09 18:51:12.000000000 -0400
> .. -1239,9 +1239,6 ..
> echo " ------ Configuring the netCDF libraries: --------"
> echo ""
>
> - cd netcdf/src;env FC="$fc" FFLAGS="$fncflags"
> F90FLAGS="$f90ncflags" \
> - CXX="" CC="$cc" CFLAGS="$cflags" CPPFLAGS="-DNDEBUG" \
> - ./configure;cd ../..
> fppflags="$fppflags -DBINTRAJ"
> cppflags="$cppflags -DBINTRAJ -I../netcdf/include"
> else
> --- Makefile.dist 2006-10-09 18:51:19.000000000 -0400
> +++ Makefile 2006-10-09 18:51:33.000000000 -0400
> .. -93,7 +93,4 ..
> cd leap; make clean
> -cd pmemd; make clean
> cd build_amoeba; make clean
> - -cd netcdf/src; make clean
> - -cd netcdf/lib && rm -f libnetcdf.a
> - -cd netcdf/include && rm -f *.mod
> # rm -f $(CONFIG_FILE)
> --- sander/Makefile.dist 2006-10-09 18:51:37.000000000 -0400
> +++ sander/Makefile 2006-10-09 18:51:50.000000000 -0400
> .. -249,7 +249,6 ..
> cd ../dcqtp; make libdivcon.a
>
> netcdf.mod:
> - cd ../netcdf/src; make install
> cp ../netcdf/include/*.mod .
>
> clean:
> --- ptraj/Makefile.dist 2006-10-09 18:51:56.000000000 -0400
> +++ ptraj/Makefile 2006-10-09 18:52:05.000000000 -0400
> .. -85,4 +85,3 ..
> cd ../lib ; make sys.a
>
> netcdf.mod::
> - cd ../netcdf/src; make install
> ---------------------- end ---------------
>
> Best
>
> Luis
>
>
> Jordi Camps said the following on 11/15/06 12:50:
> > Hello,
> >
> > I'm trying to compile Amber 9 with NetCDF support, but I'm
> stuck with
> > a linking problem. I get Amber working without NetCDF
> support in the
> > serial flavour, but when I add the NetCDF flag, I get a bunch of
> > unresolved symbols.
> > Here is a snip of the first error lines:
> > ../netcdf/lib/libnetcdf.a(netcdf.o): In function
> > `__netcdf__nf90_inq_libvers':
> > netcdf.f90:(.text+0x13): undefined reference to
> `nf_inq_libvers_'
> > ../netcdf/lib/libnetcdf.a(netcdf.o): In function
> > `__netcdf__nf90_strerror':
> > netcdf.f90:(.text+0x47): undefined reference to `nf_strerror_'
> > ../netcdf/lib/libnetcdf.a(netcdf.o): In function
> > `__netcdf__nf90_create':
> > netcdf.f90:(.text+0xaf): undefined reference to `nf__create_'
> > netcdf.f90:(.text+0xeb): undefined reference to `nf__create_'
> > netcdf.f90:(.text+0xf7): undefined reference to `nf_create_'
> > ../netcdf/lib/libnetcdf.a(netcdf.o): In function
> > `__netcdf__nf90_enddef':
> > netcdf.f90:(.text+0x188): undefined reference to `nf_enddef_'
> > netcdf.f90:(.text+0x1f6): undefined reference to `nf__enddef_'
> > It is a linking problem, but I'm being unable to resolve the cause.
> > I'm on a
> > x86_64 (Opteron) system running Linux and GCC (gfortran) compilers
> > version 4.1.0.
> > Did you get this error before? Could you tell me how you
> will try to
> > resolve this issue?
> >
> > Thanks in advance!
> >
> > --
> > Jordi Camps Puchades
> > jcamps.lsi.upc.edu
> > Supercomputing research, support and development
> >
> > Barcelona Supercomputing Center | Instituto Nacional de
> Bioinformática
> > | GNHC-2 UPC-CIRI
> > (http://inb.lsi.upc.edu)
> > http://www.bsc.es | http://www.inab.org
> > Tel. : 934 137 602 | Tel. : 934 037 155
> > Fax : 934 137 721 | Fax : 934 037 157
> > c/ Jordi Girona, 29 | c/ Josep Samitier, 1-5
> > Edifici Nexus II, despatx 1B | PCB, Edifici Modular, PBC32
> > E-08034 Barcelona | E-08028 Barcelona
> > Catalunya (Spain) | Catalunya (Spain)
> >
> >
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Received on Sun Nov 19 2006 - 06:07:26 PST