AMBER Archive (2006)

Subject: RE: AMBER: Issue with installation of Amber v9.0 parallel compilation

From: Ross Walker (
Date: Thu Oct 19 2006 - 23:55:00 CDT

Dear Pavin,

When you see errors like this:

evb_init.o(.text+0x790): In function `evb_init_':
: undefined reference to `mpi_bcast_'

It almost certainly means that the compiler you used to compile the mpi
library was a different one to the one used to compile amber. You need to go
back to your openmpi installation and run the configure, make and
installation again ensuring that you specify the correct compilers.

Typically you do this with arguments to configure along the lines of

./configure --prefix=/foo/bar CC=icc CXX=icc FC=ifort F77=ifort

but don't take my word for it here, I have not tried openmpi so you will
need to read the openmpi installation instructions.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

> -----Original Message-----
> From:
> [] On Behalf Of
> Sent: Thursday, October 19, 2006 21:18
> To:
> Subject: AMBER: Issue with installation of Amber v9.0
> parallel compilation
> Dear Sir,
> This is with reference to above subject. We are trying to install the
> parallel version of Amber v9.0, We have installed the openmpi-1.0
> compiled with intel compiler (intel_fc_80,intel_cc_80). When I try
> to compile the amber parallel version I get error as mentioned in
> file 'amber_error.txt' the intial few modules are compiled without any
> errors, I get the errors in the module 'sander.MPI'.
> We even tried to compile the sander.MPI individually but received the
> same error as mentioned in 'amber_error.txt'. For your reference I am
> attaching the text files of error messages :
> 1.amber_error.txt
> 2.config.h
> Kindly suggest.
> with best regards
> Pravinkumar
> (See attached file: amber_error.txt)
> (See attached file: config.h)
> --------------------------------------------------------------
> --------------------------------------------------
> This Message and any attachment (the "message") is intended
> solely for the addressees and is confidential.
> If you receive this message in error, please delete it and
> immediately notify the sender.
> Any use not in accord with its purpose, any dissemination or
> disclosure, either whole or partial,
> is prohibited except formal approval. The internet can not
> guarantee the integrity of this message.
> Jubilant Organosys Ltd. (and its subsidiaries) shall (will)
> not therefore be liable for the message if modified.

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