CONTEXT
During installation BioBASH gets the number of cores in the system and sets the ambient variable: $BIOBASH_CORES.
This variable is therefore used for os::default_number_of_cores to determine the default number of cores that BioBASH scripts will use.
PROBLEM
We have not implemented a consistent method to determine the "optimal" default number of cores to use based on the system.
So by default BioBASH sets this default to: 1 core. Basically because of this:
By default BioBASH uses 1 core, one attempt was to use a fraction of total cores in the system (something like: 1/3(total number of cores), nevertheless this approach was dismissed, since in huge infrastructures this could cause more harm than benefit, because we could be trying to split a small process in several processes and make things slower (this has not been tested throughly. Needs to be done). One could make a bet and set the default number of cores to "2", because there is a low, low probability that someone is trying to run BioBASH in a single-core processor CPU (such as the Celeron G470 or an Intel Atom), but no one knows.
SOLUTION
Use the BIOBASH_CORES variable to set reasonable limits for default number of cores. For instance in huge systems with, let's say, 100 cores, one could set a reasonable number of cores assuring that it WON'T MAKE SMALL PROCESSES SLOWER, but that intermediate to large processes will run smoothly.
If the systems has a low number of cores this limits should also be assesed. Thats the solution that we want to find.
CONTEXT During installation BioBASH gets the number of cores in the system and sets the ambient variable: $BIOBASH_CORES. This variable is therefore used for os::default_number_of_cores to determine the default number of cores that BioBASH scripts will use.
PROBLEM We have not implemented a consistent method to determine the "optimal" default number of cores to use based on the system. So by default BioBASH sets this default to: 1 core. Basically because of this:
By default BioBASH uses 1 core, one attempt was to use a fraction of total cores in the system (something like: 1/3(total number of cores), nevertheless this approach was dismissed, since in huge infrastructures this could cause more harm than benefit, because we could be trying to split a small process in several processes and make things slower (this has not been tested throughly. Needs to be done). One could make a bet and set the default number of cores to "2", because there is a low, low probability that someone is trying to run BioBASH in a single-core processor CPU (such as the Celeron G470 or an Intel Atom), but no one knows.SOLUTION Use the BIOBASH_CORES variable to set reasonable limits for default number of cores. For instance in huge systems with, let's say, 100 cores, one could set a reasonable number of cores assuring that it WON'T MAKE SMALL PROCESSES SLOWER, but that intermediate to large processes will run smoothly. If the systems has a low number of cores this limits should also be assesed. Thats the solution that we want to find.