README.md

In rjbgoudie/mngr: Make, Rake, Workflows etc for R

mngr

mngr is a system for automating runs of R files for statistical analyses.

Workflows are defined in a file called Mngrfile.R in the directory of the analysis.

All R files in the current directory can be made into a 'task' using rfiles()

Dependencies between tasks are set up using the %d% operator (or %depends%).

Arms

Often, we want to run many variants of a particular analysis. Each variant of an analysis is called an `arm' in mngr. If all combinations are required, then add the following to the Mngrfile.R

arms_factorial(initial_value = c(1, 4, 7),
               seed = c(3, 4))

This will mean that, for example, in the first arm, initial_value = 1 and seed = 3. The variables will be set when R starts up.

So that each arm does not overwrite each other, helper functions are available to place data files and plots etc in appropriate places:

1. rds_file("myobject") will return the path to $OUTPUT/$GITBRANCH/$ARM/rds/myobject.rds
2. pdf_file("myplot") will return the path to $OUTPUT/$GITBRANCH/$ARM/plots/myplot.pdf
3. tiff_file("myplot") will return the path to $OUTPUT/$GITBRANCH/$ARM/rds/myplot.tiff
4. png_file("myplot") will return the path to $OUTPUT/$GITBRANCH/$ARM/rds/myplot.png

All of these are wrappers to file_path.

Slurm

Submit scripts should go in ~/.mngr/slurm/QUEUE where QUEUE is the name of the queue (unless you change the value of mngr_slurm_submit_path -- see below).

If no queue is specified in an Mngrfile, ~/.mngr/slurm/default will be used

Cores, memory, hours, and throttling constraints can be set for individual tasks using %cores%, %memory%, %hours% and %throttle%.

Options

Several settings are controlled by the standard options mechanism in R.

These settings should be made in ~/.mngr/config.R. So that you can use mngr interactively, you will also want to source this config file in your .Rprofile

1. Scheduler: mngr_scheduler should take the value "slurm" to use the Slurm Workload Manger for running the jobs on a cluster, or "local" to run the jobs on locally, using a simple R-based scheduler.

When the default is to use Slurm, the --local flag to mngr will override this.

1. Filepaths: mngr_dir_output and mngr_dir_run - see 'File locations and paths' section below for details.

Further customisation can be achieved with the mngr_dir_slurm_logs, mngr_dir_r_logs_latest, mngr_dir_r_logs and mngr_dir_state optins.

1. Use tempfile for saving RDS files. On some filesystems (e.g NFS network shares), it can be slow to write out RDS files using saveRDS. Instead, it is much quicker to write the file first to a local filesystem, and then move the final file to the network share.

Setting mngr_use_tempfile to TRUE will turn this option on: when saveRDS is used, the R object is first written to tempfile(), and then moved to the ultimate final location.

1. Slurm submit directory: mngr_slurm_submit_path. This should be set to the path containing Slurm submit scripts. The directory can contain several submit scripts, for example for different Slurm queues.

The default value is ~/.mngr/slurm/.

1. Global throttle: mngr_global_throttle. The maximum number of tasks to run simulataneously (for local scheduler; default set by parallel::detectCores()) or the maximum number of arms of a task to run (for slurm; default is 50).

File locations and paths

There are several file locations relevant to mngr:

1. Where the actual R files are stored, which must be within a git repository. We call the top level directory of this git repository $GIT_TOPLEVEL
2. Where the R files will be run from: mngr checks out the git repository to a separate location, when running the analysis, so that the original working copy of the R files can be edited while the original analysis is running, without changing what runs.

The location of this is set by the option mngr_dir_run.

This should be a function that converts $GIT_TOPLEVEL to the equivalant run directory. By default $HOME/path/to/$GIT_TOPLEVEL/ will be converted to $HOME/run/$GIT_TOPLEVEL.

Note that the function must return the supplied dir if dir is in the run directory already.

1. The "output" location: this is where all of the plots, rds files, and logs are stored. You may wish for this to on a separate drive to the R source, since the output may be large and can be reproduced, so you might not need to back the results up so carefully.

The location of this is set by the option mngr_dir_output.

This should be a function that converts a path (within the run directory) to the corresponding path in the results location. By default, mngr_dir_output is set so that the results will be saved within the run directory

Installation

# Install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("rjbgoudie/mngr")

Other systems

mngr is somewhat inspired by Make and Rake, but mngr is customised to statistical workflows. In particular, versions of analyses are handled using `git': different branches can be run simultaneously and independently, and the output will be stored separately.

rjbgoudie/mngr documentation built on May 27, 2019, 9:13 a.m.