poet/docs/Output.md

Output Files

POET will place all simulation data and other files inside the given <OUTPUT_DIRECTORY>. The directory will look like this:

.
└── <OUTPUT_DIRECTORY>/
    ├── iter000.rds
    ├── iter000.dht
    ├── ...
    ├── iter<n>.rds
    ├── iter<n>.dht
    ├── setup.rds
    └── timings.rds

Description

All .rds file can be read into an R runtime using e.g. readRDS("<FILE>"). The following description can be given to the files:

File	Description
iter<n>.rds	Defines the state of the grid after n iteration, especially the state after transport (T) and chemistry (C)
iter<n>.dht	DHT-snapshot of the n th iteration
setup.rds	Summary of all simulation parameters given at startup
timings.rds	Various measured timings by POET

Timings

POET provides built-in time measurements of (sub) routines. The corresponding values can be found in <OUTPUT_DIRECTORY>/timings.rds and possible to read out within a R runtime with readRDS("timings.rds"). There you will find the following values:

Value	Description
simtime	time spent in whole simulation loop without any initialization and cleanup
simtime_transport	measured time in transport subroutine
simtime_chemistry	measured time in chemistry subroutine (actual parallelized part)

chemistry subsetting

If running parallel there are also measured timings which are subsets of simtime_​chemistry.

Value	Description
chemistry_loop	time spent in send/​recv loop of master
chemistry_sequential	sequential part of master chemistry
idle_master	idling time (waiting for any free worker) of the master
idle_worker	idling time (waiting for work from master) of the workers
phreeqc_time	accumulated times for Phreeqc calls of every worker

DHT usage

If running in parallel and with activated DHT, two more timings and also some profiling about the DHT usage are given:

Value	Description
dht_fill_time	time to write data to DHT
dht_get_time	time to retreive data from DHT
dh_hits	count of data points retrieved from DHT
dht_miss	count of misses/count of data points written to DHT
dht_evictions	count of data points evicted by another write operation