Recently I posted questions regarding my attempts to compile and execute Amber 8 on a dual Xeon EM64T running RHEL 3.0 update 4 x86_64 with the most recent version of Intel's Fortran Compiler, 8.1.024. While I was able to compile all of the code, testing failed repeatedly with sander, among other modules, with SIGSEV errors. MPICH2 also failed to run properly. It seems like other users are having the same problems and no one seems to know what to do about it, at least that's what I'm gathering from the lack of response to the questions. Ross Walker was very helpful as he is running the same hardware, albeit with SUSE. I had my sysadmin scrub the computer clean of the 64 bit OS and install the 32 bit version, to his dismay ("why run a 32 bit OS on a 64 bit machine?", he asked me. The are lots of answers to that question! ) Amber 8 compiled with nary a complaint the first time, with the Intel MKL v7.2, as did MPICH version 2 Release 1.0.1. I am now happily running both sander !
an!
d pmemd and pmemd runs quite happily in parallel (thanks, Dr. Duke, for the config.h's you posted). So, my advice to all those struggling to get Amber 8 to run on the EM64T is to use a 32 bit OS first and see if you can get it runnning on that and only if you have the time and patience would I recommend trying it on a 64 bit OS.
Lee Shekter
Assistant Professor (Adjunct) Medical Science
Brown University
Divison of Biology and Medicine
Box G
Providence, RI 02912-9107
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Received on Mon Apr 18 2005 - 19:53:00 PDT
