RE: Can't compile Sander with parallel on Linux cluster

From: Thomas A. Spraggins <>
Date: Fri 16 Mar 2001 12:37:24 -0500

I used the pgf compilers for Amber6 without any real problems. You'll want
to use "mpif90" for your FC definition, so the mpich scripts can take of
including the proper includes and libraries; otherwise, no sweat.
PGF-compiled code generally runs quite a bit faster than g77; I don't have
the benchmarks handy, but my recollection was that the difference, while
significant, wasn't as big as I've seen for other applications.

You need to make sure not to mix-and-match with the compilers used for the
mpich install and the subsequent Amber build. That definitely causes major

Tom Spraggins

-----Original Message-----
From: Ross Walker []
Sent: Friday, March 16, 2001 10:06 AM
Subject: RE: Can't compile Sander with parallel on Linux cluster

Hi Chomsri,

What has happened is that when you have installed and configured mpich it
has looked for fortran compilers on your system and picked up the absoft
compiles and is using these. The Absoft compilers do not work properly with

Try the following:

1) Resinstall MPICH manually specifing the compilers

        e.g ./configure -prefix=/usr/local/mpich-1.2.1 -fc=g77 -cc=gcc

Then do make / make install etc.

Then try recompiling amber. Make sure you do a make clean in ./amber6/src

if this doesn't work try replacing all occurances of mpif77 and mpicc in the
machine file with g77 and gcc respectively.

Also, I would ensure that /usr/local/mpich-1.2.1/bin is in your path.

I also trust you uninstalled v1.2.0 of mpi? If not then you need to check
which one is favoured as far as libraries etc go.

e.g which mpirun

Hope this helps

All the best

> -----Original Message-----
> From: chomsri upkaew []
> Sent: 16 March 2001 14:02
> To:
> Subject: Can't compile Sander with parallel on Linux cluster
> Dear Ross,
> Many thanks for your suggestion. I did as your suggestion, however, I
> obtained message;
> cd sander; make install
> make[1]: Entering directory `/users/siriwong/Program/amber6/src/sander'
> .../Compile L2 -P -DDPREC sander.f
> cat sander.f | /lib/cpp -traditional
> -I/users/siriwong/Program/mpich-1.2.1/include -P -DDPREC -DLinux
> -DISTAR4 -DREGNML -DMPI > _sander_.f
> mpif77 -c -O3 -m486 -malign-double -ffast-math -fomit-frame-pointer
> -fno-globals -ff90 -funix-intrinsics-hide _sander_.f
> /usr/absoft/bin/f77: illegal option -- 3
> usage: f77 [options] file [file] ... (man f77 for further details)
> make[1]: *** [sander.o] Error 1
> make[1]: Leaving directory `/users/siriwong/Program/amber6/src/sander'
> make: *** [install] Error 2
> Please let me know how to solve this.
> Sincerely Yours,
> Uchom
> -------------------------------------
> I have it working no problem. You need to have mpich-1.2.1 as there are
> known issues with 1.2.0 (e.g parallel IO is broken) under linux. Go to
> to download a copy
> of the 1.2.1
> source.
> I would avoid using the portland group compilers for compiling Amber with
> mpi support as I have encountered numerous problems such as Unit
> 5 Error on
> open. Something is very strange and hard to sort out. Stick to just the
> gnu compilers which work fine (egcs 2.95).
> I have included a copy of my machine.g77_mpich configuration file that you
> may want to compare against yours.
> All the best
> Ross
> /\
> \/
> |\oss Walker
> _________________________________________________________________________
> Get Your Private, Free E-mail from MSN Hotmail at
Received on Fri Mar 16 2001 - 09:37:24 PST
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