AMBER Archive (2008)

Subject: AMBER: amber installation on cluster

From: Pankaj R. Daga (
Date: Wed Jun 04 2008 - 12:27:57 CDT

Hi amber community


I am trying to install Amber9 on our opteron cluster. I have installed
openmpi with Intel compilers icc, icpc and ifort. The installation went


After setting the environment, I want to install parallel version of amber.
When I start configuration, config.h file is created with an error as shown
in below.


shell % ./configure -openmpi -opteron ifort_x86_64

AMBERHOME is set to /u2/daga/amber9

Setting up Amber configuration file for architecture: ifort_x86_64

Using parallel communications library: openmpi

MPI_HOME is set to /usr/local

/usr/local/bin/mpif90: error while loading shared libraries:
cannot open shared object file: No such file or directory

MKL_HOME is set to /opt/intel/mkl/

Using MKL libraries from /opt/intel/mkl/


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



When I use this config.h file for next step,


shell % make parallel

Starting installation of Amber9 (parallel) at Wed Jun 4 10:53:46 CDT 2008.

cd sander; make parallel

make[1]: Entering directory `/u2/daga/amber9/src/sander'


cpp -traditional -I/usr/local/include -P -DMPI -DMKL evb_vars.f >

cpp: invalid option -traditional

make[1]: *** [evb_vars.o] Error 1

make[1]: Leaving directory `/u2/daga/amber9/src/sander'

make: *** [parallel] Error 2



Could you please explain me where am I wrong? Do I need to change the
config.h file when I use Intel compilers?


Thanks and regards




If your ship doesn't come in, swim out to it...Jonathan Winters
Pankaj R. Daga |
Dept. of Medicinal Chemistry | e-mail:
417 Faser Hall, | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |


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