Hi Pankaj,
Your MPI installation is not successfully installed. Note the fact that
mpif90 can't find the shared libraries. This is likely because your
LD_LIBRARY_PATH was not set correctly. Check the openmpi documentation for
anything you should add to bashrc / cshrc. If it doesn't suggest sourcing
any specific environment setup files then try adding:
export LD_LIBRARY_PATH=/path/to/openmpi/lib/:$LD_LIBRARY_PATH
then resource your .bashrc file.
Then try running mpif90 -show and see if it complains.
You also need to make sure that openmpi was compiled with the same compiler
as you are using for AMBER.
All the best
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Pankaj R. Daga
Sent: Wednesday, June 04, 2008 10:28 AM
To: amber.scripps.edu
Subject: AMBER: amber installation on cluster
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
well.
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: libintlc.so.5:
cannot open shared object file: No such file or directory
MKL_HOME is set to /opt/intel/mkl/10.0.1.014
Using MKL libraries from /opt/intel/mkl/10.0.1.014/lib/em64t
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'
./checkparconf
cpp -traditional -I/usr/local/include -P -DMPI -DMKL evb_vars.f >
_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
Pankaj
===============================================================
If your ship doesn't come in, swim out to it...Jonathan Winters
===============================================================
Pankaj R. Daga |
Dept. of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
417 Faser Hall, | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
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Received on Sun Jun 08 2008 - 06:07:15 PDT
