notes/graham_notes.md

In bbolker/McMasterPandemic: Pandemic Model

A quick update on attempting to run calibrations on Graham: As expected, our standard "pure" Nelder-Mead operation is running normally. This completes a test calibration in 17 minutes, and all the metrics look normal. A calibration using deOptim with only one core allocated doesn't complete in 20 minutes (I can try rerunning it for longer), but has otherwise normal-looking metrics. A calibration using deOptim with 4 cores (doesn't even complete in 40 minutes, and has an extremely low CPU usage indicating that it is not being used fully. Note that I accidentally over-allocated memory for the Nelder-Mead and deOptim 1-core runs, resulting in low memory efficiency.

The calibrate call is as follows (for the 4-core deOptim): ont_cal1 <- calibrate( data = ont_all_sub, base_params = params, opt_pars = opt_pars, time_args = list(params_timevar = timevar_df), sim_args = list(step_args = list()), use_DEoptim = TRUE, DE_cores = 4 )

(Pure Nelder-Mead) [mso@gra-login3 scratch]$ seff 49577068 perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "C.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). Job ID: 49577068 Cluster: graham User/Group: mso/mso State: COMPLETED (exit code 0) Cores: 1 CPU Utilized: 00:16:53 CPU Efficiency: 99.31% of 00:17:00 core-walltime Job Wall-clock time: 00:17:00 Memory Utilized: 326.91 MB Memory Efficiency: 7.98% of 4.00 GB

(deOptim 1-core) [mso@gra-login3 scratch]$ seff 49577069 Job ID: 49577069 Cluster: graham User/Group: mso/mso State: TIMEOUT (exit code 0) Cores: 1 CPU Utilized: 00:19:52 CPU Efficiency: 98.27% of 00:20:13 core-walltime Job Wall-clock time: 00:20:13 Memory Utilized: 354.03 MB Memory Efficiency: 8.64% of 4.00 GB

(deOptim 4-core) [mso@gra-login1 scratch]$ seff 49578001 perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "C.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). Job ID: 49578001 Cluster: graham User/Group: mso/mso State: TIMEOUT (exit code 0) Nodes: 1 Cores per node: 4 CPU Utilized: 00:07:32 CPU Efficiency: 6.19% of 02:01:40 core-walltime Job Wall-clock time: 00:30:25 Memory Utilized: 327.13 MB Memory Efficiency: 15.97% of 2.00 GB

bbolker/McMasterPandemic documentation built on Aug. 25, 2024, 6:35 p.m.