[petsc-users] installation on cloud platform

Barry Smith bsmith at mcs.anl.gov
Mon Jan 4 17:10:42 CST 2016


  There are competitors to the "regular" cloud machines like Amazon focused specifically  on HPC that "come with" MPI and use high speed networks so are much like if you built a custom HPC machine. For example http://www.rescale.com/software/  

   I don't have direct experiences with any of these systems but suspect that if you really want to scale to a bunch of nodes you are likely far better off with the HPC cloud servers than with general purpose systems even if they have a higher cost (you get what you pay for).


> On Jan 4, 2016, at 4:48 PM, Marco Zocca <zocca.marco at gmail.com> wrote:
> Hi Satish,
> thank you for the input;
> I was really looking for something that lets one abstract out "where"
> the code lives, so as to possibly work both in a single-node and
> cluster setting.
> This is why a "container" approach sounds meaningful. Configure once, run many.
> For message-passing codes such as our case, there's this
> `docker-compose` [ https://docs.docker.com/compose ] which aggregates
> the compilation and network setup steps.
> I have found this approach [
> http://qnib.org/2015/04/14/qnibterminal-mpi-hello-world/ ] that runs
> an MPI benchmark using `docker-compose`. The "Consul" library takes
> care of the DNS resolution as far as I can tell, and SLURM is the
> queue manager.
> The downsides: it's yet another third party tool (albeit a widespread
> one), with yet another scripting syntax (very much similar but
> incompatible with shell script).
> Latencies will be much larger, I expect, and also one should pay a
> much higher attention to security (building on top of someone else's
> images, freely available from the Docker Hub, is tantamount to running
> arbitrary code at compile time).
> There are however trusted Docker images, containing various
> combinations of Linux distributions and software.
> I'm very much looking forward to continuing this discussion;
> Kind regards,
> Marco
>> Are you interested in using 1 node [with multiple cores] - or multiple
>> nodes - aka cluster on amazon?
>> For a single node - I don't think any additional config should be
>> necesary [/etc/hosts - or ssh keys]. It should be same as any laptop
>> config.
>> Its possible that 'hostname' is not setup properly on amazon nodes - and
>> MPICH misbehaves.  In this case - you might need any entry to
>> /etc/hosts. Perhaps something like:
>> echo `hostname` >> /etc/hosts
>> If cluster - then there might be a tutorial to setup a proper cluster with AWS. Googles gives
>> http://cs.smith.edu/dftwiki/index.php/Tutorial:_Create_an_MPI_Cluster_on_the_Amazon_Elastic_Cloud_%28EC2%29
>> BTW: --download-mpich is a convient way to install MPI. [we default to
>> device=ch3:sock]. But you might want to figureout if there is a better
>> performing MPI for the amazon config.  [perhaps mpich with nemesis
>> works well. Or perhaps openmpi. Both are available prebuit on
>> ubunutu...]
>> Satish
>>>>>      has anyone here tried/managed to install PETSc on e.g. Amazon AWS or
>>>>>    the Google Compute Engine?
>>>>>    I believe some extra components are needed for coordination, e.g.
>>>>>    Kubernetes or Mesos (in turn requiring that the library be compiled
>>>>>    within some sort of container, e.g. Docker), but I'm a bit lost amid
>>>>>    all the options.

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