Open kimberlynroosa opened 6 days ago
inference, operations
medium priority
kimbe@kmr-laptop MINGW64 ~/Documents/flepimop_dir/flepimop_sample (main) $ Rscript $FLEPI_PATH/flepimop/main_scripts/inference_main.R -c config_sample_2pop_inference.yml Warning messages: 1: replacing previous import 'foreach::when' by 'purrr::when' when loading 'flepicommon' 2: replacing previous import 'foreach::accumulate' by 'purrr::accumulate' when loading 'flepicommon' [1] "Starting" [1] "Running 20 jobs in parallel" [1] "Making cluster with 20 cores." seir_modifiers_scenarios : Ro_all outcome_modifiers_scenarios : test_limits slots : 1 config : config_sample_2pop_inference.yml run_id : 20240923_143204EDT seir_modifiers_scenarios : all outcome_modifiers_scenarios : all jobs : 20 iterations_per_slot : 1 this_slot : 1 this_block : 1 stoch_traj_flag : FALSE ground_truth_start : ground_truth_end : flepi_path : C:\Users\kimbe\Documents\flepimop_dir\flepiMoP python : C:\Users\kimbe\AppData\Local\Programs\Python\Python311\python rpath : Rscript is-resume : FALSE is-interactive : FALSE reset_chimeric_on_accept : TRUE save_seir : FALSE save_hosp : TRUE memory_profiling : FALSE memory_profiling_iters : 100 subpop_len : 5 incl_aggr_likelihood : TRUE help : FALSE [1] "⚠️ No seeding: section found in config >> not using or fitting seeding." [1] "Running 1 simulations for slot 1" Warning: The following named parsers don't match the column names: source Joining with by = join_by(date, subpop) [1] "Running WITH inference" [1] "Chimeric reset is TRUE" [1] "config" "run_id" [3] "seir_modifiers_scenarios" "outcome_modifiers_scenarios" [5] "jobs" "iterations_per_slot" [7] "this_slot" "this_block" [9] "stoch_traj_flag" "ground_truth_start" [11] "ground_truth_end" "flepi_path" [13] "python" "rpath" [15] "is-resume" "is-interactive" [17] "reset_chimeric_on_accept" "save_seir" [19] "save_hosp" "memory_profiling" [21] "memory_profiling_iters" "subpop_len" [23] "incl_aggr_likelihood" "help" [25] "total_ll_multiplier" Warning: To save space, intermediate SEIR files will not be saved for every iteration of the MCMC inference procedure. To save these files, set option save_seir TRUE. [1] "Running seir modifier scenario: Ro_all" [1] "Running outcome modifier scenario: test_limits" gempyor >> Running DETERMINISTIC simulation; gempyor >> ModelInfo sample_2pop_Ro_all_test_limits; index: 1; run_id: 20240923_143204EDT, gempyor >> prefix: sample_2pop_Ro_all_test_limits/20240923_143204EDT/; [1] "gempyor_inference_runner created successfully." [1] "RUNNING: MCMC initialization for the first block" Error: IOError: Failed to open local file 'C:/Users/kimbe/Documents/flepimop_dir/flepimop_sample/model_output/sample_2pop_Ro_all_test_limits/20240923_143204EDT/init/global/intermediate/000000001.000000001.000000000.20240923_143204EDT.init.parquet'. Detail: [Windows error 1224] The requested operation cannot be performed on a file with a user-mapped section open. Error in unserialize(socklist[[n]]) : error reading from connection Calls: %dopar% ... recvOneData -> recvOneData.SOCKcluster -> unserialize Execution halted
by = join_by(date, subpop)
No response
MINGW64
Label
inference, operations
Priority Label
medium priority
Describe the bug/issue
kimbe@kmr-laptop MINGW64 ~/Documents/flepimop_dir/flepimop_sample (main) $ Rscript $FLEPI_PATH/flepimop/main_scripts/inference_main.R -c config_sample_2pop_inference.yml Warning messages: 1: replacing previous import 'foreach::when' by 'purrr::when' when loading 'flepicommon' 2: replacing previous import 'foreach::accumulate' by 'purrr::accumulate' when loading 'flepicommon' [1] "Starting" [1] "Running 20 jobs in parallel" [1] "Making cluster with 20 cores." seir_modifiers_scenarios : Ro_all outcome_modifiers_scenarios : test_limits slots : 1 config : config_sample_2pop_inference.yml run_id : 20240923_143204EDT seir_modifiers_scenarios : all outcome_modifiers_scenarios : all jobs : 20 iterations_per_slot : 1 this_slot : 1 this_block : 1 stoch_traj_flag : FALSE ground_truth_start : ground_truth_end : flepi_path : C:\Users\kimbe\Documents\flepimop_dir\flepiMoP python : C:\Users\kimbe\AppData\Local\Programs\Python\Python311\python rpath : Rscript is-resume : FALSE is-interactive : FALSE reset_chimeric_on_accept : TRUE save_seir : FALSE save_hosp : TRUE memory_profiling : FALSE memory_profiling_iters : 100 subpop_len : 5 incl_aggr_likelihood : TRUE help : FALSE [1] "⚠️ No seeding: section found in config >> not using or fitting seeding." [1] "Running 1 simulations for slot 1" Warning: The following named parsers don't match the column names: source Joining with
by = join_by(date, subpop)[1] "Running WITH inference" [1] "Chimeric reset is TRUE" [1] "config" "run_id" [3] "seir_modifiers_scenarios" "outcome_modifiers_scenarios" [5] "jobs" "iterations_per_slot" [7] "this_slot" "this_block" [9] "stoch_traj_flag" "ground_truth_start" [11] "ground_truth_end" "flepi_path" [13] "python" "rpath" [15] "is-resume" "is-interactive" [17] "reset_chimeric_on_accept" "save_seir" [19] "save_hosp" "memory_profiling" [21] "memory_profiling_iters" "subpop_len" [23] "incl_aggr_likelihood" "help" [25] "total_ll_multiplier" Warning: To save space, intermediate SEIR files will not be saved for every iteration of the MCMC inference procedure. To save these files, set option save_seir TRUE. [1] "Running seir modifier scenario: Ro_all" [1] "Running outcome modifier scenario: test_limits" gempyor >> Running DETERMINISTIC simulation; gempyor >> ModelInfo sample_2pop_Ro_all_test_limits; index: 1; run_id: 20240923_143204EDT, gempyor >> prefix: sample_2pop_Ro_all_test_limits/20240923_143204EDT/; [1] "gempyor_inference_runner created successfully." [1] "RUNNING: MCMC initialization for the first block" Error: IOError: Failed to open local file 'C:/Users/kimbe/Documents/flepimop_dir/flepimop_sample/model_output/sample_2pop_Ro_all_test_limits/20240923_143204EDT/init/global/intermediate/000000001.000000001.000000000.20240923_143204EDT.init.parquet'. Detail: [Windows error 1224] The requested operation cannot be performed on a file with a user-mapped section open. Error in unserialize(socklist[[n]]) : error reading from connection Calls: %dopar% ... recvOneData -> recvOneData.SOCKcluster -> unserialize Execution haltedTo Reproduce
No response
Environment, if relevant
MINGW64