From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Sep 23 2020 - 09:40:04 CDT
Axel has explained well already the rationale behind not doing continuous
upgrades for shared systems that serve a multitude of purposes, each of
which has complex dependencies.
I would only add that for many institutions security of these systems is
also a major concern, and it is better for them to use an "old" but tested
environment than one that changes too quickly. CentOS 6 is not just old
but almost dead at this point: whoever administers Boyan's server must
upgrade soon.
Back to the original question, this NAMD build will not run natively on
CentOS 7 either for the same reason (Glibc version). But it runs fine
through e.g. a Singularity container with the --nv flag to allow direct
access from the container to the GPUs.
A reasonable arrangement would be for the admins to upgrade the server to
the most recent OS that they are able to manage, but also install Docker or
Singularity to allow people to use a more recent software stack if they
need to.
Giacomo
On Wed, Sep 23, 2020 at 3:50 AM Pratik Narain Srivastava <
pratik.narain_at_gmail.com> wrote:
> Sanjay ji I have been using linux since 2009 on my home as well as work
> systems. I usually stick to ubuntu LTS releases while occasionally delving
> into arch. And I have not had a single major breakage on my work systems
> since atleast 2016. I have never understood the appeal for centos or even
> RHEL apart from its commercial support. And one cannot expect moving
> technologies to keep supporting old environments indefinitely.
>
> On Tue, Sep 22, 2020 at 3:18 AM 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.
>>
>>
>>
>> *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 I personally have never understood the appeal for outdated software in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]
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_biomembranenmr&d=DwMF-g&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=f2k7pupr5fmenaKc0glXLF049j1Pb8ZdGSK5XvDdGsg&s=BFflxFSN772EpbEAZECF09cV169T3Fa3YAaV9SJFxCI&e=>
>>
>>
>>
>>
>>
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>>
>>
>
> --
> Pratik Narain Srivastava,
> c/o Dr. Satish Mishra
> SRF, LSN-204
> MPI division,
> CSIR-CDRI, Lucknow
> Ph. 9454285924
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Research collaborator, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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