|
2 | 2 |
|
3 | 3 | ## TL;DR |
4 | 4 |
|
5 | | -Here is an example on how to evaluate R expressions on a Slurm |
6 | | -high-performance compute (HPC) cluster from within R. |
| 5 | +Here is an example of how to evaluate R expressions on a Slurm |
| 6 | +high-performance computing (HPC) cluster from within R. |
7 | 7 |
|
8 | 8 | ``` r |
9 | | - |
10 | 9 | library(future) |
11 | 10 |
|
12 | 11 | # Limit runtime to 10 minutes and memory to 400 MiB per future, |
@@ -55,12 +54,11 @@ leverage the compute power of high-performance computing (HPC) clusters |
55 | 54 | via a simple switch in settings - without having to change any code at |
56 | 55 | all. |
57 | 56 |
|
58 | | -For instance, the below two future R expressions will be processed by |
59 | | -parallel R workers that launched on different compute nodes by the |
| 57 | +For instance, the following two future R expressions will be processed |
| 58 | +by parallel R workers launched on different compute nodes by the |
60 | 59 | specified job scheduler: |
61 | 60 |
|
62 | 61 | ``` r |
63 | | - |
64 | 62 | library(future) |
65 | 63 | plan(future.batchtools::batchtools_slurm) |
66 | 64 |
|
@@ -89,26 +87,25 @@ used. *The user has full control of how futures are evaluated*. For |
89 | 87 | instance, to use local batchtools futures, run the demo as: |
90 | 88 |
|
91 | 89 | ``` r |
92 | | - |
93 | 90 | library(future) |
94 | 91 | plan(future.batchtools::batchtools_local) |
95 | 92 | demo("mandelbrot", package = "future", ask = FALSE) |
96 | 93 | ``` |
97 | 94 |
|
98 | | -## Available batchtools backend |
| 95 | +## Available batchtools backends |
99 | 96 |
|
100 | 97 | The **future.batchtools** package implements a generic future wrapper |
101 | 98 | for all batchtools backends. Below are the most common types of |
102 | 99 | batchtools backends. For other types of parallel and distributed |
103 | 100 | backends, please see <https://www.futureverse.org/backends.html>. |
104 | 101 |
|
105 | | -| Backend | Description | Alternative in future package | |
106 | | -|:---|:---|:---| |
107 | | -| `batchtools_lsf` | Futures are evaluated via a [Load Sharing Facility (LSF)](https://en.wikipedia.org/wiki/Platform_LSF) job scheduler | N/A | |
108 | | -| `batchtools_openlava` | Futures are evaluated via an [OpenLava](https://en.wikipedia.org/wiki/OpenLava) job scheduler | N/A | |
109 | | -| `batchtools_sge` | Futures are evaluated via a [Sun/Son of/Oracle/Univa/Altair Grid Engine (SGE)](https://en.wikipedia.org/wiki/Oracle_Grid_Engine) job scheduler | N/A | |
110 | | -| `batchtools_slurm` | Futures are evaluated via a [Slurm](https://en.wikipedia.org/wiki/Slurm_Workload_Manager) job scheduler | N/A | |
111 | | -| `batchtools_torque` | Futures are evaluated via a [TORQUE](https://en.wikipedia.org/wiki/TORQUE) / PBS job scheduler | N/A | |
112 | | -| `batchtools_custom` | Futures are evaluated via a custom batchtools configuration R script or via a set of cluster functions | N/A | |
113 | | -| `batchtools_multicore` | parallel evaluation by forking the current R process | `plan(multicore)` | |
114 | | -| `batchtools_local` | sequential evaluation in a separate R process (on current machine) | `plan(cluster, workers = I(1))` | |
| 102 | +| Backend | Description | Alternative in future package | |
| 103 | +|:-----------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------| |
| 104 | +| `batchtools_lsf` | Futures are evaluated via a [Load Sharing Facility (LSF)](https://en.wikipedia.org/wiki/Platform_LSF) job scheduler | N/A | |
| 105 | +| `batchtools_openlava` | Futures are evaluated via an [OpenLava](https://en.wikipedia.org/wiki/OpenLava) job scheduler | N/A | |
| 106 | +| `batchtools_sge` | Futures are evaluated via a [Sun/Son of/Oracle/Univa/Altair Grid Engine (SGE)](https://en.wikipedia.org/wiki/Oracle_Grid_Engine) job scheduler | N/A | |
| 107 | +| `batchtools_slurm` | Futures are evaluated via a [Slurm](https://en.wikipedia.org/wiki/Slurm_Workload_Manager) job scheduler | N/A | |
| 108 | +| `batchtools_torque` | Futures are evaluated via a [TORQUE](https://en.wikipedia.org/wiki/TORQUE) / PBS job scheduler | N/A | |
| 109 | +| `batchtools_custom` | Futures are evaluated via a custom batchtools configuration R script or via a set of cluster functions | N/A | |
| 110 | +| `batchtools_multicore` | parallel evaluation by forking the current R process | `plan(multicore)` | |
| 111 | +| `batchtools_local` | sequential evaluation in a separate R process (on current machine) | `plan(cluster, workers = I(1))` | |
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