Re: WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM?

From: Richard Overstreet (roverst_at_g.clemson.edu)
Date: Sun Mar 01 2015 - 16:56:39 CST

1) *Which version of NAMD should I install from the following list?
*Linux-x86_64-multicore
<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1316>
may work but Ideally you would want to download the sources and
dependencies then compile/install for your specific system.
2) *Do I need to install any additional drivers and softwares in
addition to ubunto itself (nvidia drivers, cuda, ...)?
*
You won't use CUDA since you don't have a CUDA enabled card. I would
suggest downloading the namd 2.10 source and checking the readme file.
By the way you usually don't want nightly builds unless you are a developer.

-Richard
On 03/01/2015 03:58 PM, Amin Dehkharghani wrote:
> 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,
> ---------------------------------------------------------------------------
> Amin Dehkharghani
> School of Mechanical Engineering
> Sharif University of Technology

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