From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Tue Oct 31 2017 - 13:34:12 CDT
Hi NAMD Users,
I am working with the HPC manager at my university to get a multi-node
build of NAMD installed on it. We are a bit at a cross-roads trying to
determine the best build, and whether or not compiling it is necessary with
the given binaries.
Coeus HPC Specs <https://www.pdx.edu/oit/linux-parallel-computing-clusters>:
- 128 compute nodes each with 20 cores and 128 GB RAM
- Dual Intel Xeon E2630 v4
<https://ark.intel.com/products/92981/Intel-Xeon-Processor-E5-2630-v4-25M-Cache-2_20-GHz>,
10 cores @ 2.2 GHz
- 128 GB 2133 MHz RAM
- 200 GB SSD drive
- 12 Intel Phi processor nodes each with 64 cores and 96 GB RAM
- Intel Xeon Phi 7210
<https://ark.intel.com/products/94033/Intel-Xeon-Phi-Processor-7210-16GB-1_30-GHz-64-core>,
64 cores @ 2.2 GHz
- 96 GB 2133 MHz RAM
- 200 GB SSD drive
- 2 large-memory compute nodes each with 20 cores and 128 GB RAM
- Dual Intel Xeon E2650 v4
<https://ark.intel.com/products/92981/Intel-Xeon-Processor-E5-2630-v4-25M-Cache-2_20-GHz>,
12 cores @ 2.2 GHz
- 768 GB 1866 MHz RAM
- 6 TB local storage
- Data Transfer Node to support high-bandwidth data transfers
- Dual Intel Xeon E2650 v4, 12 cores @ 2.2 GHz
- 256 GB 2133 MHz RAM
- ~40 TB local disk storage in a RAID 6 array
- *Intel Omni-Path* high-performance (100 Gbps) network fabric
- 1 Gb ethernet cluster management and IPMI networks
To the best of my knowledge, the correct build to use would be
Linux-x86_64-ibverbs-smp
<http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD>,
however the more I read about multi-node NAMD builds, the more confused I
get. Also, could I just download the binaries to my cluster-home directory
then run the multi-node version?
I am currently doing all of my research from a few GPU desktops, and need
the HPC.
Thank you for hearing me out!
~ Bassam
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