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

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Mon Mar 02 2015 - 10:45:28 CST

Hi,

Linux-x86_64-multicore will definitely work, but if you want to take
advantage of your graphics card, you'll want Linux-x86_64-multicore-CUDA. I
use it on computers with very similar profiles. To use CUDA on your Ubuntu
14.04 installation, you will probably need to install the NVIDIA graphics
drivers (you can find instructions for how to do this for Ubuntu online)
and the CUDA libraries. Here's what I have in my notes for installing CUDA,
which may or may not be the best way to do it:

## Get the deb from https://developer.nvidia.com/cuda-downloads
## $ sudo dpkg -i cuda-repo-ubuntu1404_6.5-14_amd64.deb
## $ sudo apt-get update
## $ sudo apt-get install -y cuda
## Add to .bashrc:
## export CUDA_HOME=/usr/local/cuda-6.5
## export LD_LIBRARY_PATH="$CUDA_HOME/lib64:$LD_LIBRARY_PATH"
## export PATH="$CUDA_HOME/bin:$PATH"

Jeff

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Sun, Mar 1, 2015 at 2:58 PM, Amin Dehkharghani <
amin.dehkharghani_at_gmail.com> 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
>

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:20:56 CST