all_run_times | Parse all run times |
arm_id | Unique name for arm |
arms_factorial | Build factorial arms |
cat_df | Concatenate and print a data.frame |
copy_dir_retain_dates | Copy directories, retaining last modified dates of files |
count_rout_errors | Count errors in file |
count_rout_warnings | Count warnings in file |
dir_git_toplevel | Get the toplevel git directory |
dir_run_branch | Corresponding (branch-specific) run directory |
dir_run_branch_toplevel | Toplevel directory of the (branch-specific) run directory |
file_last_line | Get the final line of a file |
file_path | Build a file path |
find_mngrfile | Find Mngrfile |
get_jobids | Extract Job ID from squeue output |
git_abbrev_ref | Abbreviated name for HEAD commit in git repository |
git_clone_or_pull | Clone or pull to the run dir |
git_short_sha | Short SHA for HEAD commit in git repository |
grapes-cores-grapes | Set the number of cores for a task |
grapes-d-grapes | Set up task dependencies |
grapes-hours-grapes | Set the number of hours for a task (walltime) |
grapes-memory-grapes | Set the memory requirements for a task |
grapes-merge-grapes | Merge arms |
grapes-split-grapes | Split arms |
grapes-task-grapes | Create a new task |
grapes-throttle-grapes | Throttle the number of tasks to run simultaneously |
hms | Convert seconds to formatted h:mm:ss string |
is_inside_git_work_tree | Check if dir is inside git work tree |
job_create | Create job |
job_exists | Check for job existence |
job_find_id | Find job id |
kill_pattern | Kill Slurm jobs matching pattern |
latest_logs | Summaries the latest R output |
link_to_arm_indicies | Merge rout status table with arm data |
lscheduler_add | Add to lscheduler |
merge_tables | Merge squeue and rout status tables |
mngr | Mngr |
mngr_config | Set configuration options for mngr |
mngr_option_dir_output | Converting run paths to output paths |
mngr_option_dir_r_logs | Path to keep all R logs |
mngr_option_dir_r_logs_latest | Path to keep the latest R logs |
mngr_option_dir_run | Converting paths to runpaths |
mngr_option_dir_slurm_logs | Path to keep Slurm logs |
mngr_option_dir_state | Path to keep the state files |
mngr_option_global_throttle | Global throttle setting |
mngr_option_scheduler | Scheduler used for running R jobs |
mngr_option_slurm_submit_path | Path to the directory containing Slurm submit script |
mngr_option_use_tempfile | Save RDS data to a tempfile initially |
monitor | Monitor Slurm jobs |
monitor_logs | Print status of specified jobs |
parse_name | Parse job names |
parse_rout_files | Parse .Rout files to a data frame |
pdf device | |
pdf_file | path to pdf file |
png | png device |
png_file | path to png file |
prereq_arm_ids | Arm IDs for the prerequisite tasks |
pretty_print_arm_values | Print the arm values prettily |
pretty_print_squeue | Pretty print squeue output |
pretty_print_time | Pretty print the time |
pretty_success_status | Pretty print ticks and crosses |
qdel | A wrapper around Sluerm qdel |
rds_file | path to rds file |
read_rds_merge | Load and merge all RDS files |
rfile | Add rfile as a slurm task |
rfile_create | Create rfile task |
rfiles | Add all R files in the current directory as tasks |
run | Execute a task |
run_jobs | Run jobs |
run_time_seconds | Parse the run time of a file |
save | save file |
saveRDS | Save an R object to a rds file |
sinfo | Information about slurm cluster |
slurm_add_jobids | Add Job ID to list of Job IDs |
slurm_summary | Return a brief summary of the Slurm queue status |
squeue | Wrapper around Slurm's squeue function |
startup | Startup mngr |
sub_path | Manipuate a path |
success | Determine whether R job ran successfully |
system_in_dir | Evalutate system command in directory |
task_create | Create task |
task_exists | Check for task existence |
task_get | Get a task |
tiff | tiff device |
tiff_file | path to tiff file |
with_dir | Evaluate expression in a particular working directory |
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