Package: clusters 0.0.51

Eliot J B McIntire

clusters: Utilities to manage, estimate speed, optimize use of parallel clusters

Miscellaneous utilities developed by the Predictive Ecology Group (<http://predictiveecology.org>).

Authors:Eliot J B McIntire [aut, cre], His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]

clusters_0.0.51.tar.gz
clusters_0.0.51.zip(r-4.7-any)clusters_0.0.51.zip(r-4.6-any)clusters_0.0.51.zip(r-4.5-any)
clusters_0.0.51.tgz(r-4.6-any)clusters_0.0.51.tgz(r-4.5-any)
clusters_0.0.51.tar.gz(r-4.7-any)clusters_0.0.51.tar.gz(r-4.6-any)
clusters_0.0.51.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
clusters/json (API)

# Install 'clusters' in R:
install.packages('clusters', repos = c('https://predictiveecology.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/predictiveecology/clusters/issues

On CRAN:

Conda:

2.48 score 1 stars 1 packages 6 scripts 28 exports 40 dependencies

Last updated from:483d517e61. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE182
source / vignettesOK252
linux-releaseNOTE143
macos-releaseNOTE144
macos-oldrelNOTE108
windows-develNOTE156
windows-releaseNOTE162
windows-oldrelNOTE154
wasm-releaseOK139

Exports:.sshKeepaliveOptsclusterSetupDEoptimIterative2dirNewfreeCoresLessReservedgetHostCombinationliveReservationsmakeClusterPSOCKmakeHostsmirrorTerraOptionsmonitorClusternumActiveThreadsplan_psock_minramUsageGBreadTransferredObjectsreleaseCoresreservationsPathreserveCoresresourcesUsedrmIncompleteDupsrunTestsshipSystemLibssummaryOutputFoldertableFilestermsInDEoptimtransferDirNameverifyClusterHostsvisualizeDE

Dependencies:callrclicpp11crayondata.tableDEoptimdigestfarverfilelockfpComparefsggplot2gluegtableisobandlabelinglifecyclelobstrotelpakparallellyprettyunitsprocessxpsqs2R6RColorBrewerRcppRcppParallelreproducibleRequirerlangrstudioapiS7scalesstringfishsysvctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
SSH options that let the master notice a worker has died.sshKeepaliveOpts
Setup a cluster for DEoptimclusterSetup
Run DEoptim in cached chunks of generationsDEoptimIterative2
Remove duplicate figures, keeping most recent duplicate onlydirNew
Subtract live reservations from measured free coresfreeCoresLessReserved
Pick how many workers to run on each hostgetHostCombination
Lightweight wrapper for parallelly::makeClusterPSOCKmakeClusterPSOCK
Build host names from the last octets of their addressesmakeHosts
Give cluster workers the master's terra memory settingsmirrorTerraOptions
Watch active threads and memory across a cluster's hostsmonitorCluster
Estimate the number of active threads currently being usednumActiveThreads
Minimal HT-aware PSOCK cluster planner (parallelly-only)plan_psock_min
Plot the outputs from 'testMachine'plotMachine
Get RAM usage in GB on the current machineramUsageGB
Read objects transferred to a worker, failing loudly if the transfer did not arrivereadTransferredObjects
Core reservations shared between concurrent cluster buildsliveReservations releaseCores reservationsPath reserveCores
Assess the machine resources usedresourcesUsed
This is for cleaning up cases where an interrupted optimization is leading to multiple files for the same .runName. This will remove duplicates, keeping only the most recent.rmIncompleteDups
Runs test on each machine in 'hosts'runTests
Ship missing system shared libraries to worker hosts, without rootshipSystemLibs
Summary - wrapper around 'dirNew' and 'tableFiles'summaryOutputFolder
Tabulate the filenames into groups based on 'pattern'tableFiles
'termsInDEoptim'termsInDEoptim
Test machinestestMachine
Build the per-job worker transfer directory nametransferDirName
Verify that every cluster host can actually run a workerverifyClusterHosts
Make histograms of 'DEoptim' object 'pars'visualizeDE