HPCD::SLURM::Stage
use HPCD::SLURM::Stage;
This module defines SLURM-specific stage attributes and contains the method that decides if the program has failed due to memory shortage, and if so if the program can be retried with a larger memory limit.
The only two resources user can define via user_input are (hard) time and (hard) memory.
The default memory limit is 2G, and default time limit is there is no limit.
A list of possible retry memory limits (when a program fails because of lack of memory it will look through this list to find and retry with the next biggest memory available). Should be in ascending order. Default is qw(2G 4G 16G 32G).
Analyzes and returns the completion state. Exit status 0 => pass, otherwise, if the program fails due to lack of memory and the program can be retried with the next biggest memory, then returns retry, else returns fail.
Searches for the next biggest memory in _use_retry_resources_required for retry.
Takes in a memory size (units: KMG or none(no unit means the unit is byte already)) and converts it to a number representing the original size in bytes. Example: &_res_to_num('1024') returns 1024 (because 1024 bytes = 1024 bytes) &_res_to_num('2K') returns 2048 (because 2KB = 2048 bytes) &_res_to_num('1M') returns 1048576 (because 1MB = 1048576 bytes)
Takes in a number in bytes and converts it into designated units (K/M/G). Example: &_num_to_res(2048) returns '2K' &_num_to_res(1048576) returns '1M'
Gives out warning based on memory usage account information and decides if the program fails because of lack of memory. If so, invoke _can_retry_from_vmem and return the memory limit for retry, otherwise return 0.
John Macdonald - Boutros Lab
Anqi (Joyce) Yang - Boutros Lab
Paul Boutros, Phd, PI - Boutros Lab
The Ontario Institute for Cancer Research
To install HPCD::SLURM, copy and paste the appropriate command in to your terminal.
cpanm
cpanm HPCD::SLURM
CPAN shell
perl -MCPAN -e shell install HPCD::SLURM
For more information on module installation, please visit the detailed CPAN module installation guide.