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CHAPTER 6. JOB DISTRIBUTION
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The parallel environment feature can be used to limit the number of cores used by the CLC
Genomics Server, when running jobs on the grid. The syntax in the native specification for using
parallel environments is:
-pe $PE_NAME $MIN_CORE-$MAX_CORE
When the parallel environments feature is used, the number of allocated slots is interpreted as
the number of cores to be used. That is, the number of utilized cores is equal to the number of
slots in this case.
The parallel environment, selected by its name, must be setup by the grid administrator
(documentation provided by Oracle will cover this subject area), in such a way that the number
of slots corresponds to the number of cores. $MIN_CORE and $MAX_CORE specify a range of
cores, which the jobs submitted through this grid preset can run under. Care must be taken not
to set $MIN_CORE too high, as the job might never be run (e.g. if there is no system with that
many cores available), and the submitting user will not be warned by this fact.
An example of a native specification using parallel environments is the following:
-l cfl=1 -l qname=32bit -pe clc 1-3.
Here, the clc parallel environment is selected, and 1 to 3 cores are requested.
Older versions of the CLC Genomics Server
CLC Genomics Server version 4.0 and older utilize CPU cores equal to the number of allocated
slots, unless a parallel environment is in use, in which case the behaviour is the same as
described previously. In many situations the number of allocated slots is 1, effectively resulting
in CLC jobs running on one core only.
Configuration of PBS Pro
With PBS Pro it is not possible to specify a range of cores (at least not to our knowledge). Here
one specifies exactly how many cores are needed. This request can be granted (the process is
scheduled) or denied (the process is not scheduled). It is thus very important to choose a realistic
number. The number of cores are requested as a resource: -l nodes=1:ppn=X, where X is the
number of cores. As this resource is also designed to work with parallel system, the number of
nodes is allowed to be larger than 1. For the sake of scheduling cores, it is vital that this parameter
is kept at 1. An example of a native specification is: -q bit32 -l nodes=1:ppn=2, which
will request two cores and be queued in the bit32 queue.
6.2.8
Other grid worker options
Additional java options can be set for grid workers by creating a file called clcgridworker.vmoptions
in the same folder as the deployed clcgridworker script, that is, the clcgridworker script
within the folder specified in the Path to CLC GridWorker field of the grid preset.
For example, if a clcgridworker.vmoptions was created, containing the following two lines,
it would, for the CLC Grid Worker specified in a given preset, set memory limits for the CLC
Science Server java process and a temporary directory available from the grid nodes, overriding
the defaults that would otherwise apply:
-Xmx1000m
-Djava.io.tmpdir=/path/to/tmp