AMBER Archive (2008)

Subject: Re: AMBER: Installation problem of AMBER on cluster

From: David A. Case (
Date: Sat May 03 2008 - 18:56:32 CDT

On Sat, May 03, 2008, sudipta sinha wrote:
> * $./configure -static -mpich2 g95*

As a wild guess, leave out the -static flag. Lots of mpi implementations
won't support that.

Second, make sure that you can compile and run simple (test) MPI programs,
such as those that come with mpich2.

> I have not set the MKL_HOME environment variable. How to set this
> environment variable? We couldn't find /opt/intel/mkl/8.0 in our machine.

If you don't have MKL, you don't need to set that variable.

> Is this environment variable setting mandatory.


> evb_init.o(.data+0x460): undefined reference to `mpi_conversion_fn_null_'

Another wild guess here: you may have compiled mpich2 with g95, but left
out the -fno-second-underscore flag (which is used by sander). Both the
mpi implementation and sander have to be compiled with the same compiler and
the same flag.

...hope this helps...dac

[Just an advertisement: Amber10 ships with the code for LAM, and the Makefile
compiles everything the same way, with all the right environment variables,
and so on. So we are working to make things more straightforward for parallel

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