AMBER Archive (2008)

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

From: sudipta sinha (
Date: Sun May 04 2008 - 07:31:22 CDT

Dear sir,

            I couldn't understand how I compile MPICH2 with the
-fno-second-underscore flag?. There is no
-fno-second-underscore flag in MPICH2. I have confirmed this by the help

*$./configure -help
It doesn't show the -fno-second-underscore flag. So where I put this flag
i,e what I am telling that "can I put this flag in .bashrc file?". If so,
how shall I put this?

Another issue is coming from selection of MPI. Actually I am facing lot
of troubles with this MPICH2. I have seen from AMBER forum some
people also had faced with this problem. Out of this I am giving one
representative link. Those people were solved their problem by using
OPENMPI. So I would request you, kindly recommend me which MPI is best for
AMBER installation (with package name, version etc. etc.) out of LAM/MPI,
MPICH2, MPICH, OPENMPI etc. I have also checked that all MPI package compile
and run small representative example programs those are coming with those

Thanks and regards

On Sun, May 4, 2008 at 5:26 AM, David A. Case <> wrote:

> 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.
> No.
> > 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
> compiles....]
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