AMBER Archive (2008)

Subject: Re: AMBER: Amber9 Installation Problem

From: Cenk Andac (
Date: Wed Mar 19 2008 - 15:55:23 CDT

One more though,
  please make sure that your gcc is x86_64 but not x86.
  gcc -v should tell you about the version.

Cenk Andac <> wrote:
    well, I have just noticed that the version of gcc you use is not compatible with the ifort version you are using.
  Sometimes ifort v9.x.x seems to be more compatible with older versions of gcc.
  and i am not so sure if you can still download ifort v9 from intel's website.

Cenk Andac <> wrote:
  I usually patch bugfixes before installing AMBER.
  I have not tried installing AMBER using g95 before. Perhaps someone else may help you out with g95 installation of AMBER.
  As for the installation of AMBER using ifort and mkl :
  1) make sure that LD_LIBRARY_PATH is set-up correctly for MKL and IFORT libraries.
  2) MKL_HOME is set correctly
  3) A path is set to ifort's binary directory and also make sure that ifort is sourced
  4) if your cpu's are intel- or AMD64-based try the following configuration
     ./configure -bintraj -p4 ifort_x86_64
     you may also try a static configuration as you have tried before.
  good luck
  jenk wrote:
  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!


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        Cenk Andac, M.S., Ph.D. Student
School of Pharmacy at
Gazi University-Ankara Turkiye

  Address: Bandirma Sok. No:6

  Etiler, Ankara, 06330 Turkey

  Cell: +90-(536)-4813012

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