[Beowulf] Docker in HPC

Bogdan Costescu bcostescu at gmail.com
Thu Nov 28 04:13:44 PST 2013


On Wed, Nov 27, 2013 at 1:18 PM, John Hearns <hearnsj at googlemail.com> wrote:
> Regarding ISV codes, today you frequently see a vendor supplying an entire
> tree of software,
> complete with an MPI  plus a version of Python with libraries, plus X, Y,Z.
> They do this because they have to ship software which works to users, and
> don't want the inevitable
> 'Oh - my sysadmin installed Python 2.7 and your software does not work with
> that' type of query.
> I don't see that it is that far a step to packaging up Docker containers.

I actually don't see the novelty here at all. I use since 10+ years
versioned and dependency-expressing directories (e.g.
openmpi/1.6.4/gcc/4.7.2 instead of simply openmpi/gcc to mean that
openmpi-1.6.4 was compiled with gcc-4.7.2) to install HPC related
software. I also try as much as possible to use -rpath with these
versioned directories, so that dynamic libs dependencies never change.
When I started using modules/dotkits/etc. I have taken the same
convention there. This way the repeatability is guaranteed both for
the user (for reproduction of scientific data) and the admin (for
reliable bug reports). For convenience, I can set softlinks like
"current" or "latest" to make it easier for developers to stay in sync
with updates; modules can even automate this.

As possibly many on this list, I have also wondered about the
explosion of different versions to maintain that such a scheme would
imply. But, as Peter Clapham mentioned, there is a certain life-time
for all software (including libraries and compilers), so in more than
95% of cases only few combinations are needed; f.e. a single version
of GROMACS is compiled against a single version of FFTW, one version
of OpenMPI and one version of MVAPICH2, which are all compiled with a
single version of gcc. OpenMPI is particularly nice in this context as
it can discover and use at runtime the best interconnect - there is no
need to keep several parallel versions which only differ in the
supported hardware and then have to compile user apps against each of
them.

A thorny problem for HPC is the rather strong dependency of certain
libraries on drivers/kernel. F.e. certain versions of MPI libraries
require certain versions of the OFED stack which come with certain
versions of IB/OF drivers which require certain kernel versions. So,
in the end, the much touted independence from the underlying system is
voided. Containers cannot solve this problem by design; virtualization
can (with some hardware support), as the VM carries a complete
computing environment including drivers/kernel.

Packing only the required libraries (which AFAIU is what the Docker
containers are doing to keep the size low) is something the HPC scene
has known for ~10 years... Anyone remembers bproc/Scyld ? It was
transferring on demand the required libs; sure, one had to keep the
versioned libs on the master to have them available to the app...

Cheers,
Bogdan


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