AMBER Archive (2000)

Subject: Re: Issues with compiling AMBER6 (MPI) on Linux

From: Guanglei Cui (gcui_at_ic.sunysb.edu)
Date: Wed Mar 01 2000 - 21:03:51 CST

Hi, Dave,
   This time I try the same thing on my home pc. It has kernel
2.2.12-20, egcs-2.91.66 and mpich1.2.0. Now the error is different. It's
something like:
...
Expression at (^) has incorrect data type or rank for its context
_sander_.f:563:
         PARAMETER (MPI_REAL16=)
                               ^
Expression at (^) has incorrect data type or rank for its context
_sander_.f:564:
         PARAMETER (MPI_COMPLEX8=)
                                 ^
Expression at (^) has incorrect data type or rank for its context
_sander_.f:565:
         PARAMETER (MPI_COMPLEX16=)
                                  ^
Expression at (^) has incorrect data type or rank for its context
_sander_.f:566:
         PARAMETER (MPI_COMPLEX32=)
...

Have you ever met this before? It didn't happen when I compiled it on
Redhat 5.1 clusters. 

-- 
Guanglei Cui
Department of Chemistry
State University of New York
Stony Brook, NY 11794-3369

dek_at_nano.nmr.ucsf.edu wrote:
> 
> 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
> AMBER: AMBER6
> 
> 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)
> 
> Dave