Apologies if these question was already answered:
I did some research but couldn't come up with a definite answer/solution
for this question/problem.
Let's say I have a simple workflow consisting of 5 steps:
1.) retrieve data from a database using a REST service
2.) storing retrieved data as a csv and staging/copying it to the local HPC
cluster
3.) dispatching first job (SGE) on the cluster for some primary analysis
4.) dispatching second job (SGE) on the cluster for secondary analysis
5.) staging out the files from cluster
Step 1, 2 are quite easy however I haven an issue with step 3-5.
So step 4 should only be started once step 3 is finished. However I didn't
find any native solution in taverna to check if the job is finished before
I start step 4.
Furthermore these jobs can run quickly or take some time (depending on
cluster usage).
Is there an easy solution to this asynchronous problem?
I can think of 2 ways how to solve it:
1.) create a service/nested workflow that checks the output files on the
cluster
2.) create a service/nested workflow that checks the SGE job status (see
http://www.myexperiment.org/workflows/174.html)
I know there are also some plugins which might abstract away these things
(PBS, Unicore).
But I would be interested in best practices in solving the HPC/Taverna
interaction.
thanks in advance
Uemit
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