Re: [AMBER-Developers] 28 Mar release candidates for Amber11/AmberTools-1.4

From: Jason Swails <>
Date: Mon, 29 Mar 2010 13:44:03 -0400


Quick issue with the configure script: On line 966, changing the "=="
to '-eq' makes the configure script sh-compliant. Without that, I get
this printout on my Ubuntu machine (which uses dash)

swails.Batman:~/newamber/03.29.10/amber11/AmberTools/src$ ./configure gnu
Your AMBERHOME environment variable should be set to

Obtaining the gnu suite version:
      gcc -v
The version is 4.4.1

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

Validating the C++ compiler version:
     g++ -v
The version is 4.4.1

Testing the gfortran compiler:
     gfortran -O0 -o testp testp.f

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
     gcc -o testp testp.c.o testp.f.o -lgfortran

Testing pointer size:
test_pointer_size test_pointer_size.c
[: 972: 1: unexpected operator
Detected 64 bit operating system.

Testing flex:

Configuring NetCDF; (may be time-consuming)

    NetCDF configure succeeded.

Configuring fftw-2.1.5; (may be time-consuming)

    fftw-2.1.5 configure succeeded.

The configuration file, config.h, was successfully created.

The next step is to type 'make install'

ln: creating symbolic link `./sander': File exists

The suggested change gets rid of the [: 972: 1: unexpected operator
line. Also, perhaps we throw something in (like a 2>/dev/null or an
"and it doesn't already exist" to the if statement) to the ln to
suppress the last message if the link already exists? Not a big deal,
merely an aesthetic issue

All the best,
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Mon Mar 29 2010 - 11:00:03 PDT
Custom Search