From: Asmi Mahmood (asmi_mahmood_at_yahoo.com)
Date: Mon Aug 17 2020 - 02:36:33 CDT
Sir i am running namd in linux using commands : namd2 p+20 nvt.namd after normal namd installation on linux.
But during finding solution for this slow speed, i came across with these two links in which charm tcl and fftw compilation is being made. i wonder i am not applying any of these plz guide
https://nishaagrawal.wordpress.com/2013/08/23/namd-v2-9-installation/
my log file for the production run is attached plz give a look on it too.
i invested so much on this and still cant have desired speed. plz guide me
On Monday, 17 August 2020, 12:15:41 pm GMT+5, Raman Preet Singh <ramanpreetsingh_at_hotmail.com> wrote:
________________________________
From: owner-namd-l-digest_at_ks.uiuc.edu <owner-namd-l-digest_at_ks.uiuc.edu> on behalf of namd-l digest <owner-namd-l-digest_at_ks.uiuc.edu>
Sent: Monday, August 17, 2020 11:37:01 AM
To: namd-l-digest_at_ks.uiuc.edu <namd-l-digest_at_ks.uiuc.edu>
Subject: namd-l digest V1 #2923
namd-l digest Monday, August 17 2020 Volume 01 : Number 2923
In this issue:
namd-l: Hi
namd-l: Low simulation speed with 24 processors
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Date: Sun, 16 Aug 2020 17:38:21 +0000 (UTC)
From: Asmi Mahmood <asmi_mahmood_at_yahoo.com>
Subject: namd-l: Hi
I am running MD simulations on Dell precision 5610 with 24 processors and 12 cores with 32 GB RAM. On windows 10, 10 ns simulations were taking 4 days. I learned from different sources from internet that running on Linux gives better speed. So I run 10ns simulation on the same system but on Ubuntu 20.04 with latest versions of NAMD and vmd in VM. The speed is same. That I m not expecting with these numbers of CPU. What could be the possible reason. If any form of input or output files r needed I can attach on asking.
Sent from Yahoo Mail on Android
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Date: Sun, 16 Aug 2020 17:39:26 +0000 (UTC)
From: Asmi Mahmood <asmi_mahmood_at_yahoo.com>
Subject: namd-l: Low simulation speed with 24 processors
I am running MD simulations on Dell precision 5610 with 24 processors and 12 cores with 32 GB RAM. On windows 10, 10 ns simulations were taking 4 days. I learned from different sources from internet that running on Linux gives better speed. So I run 10ns simulation on the same system but on Ubuntu 20.04 with latest versions of NAMD and vmd in VM. The speed is same. That I m not expecting with these numbers of CPU. What could be the possible reason. If any form of input or output files r needed I can attach on asking.
Sent from Yahoo Mail on Android
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End of namd-l digest V1 #2923
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You mentioned VM so I assume you are using something like VMWare or Virtual box on Win 10. VM is usually slower. Instead of VM, try WSL or WSL2 in Win 10 if migration to Linux is not possible (the only pain for a Windows user is there is no GUI in WSL yet). It gives performance almost comparable to native Linux (the performance is only 5-10% lower in WSL under worst cases)
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