[Beowulf] HPC workflows

John Hearns hearnsj at googlemail.com
Wed Nov 28 04:25:15 PST 2018

Bogdan, Igor. Thankyou very much for your thoughtful answers. I don not
have much time today to do your replies the justice of a proper answer.
Regarding the ssh filesystem, the scenario was that I was working for a
well known company.
We were running CFD simulations on remote academic HPC setups. There was
more than one site!
The corporate firewall allowed us an outgoing ssh connection. I found it a
lot easier to configure an sshfs mount so that engineers could transfer
programs and scripts between their locla system and the remote system,
rather than using a graphical or a command line ssh client.
The actual large data files were transferred by yours truly, via a USB disk

I did not know about gitfs (my bad). That sounds interesting.

On Wed, 28 Nov 2018 at 13:09, INKozin <i.n.kozin at googlemail.com> wrote:

> On Wed, 28 Nov 2018 at 11:33, Bogdan Costescu <bcostescu at gmail.com> wrote:
>> On Mon, Nov 26, 2018 at 4:27 PM John Hearns via Beowulf <
>> beowulf at beowulf.org> wrote:
>>> I have come across this question in a few locations. Being specific, I
>>> am a fan of the Julia language. Ont he Juia forum a respected developer
>>> recently asked what the options were for keeping code developed on a laptop
>>> in sync with code being deployed on an HPC system.
>> I think out loud that many HPC codes depend crucially on a $HOME
>>> directory being presnet on the compute nodes as the codes look for dot
>>> files etc. in $HOME. I guess this can be dealt with by fake $HOMES which
>>> again sync back to the Repo.
>> I don't follow you here... $HOME, dot files, repo, syncing back? And why
>> "Repo" with capital letter, is it supposed to be a name or something
>> special?
> I think John is talking here about doing version control on whole HOME
> directories but trying to be mindful of dot files such as .bashrc and
> others which can be application or system specific. The first thing which
> comes to mind is to use branches for different cluster systems. However
> this also taps into backup (which is another important topic since HOME
> dirs are not necessarily backed up). There could be a working solution
> which makes use of recursive repos and git lfs support but pruning old
> history could still be desirable. Git would minimize the amount of storage
> because it's hash based. While this could make it possible to replicate
> your environment "wherever you go", a/ you would drag a lot history around
> and b/ a significantly different mindset is required to manage the whole
> thing. A typical HPC user may know git clone but generally is not a git
> adept. Developers are different and, who knows John, maybe someone will
> pick up your idea.
> Is gitfs any popular?
> In my HPC universe, people actually not only need code, but also data -
>> usually LOTS of data. Replicating the code (for scripting languages) or the
>> binaries (for compiled stuff) would be trivial, replicating the data would
>> not. Also pulling the data in or pushing it out (f.e. to/from AWS) on the
>> fly whenever the instance is brought up would be slow and costly. And by
>> the way this is in no way a new idea - queueing systems have for a long
>> time the concept of "pre" and "post" job stages, which could be used to
>> pull in code and/or data to the node(s) on which the node would be running
>> and clean up afterwards.
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