AMBER Archive (2008)

Subject: AMBER: Amber9 Installation Problem

Date: Wed Mar 19 2008 - 11:28:35 CDT

Hello all,

I am currently trying to install Amber 9 on a 64 bit Xeon machine with
RHEL 5.1 as the operating system. I used gcc [version: gcc (GCC) 4.1.2
20070626 (Red Hat 4.1.2-14) ] and g95 [version: G95 (GCC 4.0.3 (g95
0.90!) Jul 27 2006)] (./configure g95) and the compilation was
succesful, and I did not notice any errors along the way. But, when I
ran the test suite, several of the tests gave results that were
significantly far from what was expected, and in particular the ptraj
module completely crashed with the following errors:
# make test.ptraj
cd ptraj_matrix; ./Run.matrix

ptraj: analyze fluctuation matrices
Segmentation fault
   ./Run.matrix: Program error

make: *** [test.ptraj] Error 1

Does anyone have any ideas what the problem might be? I am guessing
that something is wrong with the fortran compilation? Does anyone know
if some other version of the compilers would be more useful?

Looking through the archives I noticed that a 32 bit installation is
sometimes recommended. What options should I change in the config.h
file or Makefiles to attempt that?

Also, looking through the archives I noticed that the intel compiler
was highly recommended. I tried installing Amber9 with gcc as the c
compiler and the trial version of the Intel fortran compiler [version
10.1.012] and got the following output:

# export MKL_HOME=/opt/intel/mkl/
# ./configure -static ifort_x86_64
AMBERHOME is set to /usr/local/Amber/amber9
Setting up Amber configuration file for architecture: ifort_x86_64
Using parallel communications library: none
MKL_HOME is set to /opt/intel/mkl/
Using MKL libraries from /opt/intel/mkl/

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

[root_at_auzanneau8 src]# make serial
Starting installation of Amber9 (serial) at Tue Mar 18 11:34:50 EDT 2008.
cd lib; make install
make[1]: Entering directory `/usr/local/Amber/amber9/src/lib'
cpp -traditional -P -DMKL new2oldparm.f > _new2oldparm.f
ifort -c -w95 -mp1 -O0 -o new2oldparm.o _new2oldparm.f
ifort: error #10149: option '-cxxlib-gcc' not supported with the
current installed GCC
make[1]: *** [new2oldparm.o] Error 1
make[1]: Leaving directory `/usr/local/Amber/amber9/src/lib'
make: *** [serial] Error 2
[root_at_auzanneau8 src]#

I also tried using both Intel c and fortran compilers version 10.1.012
and got the same error.

Does anyone know what version of Intel compilers might be compatible
with gcc or what version of gcc is likely to work with the Intel 10

Or am I missing something else?

Thanks alot!


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to