Re: namd3 on centos 6

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 21 2020 - 17:34:24 CDT

On Mon, Sep 21, 2020 at 5:48 PM Sanjay Hari <shari_at_universalsequencing.com>
wrote:

> 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.
>

sticking with a trusted and familiar OS is ok for as long as you don't
expect to have the latest greatest software technology and tools run on it.
RHEL 6 is an OS using technology that is over 10 years old.
there is a healthy middle ground, but RHEL 6 is very, *VERY* old. already
RHEL 7 is showing its age when you want to use "modern" programming tools.
so trying to expect to have a development version of a software with
support for the latest GPU technology run on such an old software stack is
problematic.

yes, upgrading in place for long-term supported linux versions is not a
good idea. that kind of breakage is to be expected. backward compatibility
can only go so far. it is usually a good approach to use this as an
opportunity to start over and start with a fresh new install on a new
machine with new hardware and thus get rid of all the cruft that
accumulates over the years. when doing this with new hardware (that usually
needs a newer OS anyway to be able to boot and run because of limited
driver support)
you can still have your trusted and familiar legacy system available for
anything that you cannot do with the new machine or have to learn fresh how
to do correctly.

the alternative is to switch to a linux version with continuous "rolling"
updates or that have an upgrade path to a new version every 6 months, so
that you have only a little breakage at a time that is more easily fixable
and not a big and frustrating disaster every 4-5 years (or more).

ciao,
     Axel.

>
>
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> *On Behalf Of
> *Pratik Narain Srivastava
> *Sent:* Saturday, September 19, 2020 10:04 AM
> *To:* namd-l_at_ks.uiuc.edu; Boyan Bonev <boyan.bonev_at_nottingham.ac.uk>
> *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 I personally have never understood the appeal for outdated software in the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 <Boyan.Bonev_at_nottingham.ac.uk>
> 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/libc.so.6: version `GLIBC_2.14' not found (required by namd3)
>
> /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found (required by
> namd3)
>
> /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found (required by
> namd3)
>
> /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by
> namd3)
>
> /usr/lib64/libstdc++.so.6: 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
>
> [image: twitter]
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>
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-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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