[Beowulf] Oh.. IBM eats Red Hat

Ryan Novosielski novosirj at rutgers.edu
Mon Oct 29 10:03:28 PDT 2018

Hash: SHA1

On 10/29/2018 12:44 PM, David Mathog wrote:

> Libraries are harder.  Try to build a newer one than ships with
> CentOS and it is not uncommon to end up having to build many other
> libraries (recursive dependencies) or to hit a brick wall when a
> kernel dependency surfaces.

We have run into stuff like this in some exceptionally dopey places,
for example the NCI GDC client. There is no reason for that to need a
version newer than is supplied with CentOS 6: it's a data downloader.
On our system, we just containerize that utility with Singularity. We
strictly-speaking shouldn't need to, since we run mostly CentOS 7.x
and theoretically that's new enough, but people have reported some
problems and my recollection is that the NCI responded with "try Ubuntu.

> In biology apps of late there is a distressing tendency for
> software to only be supported in a distribution form which is
> essentially an entire OS worth of libraries packaged with the one
> (often very small) program I actually want to run.  (See
> "bioconda".)  Most of these programs will build just fine from
> source even on CentOS 6, but often the only way to download a
> binary for them is to accept an additional 1Gb (or more) of other
> stuff.

You could do the same here, depending, but that will often have the
same problem (lots of wasted space).

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