[AMBER-Developers] AT 1.3 config fails for alternate gnu location

From: Lachele Foley <lfoley.ccrc.uga.edu>
Date: Tue, 24 Nov 2009 16:28:08 -0500

I have an alternate gcc/gfortran installed on a system in /usr/local/bin (etc.). If I rearrange my PATH so that the system sees the original install (in /usr/bin), AT configures and compiles (testing now). If I leave my path so it finds the gcc/gfortran in /usr/local/bin first, the configure fails with complaints about gfortran and netcdf.

If there's a way in the configure script to specify alternate library paths, I don't see it. I can alter the config.h file, of course, but not if the configure script never makes one.

On this system:

Linux shaw.nuigalway.ie 2.6.18-128.1.10.el5xen #1 SMP Wed Apr 29 14:24:51 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux

[installer.shaw src]$ ./configure gnu
Setting AMBERHOME to /array2/programs/amber11_AT_20091124

Obtaining the gnu suite version:
      gcc -v
The version is 4.3.1

Testing the gcc compiler:
     gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c

Obtaining the C++ compiler version:
     g++ -v
The version is 4.3.1

Testing the gfortran compiler:
     gfortran -O0 -o testp testp.f
/usr/bin/ld: cannot find -lgfortranbegin
collect2: ld returned 1 exit status
./configure: line 744: ./testp: No such file or directory
Unable to compile a Fortran program using gfortran -O0
We will be unable to compile sqm

Testing flex:

Configuring NetCDF; (may be time-consuming)

    Error: NetCDF configure returned 1
    NetCDF configure failed! Check the netcdf_config.log file.

the netcdf log complains:

checking if Fortran "byte" is C "signed char"... configure: error: Could not link conftestf.o
and conftest.o

[installer.shaw src]$ which gfortran
[installer.shaw src]$ which gcc
[installer.shaw src]$ locate conftestf.o
[installer.shaw src]$ locate conftest.o
[installer.shaw src]$

Regarding gfortran:

[installer.shaw src]$ locate gfortranbegin

:-) Lachele
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
AMBER-Developers mailing list
Received on Tue Nov 24 2009 - 13:30:02 PST
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