So you intend to develop a new pure Perl compute cluster? Because if you just need to get the job done why would you not use Hadoop whether private cluster or AWS? It has a Perl APi and it will cheerfully run Perl jobs. Hadoop is an Apache project, open source free software with a large installed base.
-----Original Message----- From: John Macdonald <john.macdon...@oicr.on.ca> Date: Fri, 5 Sep 2014 13:57:47 To: Fields, Christopher J<cjfie...@illinois.edu> Cc: James E Keenan<jk...@verizon.net>; module-authors@perl.org<module-authors@perl.org> Subject: RE: Top level name proposal - ComputeCluster I'm intending that ComputeCluster (or whatever the final name turns out to be) will be domain-agnostic at the top level interface at least. However, my lab will be using it for genome analysis pipelines, and I suspect a significant proportion of the potential other users will also be in this field (as shown by the repsonses on this discussion already) so there could be domain-specific submodules - either within this namespace or in other namespaces simply using this module set. Chris, Alex, and anyone else who is interested as a potential future user/contributor, feel free to email me outside of this module-authors discussion about how the actual module will develop. John Macdonald Software Engineer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario Canada M5G 0A3 Tel: Email: john.macdon...@oicr.on.ca Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________________ From: Fields, Christopher J [cjfie...@illinois.edu] Sent: September 5, 2014 9:47 AM To: John Macdonald Cc: James E Keenan; module-authors@perl.org Subject: Re: Top level name proposal - ComputeCluster Yup, I agree. I think Cluster is too generic and can mean a lot of things (I think of cluster analysis myself). Maybe something more distinctive? Is it application- or domain-specific (bioinformatics, etc)? There are a few tools with similar functionality that come to mind. Most of them have catchy names; one written in Perl is Clusterflow (not on CPAN but here: https://github.com/ewels/clusterflow/). Another is the (completely unmaintained, likely broken, but possibly useful for something) biopipe project: https://github.com/bioperl/bioperl-pipeline. I have thought about retooling the latter to be less reliant on bioperl and more a stand-alone tool. There are a couple Java tools also: bpipe (https://code.google.com/p/bpipe/) and nextflow (https://github.com/nextflow-io/nextflow). And I agree with Alex; as you might guess based on my comment on biopipe, our group would be very interested in helping out on this, even if it’s at simply the testing phase (we run PBS/Torque locally). chris On Sep 5, 2014, at 8:00 AM, John Macdonald <john.macdon...@oicr.on.ca> wrote: > Cluster was my first thought for a name, but when I did a search to see what > modules already existed (bot in case someone had already written a generic > cluster module saving me the bother of starting a new one, and to see what > types of cluster had cluster-specific modules written for them) the word > cluster came up in a large number of contexts. An tightly connected group of > "things" is a cluster (e.g. nodes in a graph) - so I didn't think that the > simple name would be clear enough. The name Cluster leaves the reader with > the immediate question "Cluster of what?". > > John Macdonald > Software Engineer > > Ontario Institute for Cancer Research > MaRS Centre > > 661 University Avenue > > Suite 510 > Toronto, Ontario > > Canada M5G 0A3 > > > Tel: > > Email: john.macdon...@oicr.on.ca > > Toll-free: 1-866-678-6427 > Twitter: @OICR_news > > > www.oicr.on.ca > > This message and any attachments may contain confidential and/or privileged > information for the sole use of the intended recipient. Any review or > distribution by anyone other than the person for whom it was originally > intended is strictly prohibited. If you have received this message in error, > please contact the sender and delete all copies. Opinions, conclusions or > other information contained in this message may not be that of the > organization. > > ________________________________________ > From: James E Keenan [jk...@verizon.net] > Sent: September 5, 2014 7:25 AM > To: module-authors@perl.org > Subject: Re: Top level name proposal - ComputeCluster > > On 09/04/2014 10:23 AM, John Macdonald wrote: >> Hi, >> >> I wanted to get general comment/concensus about a top level name that I >> am proposing. >> >> I'm starting to organize a set of modules for managing jobs on a >> computer cluster. I intend it to work much like DBI - with a top level >> abstract interface that programs can use, actually implemented by >> drivers that translate the common interface into the interface used by >> the particular type of compute cluster that is being accessed. >> Initially, I will provide a driver for SGE, since that is what we have >> and use in our lab (but after I have that running, my PI can get me >> access to a couple of other type of compute cluster to add some more. >> >> For naming, I am planning to use: >> >> ComputeCluster - top level name >> - will provide switching functions to create a class of object >> for a particular cluster type >> > > Could that be shortened to simply: Cluster ?
