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
chemistry	measured time in chemistry subroutine
diffusion	measured time in diffusion subroutine

Chemistry subsetting

Value	Description
simtime	overall runtime of chemistry
loop	time spent in send/recv loop of master
sequential	sequential part of the master (e.g. shuffling field)
idle_master	idling time of the master waiting for workers
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_hits	count of data points retrieved from DHT
dht_evictions	count of data points evicted by another write operation
dht_get_time	time to retreive data from DHT
dht_fill_time	time to write data to DHT

Interpolation

If using interpolation, the following values are given:

Value	Description
interp_w	time spent to write to PHT
interp_r	time spent to read from DHT/PHT/Cache
interp_g	time spent to gather results from DHT
interp_fc	accumulated time spent in interpolation function call
interp_calls	count of interpolations
interp_cached	count of interpolation data sets, which where cached in the local map

Diffusion subsetting

Value	Description
simtime	overall runtime of diffusion