Re: AMBER: configure question

From: David A. Case <>
Date: Thu, 28 Jun 2007 09:26:34 -0700

On Thu, Jun 28, 2007, Steve Young wrote:

> I have only recently been on the mailing list since I had some issues
> with getting amber9 to compile correctly. The whole time working through
> my issues I couldn't help but ask myself why isn't there a ./configure
> script for this just like most of all the other open source applications
> out there. It seems like having a normal ./configure script that can
> help to sort out compile issues and to set up the environment properly
> could go a long ways in helping many people to compile this software
> properly. Especially when it can inform the person of potential problems
> instead of having to post compile errors to the amber listserv to get
> help from. I haven't been on this list very long but I'd think you would
> get a lot of questions on this list related to compile issues which you
> consistently need to answer over and over again. Things that a
> good ./configure script could remedy for you. Just curious,

Specific suggestions or patches are welcome. I'm not sure exactly what you
mean by a "normal ./configuration script". Amber heavily depens on fortran
compilers and math and MPI libraries, which are not standard for Autotools.
And there are often several fortran compilers on a given machine, so that
choices still have to be made. The standard autotools configure invocation
would end up looking something like this:

./configure FC=/opt/intel/9.0/bin/ifort CC=..... MKL=......,MPI=....., etc.

That is, it might end up being as complex as our home-built scripts. Note
that lots of things need attendtion, like the fact that the compiler options
are different for various compilers, and PGI fortran needs special extra
flags, that the MPI libraries can be from mpich, openmpi, vendor-supplied,

We could do more to make sure at configure time that the chosen compiler is
actually in the user's path and is functional. Right now, the configure step
works, but the first step often yields "ifort: command not found". It would
be better to have that fail at the configure step. But other problems would
persist: if the user doesn't have write permission in the build directory,
lots of things are going to fail.

I don't want to start a flame war here. Various people have proposed to
create the macros we would need for autotools. The advantage of a home-built
./configure script is that it is easy to see what it is doing, and all of the
current developers can help in maintaining it. The disadvantage is that we
ask users to parse error messages (from the build) themselves; many Amber
users are not experienced in this aspect of things and find this difficult.
My current vote is to keep incrementally improving the ./configure script we
have, but I am open to serious and detailed suggestions for other options.

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Received on Sun Jul 01 2007 - 06:07:22 PDT
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