AMBER Archive (2006)

Subject: RE: AMBER: gfortran/gcc versus ifort/icc

From: Jordi Camps (jcamps_at_lsi.upc.edu)
Date: Thu Nov 16 2006 - 10:22:55 CST

Hello,

thanks for your methodology. I've tried it, but it's still not working. In
the first place, I installed the NetCDF binary version from my distribution
repositories, but this source lacks the .mod files, so I backed up to your
method: I downloaded the apropriate binaries from the NetCDF home page and
followed your method. But now I'm getting another strange error (related to
the .mod files):
        gfortran -c -O3 -fno-second-underscore -march=nocona -ffree-form
-o bintraj.o _bintraj.f
        Fatal Error: Reading module netcdf at line 5 column 61: Expected
left parenthesis
The 5 first lines of netcdf.mod file are as follows:
        GFORTRAN module created from netcdf.f90 on Mon Feb 27 10:44:00 2006
        If you edit this, you'll get what you deserve.
        
        
        (() () () () () () () () () () () () () () () () () () () ())
It seems correctly parentized, and is an original distribution file, so I
cannot think this file is wrong.
Didn't you changed anything else?

Thank you for your help, 

--
Jordi Camps Puchades
jcamps_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] 
> En nombre de Luis Gracia
> Enviado el: miércoles, 15 de noviembre de 2006 19:35
> Para: amber_at_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_at_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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