Showing 14 of total 14 results (show query)
uscbiostats
slurmR:A Lightweight Wrapper for 'Slurm'
'Slurm', Simple Linux Utility for Resource Management <https://slurm.schedmd.com/>, is a popular 'Linux' based software used to schedule jobs in 'HPC' (High Performance Computing) clusters. This R package provides a specialized lightweight wrapper of 'Slurm' with a syntax similar to that found in the 'parallel' R package. The package also includes a method for creating socket cluster objects spanning multiple nodes that can be used with the 'parallel' package.
Maintained by George Vega Yon. Last updated 1 years ago.
41.6 match 59 stars 8.06 score 216 scripts 1 dependents
earthlab
rslurm:Submit R Calculations to a 'Slurm' Cluster
Functions that simplify submitting R scripts to a 'Slurm' workload manager, in part by automating the division of embarrassingly parallel calculations across cluster nodes.
Maintained by Erick Verleye. Last updated 2 years ago.
33.3 match 55 stars 8.30 score 303 scripts 1 dependents
mschubert
clustermq:Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM, PBS/Torque)
Evaluate arbitrary function calls using workers on HPC schedulers in single line of code. All processing is done on the network without accessing the file system. Remote schedulers are supported via SSH.
Maintained by Michael Schubert. Last updated 24 days ago.
clusterhigh-performance-computinglsfsgeslurmsshzeromq3cpp
15.9 match 149 stars 10.23 score 253 scripts
mllg
batchtools:Tools for Computation on Batch Systems
As a successor of the packages 'BatchJobs' and 'BatchExperiments', this package provides a parallel implementation of the Map function for high performance computing systems managed by schedulers 'IBM Spectrum LSF' (<https://www.ibm.com/products/hpc-workload-management>), 'OpenLava' (<https://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid Engine' (<https://www.univa.com/>), 'Slurm' (<https://slurm.schedmd.com/>), 'TORQUE/PBS' (<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>), or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>). A multicore and socket mode allow the parallelization on a local machines, and multiple machines can be hooked up via SSH to create a makeshift cluster. Moreover, the package provides an abstraction mechanism to define large-scale computer experiments in a well-organized and reproducible way.
Maintained by Michel Lang. Last updated 2 years ago.
batchexperimentsbatchjobsdocker-swarmhigh-performance-computinghpchpc-clusterslsfopenlavaparallel-computingreproducibilitysgeslurmtorque
13.8 match 175 stars 11.39 score 772 scripts 14 dependents
philchalmers
SimDesign:Structure for Organizing Monte Carlo Simulation Designs
Provides tools to safely and efficiently organize and execute Monte Carlo simulation experiments in R. The package controls the structure and back-end of Monte Carlo simulation experiments by utilizing a generate-analyse-summarise workflow. The workflow safeguards against common simulation coding issues, such as automatically re-simulating non-convergent results, prevents inadvertently overwriting simulation files, catches error and warning messages during execution, implicitly supports parallel processing with high-quality random number generation, and provides tools for managing high-performance computing (HPC) array jobs submitted to schedulers such as SLURM. For a pedagogical introduction to the package see Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Maintained by Phil Chalmers. Last updated 4 hours ago.
monte-carlo-simulationsimulationsimulation-framework
7.4 match 62 stars 13.36 score 253 scripts 46 dependents
wlandau
crew.cluster:Crew Launcher Plugins for Traditional High-Performance Computing Clusters
In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'crew.cluster' package extends the 'mirai'-powered 'crew' package with worker launcher plugins for traditional high-performance computing systems. Inspiration also comes from packages 'mirai' by Gao (2023) <https://github.com/shikokuchuo/mirai>, 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischl, and Surmann (2017). <doi:10.21105/joss.00135>.
Maintained by William Michael Landau. Last updated 1 months ago.
crewhigh-performance-computing
11.1 match 28 stars 6.81 score 68 scripts
a2-ai
slurmtools:slurm tooling
What the package does (one paragraph).
Maintained by Devin Pastoor. Last updated 2 months ago.
10.8 match 2 stars 3.56 score 6 scripts
dkaschek
dMod:Dynamic Modeling and Parameter Estimation in ODE Models
The framework provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc. The framework follows the paradigm that derivative information should be used for optimization whenever possible. Therefore, all major functions produce and can handle expressions for symbolic derivatives.
Maintained by Daniel Kaschek. Last updated 9 days ago.
3.4 match 20 stars 8.35 score 251 scripts
bioc
BgeeCall:Automatic RNA-Seq present/absent gene expression calls generation
BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (https://bgee.org).
Maintained by Julien Wollbrett. Last updated 5 months ago.
softwaregeneexpressionrnaseqbiologygene-expressiongene-levelintergenic-regionspresent-absent-callsrna-seqrna-seq-librariesscrna-seq
4.2 match 3 stars 5.56 score 9 scripts
tudo-r
BatchJobs:Batch Computing with R
Provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported. For further details see the project web page.
Maintained by Bernd Bischl. Last updated 3 years ago.
2.3 match 85 stars 8.57 score 616 scripts 3 dependents
capro-uio
tsdrtools:Convenience package for installing R-packages on UiO TSD
Some packages are hard to install on the secure closed server of the University of Oslo, TSD This package has some functions to help users more easily install packages to TSD that cannot be installed using the mini-CRAN service within TSD.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
4.3 match 6 stars 4.18 score 5 scripts
lcbc-uio
tsdrtools:Convenience package for installing R-packages on UiO TSD
Some packages are hard to install on the secure closed server of the University of Oslo, TSD This package has some functions to help users more easily install packages to TSD that cannot be installed using the mini-CRAN service within TSD.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
4.3 match 6 stars 4.18 score 5 scripts
pik-piam
brick:Building sector model with heterogeneous renovation and construction of the stock
This building stock model represents residential and commercial buildings at customisable regional and temporal resolution. The building stock is quantified in floor area and distinguished by building type (SFH/MFH) and location (rural/urban). In each building category, construction cohorts are tracked explicitly. This allows to characterise buildings specifically for each subset of buildings. The evolution of the building stock follows from the flows of constructed, renovated and demolished buildings and is optimised under cost minimisation with a benefit for heterogeneity in the choice of construction and renovation alternatives. This benefit captures heterogeneity in the preferences of the agents and the building structure.
Maintained by Robin Hasse. Last updated 20 days ago.
4.3 match 3.76 score 1 dependentsbioc
FLAMES:FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.
Maintained by Changqing Wang. Last updated 5 days ago.
rnaseqsinglecelltranscriptomicsdataimportdifferentialsplicingalternativesplicinggeneexpressionlongreadzlibcurlbzip2xz-utilscpp
1.5 match 31 stars 7.95 score 12 scripts