AMBER Archive (2009)

Subject: RE: [AMBER] amber9 in fedora10

From: Ross Walker (
Date: Wed May 13 2009 - 18:22:20 CDT

Hi Bala,

> I am installing amber9 on a system running with Fedora10. I got the
> following error when i gave 'make serial'. I didnt find any question on
> this
> error in the mail list archieve. kindly write me what is going wrong.
> The
> config.h is attached above.
> I created the config file with the command: ./configure -bintraj
> gfortran
> netcdf.f90:(.text+0x18a5): undefined reference to `nf_inq_varid_'
> ../netcdf/lib/libnetcdf.a(netcdf.o): In function
> `__netcdf_MOD_nf90_rename_var':
> netcdf.f90:(.text+0x1af5): undefined reference to `nf_rename_var_'
> collect2: ld returned 1 exit status
> make[1]: *** [sander] Error 1
> make[1]: Leaving directory `/usr/local/amber9/src/sander'
> make: *** [serial] Error 2

This suggests that netcdf may have been compiled with a different compiler
than you are using for AMBER. Did you definitely make clean before you

Another quick fix, if making clean does not work, would be to run configure
without the -bintraj option. You will lose the ability to use binary
trajectories but this at least get things compiled for you.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

AMBER mailing list