Re: Binary packages for scientific research on RHEL/CentOS

[Jason Bacon <bacon4000%gmail.com@localhost>]

On 05/16/17 18:44, Kamil Rytarowski wrote:
> On 17.05.2017 01:09, Jason Bacon wrote:
> > Binary packages aimed at research computing and HPC are now available
> > for RHEL/CentOS 6 and 7:
> >
> >      http://uwm.edu/hpc/software-management/
> >
> > These are more or less static package sets with a different prefix for
> > each quarterly build, e.g. /sharedapps/pkg-2017Q1. This layout allows
> > researchers to use the same package versions for the duration of
> > long-term studies (this is critical in many research projects) while
> > newer packages can be deployed alongside them on the same system.
> >
> > I also posted instructions for our pbulk setup, which uses a pristine OS
> > installation image in a chroot env.  Many thanks to everyone who offered
> > advice as I was experimenting with pbulk.
> Thank you for your involvement, this looks great!
>
> > I'm hoping the availability of these packages will spur a new level of
> > interest in pkgsrc within the research computing community.  I know for
> > a fact that pkgsrc has enormous potential here, as I've watched many
> > researchers struggle with software installations for the past 17 years,
> > especially on enterprise Linux, which has a virtual monopoly in HPC.
> As far as I researched my local city HPC top500 cluster uses mainline
> Linux kernel and the userland distribution... is built from scratch with
> tuned configure options. This sounds like massive waste of manpower,
> better to add options in pkgsrc packages, tune mk.conf and just generate
> binary prebuilt packages quarterly.
>
> A blog post - with successful stories - would help to convince them and
> others to research the pkgsrc option.
>
> Another market for similar setups is a corporate market with long-term
> application support, people keep deploying setups on CentOS|RHEL servers
> that are 2-3 major versions behind.. developing and installing software
> on decade old Linux distributions is usually done manually.
>
> > With this infrastructure in place, the work of creating many new
> > scientific packages will now become our primary focus.
> >
> > Comments and contributions are always welcome!
> It is worth preparing a post on TNF blog, about pkgsrc on HPC computers
> / CentOS|RHEL setups. There are already few users out there, I'm aware
> about NASA and Joyent.
>
> > Regards,
> >
> >      Jason
To put the waste of manpower in perspective: There are cases where 
literally thousands of people in research around the world are spending 
10 or 20 hours each trying to install the same software.  These are 
brilliant people who should be spending that time doing research in 
their field.  Most of them would rather not be struggling with IT tasks 
anyway, but they're just not aware of a better way.

In other cases, people are using a mishmash of different automated 
installation methods, like yum, pip, virtualenv, or using containers for 
the sole purpose of isolating software with esoteric build systems or 
bundled dependencies.  It's a real mess.  Some of us are concerned about 
the containerization trend leading to the de-evolution of scientific 
software.  If software is always isolated and doesn't have to play nice 
with others, the developers have no motivation to clean it up or make it 
more portable.

If we can get scientists on board with the idea of using pkgsrc to 
install most of their software, that trend can be reversed. So, I'm 
hoping to make pkgsrc the fastest and easiest method of deployment on 
the mainstream platforms in HPC.  We're already there for many things, 
most importantly for the tools that are often hurdles on EL such as 
newer compilers and interpreters. Thankfully the pkgsrc gcc and clang 
packages are working well on CentOS now.

The main task from here on is populating pkgsrc with as many scientific 
packages as possible.  If people can install most of what they need with 
a simple "pkg_add" or "pkgin install", then we can stop flushing 
man-years of extremely valuable time down the toilet and scientific 
discovery will be accelerated.

Cheers,

    Jason

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