I have been running RS_HGAP_Assembly.2 in SMRT portal and the job has been failing at the overlapInCore step. I was able to solve the problem by changing the nproc from 64 down to 24 so it would not use up all the available RAM on our system.
Each overlapInCore job was trying to use ~2.5GB of RAM, and the system only has 128GB. With 63 processes trying to run, the job failed. In order to optimize performance of the CA step - how do I determine how much RAM is used by each overlapInCore process?
For example, should I increase ovlThreads, while decreasing ovlConcurrency. I have 64 cores and 128GB RAM, so I'm trying to use as much available computing power as possible.
If anyone can provide insight on this, I'd appreciate it!
Best,
Jeff
From my runCA.spec file:
ovlThreads=integer (default=2)
The number of compute threads to use per overlap job.
ovlConcurrency=integer (default=1)
When not using SGE, the number of concurrent overlap jobs to run at the same time.
My current job is running with
ovlThreads = 1
ovlConcurrency = 24
Each overlapInCore job was trying to use ~2.5GB of RAM, and the system only has 128GB. With 63 processes trying to run, the job failed. In order to optimize performance of the CA step - how do I determine how much RAM is used by each overlapInCore process?
For example, should I increase ovlThreads, while decreasing ovlConcurrency. I have 64 cores and 128GB RAM, so I'm trying to use as much available computing power as possible.
If anyone can provide insight on this, I'd appreciate it!
Best,
Jeff
From my runCA.spec file:
ovlThreads=integer (default=2)
The number of compute threads to use per overlap job.
ovlConcurrency=integer (default=1)
When not using SGE, the number of concurrent overlap jobs to run at the same time.
My current job is running with
ovlThreads = 1
ovlConcurrency = 24
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