Re: [AMBER] Doubts in the installation of Amber11

From: Ben Roberts <>
Date: Mon, 31 Jan 2011 14:21:55 -0500

Hi Vani,

On 31/1/2011, at 2:15 p.m., vani panguluri wrote:

> [vani.louie2 src]$ ./configure gnu
> Your AMBERHOME environment variable should be set to /home/vani/amber11
> Obtaining the gnu suite version:
> gcc -v
> The version is 3.4.6

This is part of your problem. 3.4.6 is by now a very ancient version of the GNU compiler, and I believe it can't be used to build Amber. I'm pretty sure you'll need version 4 (I think 4.1 minimum), and the more recent stable sub-version (4.1, 4.2,...) you can obtain, the better.

> Using Intel MKL libraries in /usr/local/compilers/Intel/mkl-10.2/lib/em64t
> MKL Version 10 or 11 assumed.
> Testing the gcc compiler:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> OK
> Validating the C++ compiler version:
> g++ -v
> The version is 3.4.6
> OK
> Testing the gfortran compiler:
> gfortran -O0 -o testp testp.f
> ./configure: line 1019: gfortran: command not found
> ./configure: line 1020: ./testp: No such file or directory
> Unable to compile a Fortran program using gfortran -O0
> We will be unable to compile sqm

You will also need an installation of gfortran. When you upgrade your GNU compiler, be sure to install the same version of gfortran at the same time.

> Testing mixed C/Fortran compilation:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
> gfortran -O0 -c -o testp.f.o testp.f
> ./configure: line 1054: gfortran: command not found
> gcc -o testp testp.c.o testp.f.o -lgfortran
> gcc: testp.f.o: No such file or directory
> ./configure: line 1057: ./testp: No such file or directory
> WARNING: Unable to compile mixed C/Fortran code.

Again, this is likely because gfortran is missing.

> Testing pointer size:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size
> test_pointer_size.c
> Detected 64 bit operating system.
> Testing flex:
> OK
> Configuring NetCDF; (may be time-consuming)
> Error: NetCDF configure returned 1
> NetCDF configure failed! Check the netcdf_config.log file.
> Continuing but NetCDF will be skipped.
> Configuring fftw-2.1.5; (may be time-consuming)
> Error: fftw configure returned 1
> fftw configure failed! Check the fftw2_config.log file.
> This is the error i am getting

These errors may well be resolved when you upgrade your GNU compilers.

Hope that helps,


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Received on Mon Jan 31 2011 - 11:30:05 PST
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