RE: namd3 on centos 6

From: Sanjay Hari (
Date: Mon Sep 21 2020 - 16:46:36 CDT

In Dr. Bonev’s defense, the old adage of “if it ain’t broke don’t fix it” applies in spades to linux distros. I cannot tell you how many times I have broken dependencies after a seemingly innocuous update to something completely unrelated. The worst is when X stops and you’re left with a just shell and a blinking cursor staring at you.

From: <> On Behalf Of Pratik Narain Srivastava
Sent: Saturday, September 19, 2020 10:04 AM
To:; Boyan Bonev <>
Subject: Re: namd-l: namd3 on centos 6

Just my two cents
I personally have never understood the appeal for outdated software in the name of stability. If course you should update to the latest available version of centos. Or better, run an Ubuntu LTS version. You are after all trying to test an alpha level software written to take advantage of latest hardware and software technologies on an ancient os.

On Sat, Sep 19, 2020, 6:21 PM Boyan Bonev <<>> wrote:
Just downloaded NAMD3 alpha CUDA to test on a multi-GPGPU system and discovered that NAMD3 requires a higher version of the libraries:

/lib64/ version `GLIBC_2.14' not found (required by namd3)

/usr/lib64/ version `GLIBCXX_3.4.14' not found (required by namd3)

/usr/lib64/ version `GLIBCXX_3.4.19' not found (required by namd3)

/usr/lib64/ version `GLIBCXX_3.4.18' not found (required by namd3)

/usr/lib64/ version `GLIBCXX_3.4.15' not found (required by namd3)

Can NAMD3 run on centos 6 or does it require lentos 7? The general view seems to be that the libraries cannot be upgraded but the OS should be upgraded, instead.

Best wishes,

Dr Boyan Bonev, Senior Tutor in Biochemistry
Biomembrane NMR & DNP spectroscopy
School of Life Sciences
University of Nottingham
Queen’s Medical Centre
Nottingham NG7 2UH, UK

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