Hello,
I have access to a computer cluster made of 44 nodes. Each node has 12 cores and 48 GB ram. The main problem is that jobs have a maximum walltime of 6h then they get killed, but I can use as many nodes as I like, which means that for a job I could use i.e up to 10 nodes = 120 cores x 480 GB RAM or more.
So in order to make a tophat job to finish in 6h hours i wanted to parallelize it to a a very large number of cores with the appropriate RAM per core, and specify the number of cores through the -p parameter.
My problem is that i can' t get tophat to recognize all the cores of the multiple nodes, and I couldn't run tophat using openmpi (mpirun -np XX tophat etc).
So I'm wondering if tophat is multi-node capable or not? Is there a way to make it run on multiple nodes or do I need a recompiled version? I could find clues of tophat being run through mpi. (http://seqanswers.com/forums/archive...p/t-11472.html)
Can anyone give me suggestions or alternatives?
PS (similar situation applies to cufflinks)
Thanks,
Best regards,
Marco
I have access to a computer cluster made of 44 nodes. Each node has 12 cores and 48 GB ram. The main problem is that jobs have a maximum walltime of 6h then they get killed, but I can use as many nodes as I like, which means that for a job I could use i.e up to 10 nodes = 120 cores x 480 GB RAM or more.
So in order to make a tophat job to finish in 6h hours i wanted to parallelize it to a a very large number of cores with the appropriate RAM per core, and specify the number of cores through the -p parameter.
My problem is that i can' t get tophat to recognize all the cores of the multiple nodes, and I couldn't run tophat using openmpi (mpirun -np XX tophat etc).
So I'm wondering if tophat is multi-node capable or not? Is there a way to make it run on multiple nodes or do I need a recompiled version? I could find clues of tophat being run through mpi. (http://seqanswers.com/forums/archive...p/t-11472.html)
Can anyone give me suggestions or alternatives?
PS (similar situation applies to cufflinks)
Thanks,
Best regards,
Marco
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