Issues with compiling AMBER6 (MPI) on Linux

From: <>
Date: Wed 01 Mar 2000 13:50:10 -0800

Hi, this issue has come up a few times before with people
trying to compile AMBER on Linux.

I have been using AMBER on Linux for some time now, and have
"historical" experience with various distributions, compilers,
and implementations of MPI.

Based on that experience, I would suggest the following minimum
software configuration if you want to use AMBER with Linux
(especially with MPI).

Linux kernel: 2.2.14
Compiler: gcc-2.95.2
MPI: MPICH 1.2.0

Kernel versions previous to 2.2.14 have TCP and SMP issues which
adversely affect performance.

Compiler versions older than gcc-2.95.2 had bugs and problems. Not all
the bugs are gone, but sander runs reliably with gcc-2.95.2. note,
the features in PGCC (pentium pgcc) and EGCS (experimental gcc) have
been merged back into gcc, as of 2.95.

MPICH 1.1.2 had a number of bugs which prevented it from working correctly on Linux. MPICH 1.2.0 fixes all these bugs and increases performance.

AMBER5 and older had some issues with Linux and MPI. AMBER6 is much
more reliable than AMBER5 with Linux/MPI, and fixes a number of
bugs as well as supplying some useful new features.

If you are banging your head trying to compile AMBER, check your versions!
% uname -a
(for kernel version)

% gcc -v
(for compiler version)

Received on Wed Mar 01 2000 - 13:50:10 PST
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