Package: hipercow 1.1.8

Rich FitzJohn

hipercow: High Performance Computing

Set up cluster environments and jobs. Moo.

Authors:Rich FitzJohn [aut, cre], Wes Hinsley [aut], Paul Liétar [aut], Imperial College of Science, Technology and Medicine [cph]

hipercow_1.1.8.tar.gz
hipercow_1.1.8.zip(r-4.7)hipercow_1.1.8.zip(r-4.6)hipercow_1.1.8.zip(r-4.5)
hipercow_1.1.8.tgz(r-4.6-any)hipercow_1.1.8.tgz(r-4.5-any)
hipercow_1.1.8.tar.gz(r-4.7-any)hipercow_1.1.8.tar.gz(r-4.6-any)
hipercow_1.1.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
hipercow/json (API)

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

Bug tracker:https://github.com/mrc-ide/hipercow/issues

Pkgdown/docs site:https://mrc-ide.github.io

On CRAN:

Conda:

5.83 score 1 stars 1 packages 58 scripts 63 exports 23 dependencies

Last updated from:b7dd52258a (on main). Checks:6 NOTE, 2 OK, 1 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE348
source / vignettesOK322
linux-release-x86_64NOTE335
macos-release-arm64NOTE234
macos-oldrel-arm64NOTE454
windows-develNOTE237
windows-releaseERROR298
windows-oldrelNOTE925
wasm-releaseOK106

Exports:dide_authenticatedide_checkdide_delete_keypairdide_generate_keypairdide_pathdide_usernamehipercowhipercow_bundle_cancelhipercow_bundle_createhipercow_bundle_deletehipercow_bundle_listhipercow_bundle_loadhipercow_bundle_log_valuehipercow_bundle_resulthipercow_bundle_retryhipercow_bundle_statushipercow_bundle_waithipercow_cluster_infohipercow_configurationhipercow_configurehipercow_driverhipercow_environment_createhipercow_environment_deletehipercow_environment_existshipercow_environment_listhipercow_environment_showhipercow_envvarshipercow_example_helperhipercow_hellohipercow_inithipercow_parallelhipercow_parallel_get_coreshipercow_parallel_load_environmenthipercow_parallel_set_coreshipercow_provisionhipercow_provision_checkhipercow_provision_comparehipercow_provision_listhipercow_purgehipercow_resourceshipercow_resources_validatehipercow_rrq_controllerhipercow_rrq_stop_workers_once_idlehipercow_rrq_workers_submithipercow_unconfiguretask_canceltask_create_bulk_calltask_create_bulk_exprtask_create_calltask_create_explicittask_create_exprtask_create_scripttask_evaltask_infotask_listtask_log_showtask_log_valuetask_log_watchtask_resulttask_retrytask_statustask_submittask_wait

Dependencies:askpassaudiocallrclicurldescfilelockfsidsjsonlitelpSolveopensslpkgbuildpkgcachepkgdependsprocessxpsR6rlangsysuuidwithrzip

Administration
Rebuilding the bootstrap library | Testing a copy of hipercow on the cluster | Recreating the vignettes | Rtools, Java support and R versions (Windows) | Adding R Versions | Updating RTools | Updating Java support | stan
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Last update: 2025-10-13
Started: 2024-01-04

Using secrets on the cluster
Using cyphr
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Last update: 2025-10-13
Started: 2025-10-13

Details
Options | Influential options | hipercow.auto_install_missing_packages | hipercow.progress | hipercow.timeout | hipercow.validate_globals | hipercow.max_size_local | hipercow.default_envvars | hipercow.development | DIDE options | rrq options | hipercow.rrq_offload_threshold_size | Options from other packages | Setting options | R versions | Workflow considerations | Long running tasks | Disk space
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Last update: 2025-04-23
Started: 2024-01-04

The DIDE Cluster
Pre-requisites:- | Authentication with DIDE | About our usernames and passwords | Networks | Filesystems and paths | Cluster-based storage and home directories | Mapping network drives on your computer | Windows | macOS | Linux | Initialisation | Does it work? | Default environment variables | The Nodes | Cluster Storage | Cluster Storage on Windows Compute nodes | Cluster Storage on Linux Compute nodes
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Last update: 2025-04-23
Started: 2025-04-23

Environments
Basics | Loading packages | Loading your own functions | Defining globals | Other points | Relationship with provisioning
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Last update: 2025-04-23
Started: 2024-11-27

hipercow
Clusters and Platforms | Installing prerequisites | Filesystems and paths | Initialising | Running your first task | Using functions you have written | Getting information about tasks | Fetching information with task_info() | Fetching logs with task_log_show | Watching logs with task_log_watch | Running many tasks at once | Bulk call, or "parallel map" | Bulk expression | More on bundles | Picking bundles back up again later | Making bundles from tasks | Parallel tasks | Understanding where variables come from | Cancelling tasks | Retrying tasks
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Last update: 2025-04-23
Started: 2024-01-04

Migration from didehpc
Differences | Mapping of didehpc methods to hipercow functions | queue_didehpc | task | bundle | Configuration | Missing features | New features
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Last update: 2025-04-23
Started: 2024-01-12

Packages and provisioning
Using pkgdepends | A list of packages | Manually | Automatically, from an environment | Using a script | Using renv | Some details about the process
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Last update: 2025-04-23
Started: 2024-01-04

Parallel Tasks
Task-level parallelism | What resources does the cluster have? | Specifying multi-core resources | Running parallel tasks | Using the Parallel package | Using the future package | Specifying more work than there are cores | How many cores should each process use? | Multiple cores per process | Other ways of using cores | Specifying which nodes should run your tasks | Memory requests | Running on specific nodes | Selecting by queue | Selecting by node names | Task time limits and scheduling | The maximum runtime | Delaying tasks starting | Lowering your priority
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Last update: 2025-04-23
Started: 2024-02-05

Troubleshooting
My task failed | Caused by an error in your code | Caused by an error during startup | My task got stuck at submitted | My code works on my computer but not on the cluster | Some of my tasks work on the cluster, but others fail | My code is slower on the cluster than running locally! | I can't connect to the cluster | Asking for help
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Last update: 2025-04-23
Started: 2024-01-04

Using INLA on Windows
Local installations | Latest available version of INLA for your R version | Specific version of INLA, where available. | Hipercow provisioning | Latest version of INLA for latest R version. | Latest version of INLA for older R version
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Last update: 2025-04-23
Started: 2024-06-14

Using stan
Local installations | CmdStan on the cluster | Installation and versions | Compiling models | A worked example
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Last update: 2025-04-23
Started: 2024-06-12

Workers
Getting started | The lightweight queue pattern | Basic usage | Scaling up | Interprocess commuication pattern | Tricks and tips | Controlling the worker environment | General considerations | Stopping redundant workers | Permanence | Object storage
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Last update: 2025-04-23
Started: 2024-12-09

Readme and manuals

Help Manual

Help pageTopics
DIDE credentialsdide_authenticate
Check we can use the DIDE clusterdide_check
Generate keypairdide_delete_keypair dide_generate_keypair
Describe a path mappingdide_path
Report DIDE usernamedide_username
Cancel bundle taskshipercow_bundle_cancel
Create task bundlehipercow_bundle_create
Delete task bundleshipercow_bundle_delete
List existing bundleshipercow_bundle_list
Load existing bundlehipercow_bundle_load
Fetch bundle logshipercow_bundle_log_value
Fetch bundle resultshipercow_bundle_result
Retry task bundlehipercow_bundle_retry
Bundle statushipercow_bundle_status
Wait for a bundle to completehipercow_bundle_wait
Describe clusterhipercow_cluster_info
Report on hipercow configurationhipercow_configuration
Configure your hipercow roothipercow_configure
Create a driverhipercow_driver
Manage environmentshipercow_environment_create hipercow_environment_delete hipercow_environment_exists hipercow_environment_list hipercow_environment_show
Environment variableshipercow_envvars
Hello worldhipercow_hello
Create a hipercow roothipercow_init
Specify parallel use of coreshipercow_parallel
Get number of coreshipercow_parallel_get_cores
Set various environment variables that report the number of cores available for execution.hipercow_parallel_set_cores
Provision cluster libraryhipercow_provision
Compare installationshipercow_provision_compare
List installationshipercow_provision_check hipercow_provision_list
Purge taskshipercow_purge
Hipercow Resourceshipercow_resources
Validate a 'hipercow_resources' list for a driver.hipercow_resources_validate
Create an rrq controllerhipercow_rrq_controller
Tell workers to exit once completehipercow_rrq_stop_workers_once_idle
Submit rrq workershipercow_rrq_workers_submit
Remove a driver from a hipercow configurationhipercow_unconfigure
Cancel taskstask_cancel
Create bulk tasks from a calltask_create_bulk_call
Create bulk tasks from an expressiontask_create_bulk_expr
Create task from calltask_create_call
Create explicit tasktask_create_explicit
Create a task based on an expressiontask_create_expr
Create script tasktask_create_script
Run a tasktask_eval
Fetch task informationtask_info
List taskstask_list
Get task logtask_log_show task_log_value task_log_watch
Get task resulttask_result
Retry a tasktask_retry
Get task statustask_status
Submit a tasktask_submit
Wait for a task to completetask_wait