From: Amin Dehkharghani (amin.dehkharghani_at_gmail.com)
Date: Sun Mar 01 2015 - 14:58:08 CST
I have a system with these specifications:
Motherboard: Microsystems X9DA7-E
CPU: 2 X Intel® Xeon(R) CPU E5-2670
Graphics Card: Quadro K2000
OS: Ubunto 14.04 64bit
I want to run molecular dynamics simulations in this system as fast and
optimized as possible, and I have the following questions:
*1) Which version of NAMD should I install from the following list? *
Version Nightly Build (2015-03-01) Platforms:
- Linux-x86_64-multicore
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1258>
(64-bit
Intel/AMD single node)
- Linux-x86_64-multicore-CUDA
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1259>
(NVIDIA
CUDA acceleration)
- Source Code
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1257>
Version 2.10 (2014-12-11) Platforms:
- Linux-x86_64-multicore
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1316>
(64-bit
Intel/AMD single node)
- Linux-x86_64
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1310>
(64-bit
Intel/AMD with ethernet)
- Linux-x86_64-TCP
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1311>
(TCP
may be better on gigabit)
- Linux-x86_64-ibverbs
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1312>
(InfiniBand
via OpenFabrics OFED, no MPI needed)
- Linux-x86_64-ibverbs-smp
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1315>
(InfiniBand
plus shared memory, no MPI needed)
- Linux-x86_64-multicore-CUDA
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1314>
(NVIDIA
CUDA acceleration)
- Linux-x86_64-ibverbs-smp-CUDA
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1313>
(NVIDIA
CUDA with InfiniBand)
- Linux-x86_64-multicore-MIC
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1323>
(Intel
Xeon Phi coprocessor acceleration)
- Linux-x86_64-netlrts
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1320>
(Multi-copy
algorithms)
- MacOSX-x86_64
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1318>
(Mac
OS X for 64-bit Intel processors)
- MacOSX-x86_64-netlrts
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1319>
(Multi-copy
algorithms)
- Win64
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1321>
(Windows
7, 8, etc.)
- Win64-CUDA
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1322>
(NVIDIA
CUDA acceleration)
- Win64-MPI
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1317>
(Windows
HPC Server)
- Source Code
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1309>
*2) Do I need to install any additional drivers and softwares in addition
to ubunto itself (nvidia drivers, cuda, ...)?*
I look forward to your response as soon as possible,
Best Regards,
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Amin Dehkharghani
School of Mechanical Engineering
Sharif University of Technology
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