Re: [AMBER] problems with NAB and SHIFTS

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 15 Jun 2010 15:12:58 -0400

Hello,

What version of gfortran are you using? You can find out by the command

gfortran -v

It may be that the version of gfortran you're using is too old to make use of -lgfortran. I believe the default gcc on centos is 4.1, in which case all that needs to be done is to remove -lgfortran from your Makefile (I think). libgfortran.a should be in your default ld search path if gfortran is located in /usr/bin. If this is wrong, then your compilation will fail at link when it can't find all the functions it needs.

Another option is to install the latest stable gcc with gfortran and recompile ambertools and shifts with the new compilers.

Good luck!
Jason

--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
On Jun 15, 2010, at 2:16 PM, Jakob Toudahl Nielsen <jtn.chem.au.dk> wrote:
> gfortran is installed, running test for nab leads to the same error  
> messages corcerning lgfortran:
> 
> /usr/bin/ld: cannot find -lgfortran
> collect2: ld returned 1 exit status
> cc failed!
> 
> sorry, this problem might be easy for an experienced linux user... but  
> my guess would be that it does not know where to find gfortran - it is  
> installed in:
> 
> /usr/bin/gfortran
> 
> what can I do to fix this?
> 
> OS: CentOS 4.7 Linux 64 bit
> 
> //Jakob
> 
> 
> Citing case <case.biomaps.rutgers.edu>:
> 
>> On Tue, Jun 15, 2010, Jakob Toudahl Nielsen wrote:
>> 
>>> nab -o shifts shifts.o shifts_emp.o ring_current.o  get_banis_info.o
>>> plane.o read_obs_shifts.o ax_susc.o sbcoil.o swap_shifts.o
>>> get_pep_info.o get_sugar_info.o get_chi_info.o el.o get_dist_ang.o
>>> write_headers.o get_vdwa.o shifts_qdb.o
>>> /usr/bin/ld: cannot find -lgfortran
>> 
>> Do you have gfortran installed on your machine?  (You will need this.)
>> Did the nab test cases in AmberTools pass?  It might help to know what OS
>> you are using.
>> 
>> ....dac
>> 
>> 
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> 
> 
> 
> 
> -- 
> 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)
> 
> _______________________________________________
> 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

Received on Tue Jun 15 2010 - 12:30:03 PDT