Re: [AMBER] problems with NAB and SHIFTS

From: Jakob Toudahl Nielsen <>
Date: Wed, 16 Jun 2010 09:56:43 +0200

Thank you all for your help leading me through this very difficult

I been talking to our system administrator who suggested that it is
best to use gfortran as the driver of ld. i.e. a typical
link-statement could be:

gfortran -o program.exe mod1.o mod2.o -L/path/to/library -lfoo -lbar
- where it should be able to find the following:
    ls -l /path/to/library/libfoo.*
    ls -l /path/to/library/libbar.*

I will also expand the path to the LD_LIBRARY_PATH, before I guess
there was no specific info regarding gfortran:

>> "echo $LD_LIBRARY_PATH":
>> /com/intel/Compiler/11.1/064/mkl/lib/em64t:/com/intel/Compiler/11.1/064/lib/intel64

I need your help on where in the test/installation-scripts to apply
these changes, i.e. where is "gfortran" and "ld" called. Should I
change something in "/src/config.h"? such as modifying the FLIBS?

FLIBS= $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a -lgfortran
FLIBSF= $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a


# Information about Fortran compilation:


thanks in advance, best regards,

information regarding versions:

>> gcc --version
gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-10)

>> gfortran --version
GNU Fortran (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)

Citing case <>:

> On Tue, Jun 15, 2010, Jakob Toudahl Nielsen wrote:
>> gfortran is installed, running test for nab leads to the same error
>> messages corcerning lgfortran:
>> /usr/bin/ld: cannot find -lgfortran
> OK. First, there is no reason to work more with SHIFTS: you have to get nab
> working first.
> You should look at the output of the configure script in AmberTools. Does
> is say something like "Unable to compile mixed C/Fortran code"? This should
> be a fatal error, but is not in the distributed version of configure. So
> if your configure script is failing here, we need to get that fixed first.
> What do "gcc --version" and "gfortran --version" report? As was mentioned
> in an earlier post, finding libgfortran.a, and setting LD_LIBRARY_PATH to
> that directory, might fix this. (But if gcc and gfortran are arising from
> the same package, that ought to automatically occurr...)
> ....dac
> _______________________________________________
> AMBER mailing list

Jakob Toudahl Nielsen, post doc
Laboratory for Biomolecular NMR Spectroscopy
inSPIN, Center for Insoluble Protein Structures
Department of Chemistry, University of Aarhus
Langelandsgade 140, DK-8000 Aarhus C, Denmark
Phone: +458942 5528 or +452993 8502 (cell)
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Received on Wed Jun 16 2010 - 01:00:03 PDT
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