AMBER Archive (2008)

Subject: RE: AMBER: amber installation on cluster

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jun 04 2008 - 12:54:36 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Pankaj R. Daga
Sent: Wednesday, June 04, 2008 10:28 AM
To: amber_at_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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