AMBER Archive (2006)

Subject: AMBER: Advice on linux cluster sought

From: Feng X Zhou (feng.zhou_at_abbott.com)
Date: Mon Aug 14 2006 - 13:34:16 CDT

Dear Amber users,

   Looking at some advice/experience on building a linux cluster that runs Amber and other related programs:

   1. clustering software - has anyone compared performance/features of sclyd, scali or other clustering software? How about MPI? Does amber supports scali MPI or HP MPI? Any customization needed?

   2. AMD vs. Xeon - don't care if it is 64 bit or 32 bit - just care about performance and price....

   3. Memory use - does Amber uses a lot of memory? What it is the recommended RAM per CPU (say 3 GHz Xeon) ...

   4. I/O - how important is I/O and which parallel file system has been used - does compute nodes need I/O at all?

   5. Interconnect - with inifiniband, what MPI is suitable? What is the expected # of CPUs that scalability is expected to fall off? Are clusters of SMP machines (4 dual core CPU) OK? How does it compare with clusters of single CPU nodes?

   6. OS - RHEL 4 vs RHEL 3 - is there any performance difference?

Would appreciate any past experience/lessons learned - and maybe some performance benchmark.... thanks!

- Feng Zhou
Worldwide Infrastructure & Networks
Unix/VMS Computer Services
Phone: (847)937-8376
feng.zhou_at_abbott.com
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