+1.  This is especially useful for us, with hardware-accelerated
algorithms having limits on input size.




On 12-05-03 9:51 AM, "Peter Cock" <p.j.a.c...@googlemail.com> wrote:

>Hello all,
>
>Currently the Galaxy experimental task splitting code allows splitting
>into
>N chunks, e.g. 8 parts, with:
>
><parallelism method="multi" split_mode="number_of_parts" split_size="8"
>..." />
>
>Or, into chunks of at most size N (units dependent on the file type, e.g.
>lines
>in a tabular file or number of sequences in FASTA/FASTQ), e.g. at most
>1000
>sequences:
>
><parallelism method="multi" split_mode="to_size" split_size="1000" ... />
>
>As an aside I found it confusing that the meaning of the "split_size"
>attribute
>depend on the "split_mode" (number of jobs, or size of jobs).
>
>I would prefer to be able to set both sizes - in this case tell Galaxy to
>try
>to use at least 8 parts, each of at most 1000 sequences. Thus in a BLAST
>task, initially the split would be (up to) eight ways:
>
>8 queries => 8 jobs each with 1 query
>80 queries => 8 jobs each with 10 queries
>800 queries => 8 jobs each with 100 queries
>8000 queries => 8 jobs each with 1000 queries
>
>Then, once the max chunk size comes into play, you'd just get more jobs:
>
>9000 queries => 9 jobs each with 1000 queries
>10000 queries => 10 jobs each with 1000 queries
>20000 queries => 20 jobs each with 1000 queries
>etc
>
>The appeal of this is it takes advantage of parallelism for small jobs
>(under 100 queries) and large jobs (1000s of queries), while able to
>impose a maximum size on each cluster job.
>
>The problem is this requires changing the XML tags, and getting rid
>of the current two modes in favour of this combined one. Perhaps this:
>
><parallelism method="multi" min_jobs="8" max_size="1000" ... />
>
>The jobs threshold isn't strictly a minimum - if you have N < 8 query
>sequences, you'd just have N jobs of 1 query each.
>
>Does this sound sufficiently general? The split code is still rather
>experimental so I don't expect breaking the API to be a big issue
>(not many people are using it).
>
>Peter
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>


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