-
Notifications
You must be signed in to change notification settings - Fork 1
/
satori-R.html
544 lines (426 loc) · 39.1 KB
/
satori-R.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>R on Satori — MIT Satori User Documentation documentation</title>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="canonical" href="https://researchcomputing.mit.edu/satori-R.html"/>
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Using MPI and CUDA on Satori" href="satori-cuda-aware-mpi.html" />
<link rel="prev" title="Julia on Satori" href="satori-julia.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
<a href="index.html" class="icon icon-home"> MIT Satori User Documentation
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="satori-basics.html">Satori Basics</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-basics.html#what-is-satori">What is Satori?</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-basics.html#how-can-i-get-an-account">How can I get an account?</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-basics.html#getting-help">Getting help?</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-ssh.html">Satori Login</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-ssh.html#web-portal-login">Web Portal Login</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-ssh.html#ssh-login">SSH Login</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-getting-started.html">Starting up on Satori</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-started.html#getting-your-account">Getting Your Account</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-started.html#shared-hpc-clusters">Shared HPC Clusters</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-started.html#logging-in-to-satori">Logging in to Satori</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-started.html#the-satori-portal">The Satori Portal</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-started.html#setting-up-your-environment">Setting up Your Environment</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-started.html#transferring-files">Transferring Files</a><ul>
<li class="toctree-l3"><a class="reference internal" href="satori-getting-started.html#using-scp-or-rysnc">Using scp or rysnc</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-getting-started.html#satori-portal-file-explorer">Satori Portal File Explorer</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-started.html#types-of-jobs">Types of Jobs</a><ul>
<li class="toctree-l3"><a class="reference internal" href="satori-getting-started.html#running-interactive-jobs">Running Interactive Jobs</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-getting-started.html#running-batch-jobs">Running Batch Jobs</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-training.html">Training for faster onboarding in the system HW and SW architecture</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-workload-manager-using-slurm.html">Running your AI training jobs on Satori using Slurm</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-workload-manager-using-slurm.html#a-note-on-exclusivity">A Note on Exclusivity</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-workload-manager-using-slurm.html#interactive-jobs">Interactive Jobs</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-workload-manager-using-slurm.html#batch-scripts">Batch Scripts</a><ul>
<li class="toctree-l3"><a class="reference internal" href="satori-workload-manager-using-slurm.html#monitoring-jobs">Monitoring Jobs</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-workload-manager-using-slurm.html#canceling-jobs">Canceling Jobs</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-workload-manager-using-slurm.html#scheduling-policy">Scheduling Policy</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-workload-manager-using-slurm.html#batch-queue-policy">Batch Queue Policy</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-workload-manager-using-slurm.html#queue-policies">Queue Policies</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-workload-manager-using-slurm.html#running-jobs-in-series">Running jobs in series</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-workload-manager-using-slurm.html#note-on-pytorch-1-4">Note on Pytorch 1.4</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-troubleshooting.html">Troubleshooting</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-ai-frameworks.html">IBM Watson Machine Learning Community Edition (WML-CE) and Open Cognitive Environment (Open-CE)</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#install-anaconda">[1] Install Anaconda</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#wml-ce-and-open-ce-setting-up-the-software-repository">[2] WML-CE and Open-CE: Setting up the software repository</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#wml-ce-and-open-ce-creating-and-activate-conda-environments-recommended">[3] WML-CE and Open-CE: Creating and activate conda environments (recommended)</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#wml-ce-installing-all-frameworks-at-the-same-time">[4] WML-CE: Installing all frameworks at the same time</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#wml-ce-testing-ml-dl-frameworks-pytorch-tensorflow-etc-installation">[5] WML-CE: Testing ML/DL frameworks (Pytorch, TensorFlow etc) installation</a><ul>
<li class="toctree-l3"><a class="reference internal" href="satori-ai-frameworks.html#controlling-wml-ce-release-packages">Controlling WML-CE release packages</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-ai-frameworks.html#additional-conda-channels">Additional conda channels</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#the-wml-ce-supplementary-channel-is-available-at-https-anaconda-org-powerai">The WML CE Supplementary channel is available at: https://anaconda.org/powerai/.</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#the-wml-ce-early-access-channel-is-available-at-https-public-dhe-ibm-com-ibmdl-export-pub-software-server-ibm-ai-conda-early-access">The WML-CE Early Access channel is available at: https://public.dhe.ibm.com/ibmdl/export/pub/software/server/ibm-ai/conda-early-access/.</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-distributed-deeplearning.html">Distributed Deep Learning</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-large-model-support.html">IBM Large Model Support (LMS)</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-julia.html">Julia on Satori</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#getting-started">Getting started</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#getting-help">Getting help?</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#a-simple-batch-script-example">A simple batch script example</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#recipe-for-running-single-gpu-single-threaded-interactive-session-with-cuda-aware-mpi">Recipe for running single GPU, single threaded interactive session with CUDA aware MPI</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#running-a-multi-process-julia-program-somewhat-interactively">Running a multi-process julia program somewhat interactively</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#an-example-of-installing-https-github-com-clima-climatemachine-jl-on-satori">An example of installing https://github.com/clima/climatemachine.jl on Satori</a></li>
</ul>
</li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">R on Satori</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#getting-started-with-r">Getting Started with R</a></li>
<li class="toctree-l2"><a class="reference internal" href="#installing-packages">Installing Packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="#a-simple-batch-script-example">A Simple Batch Script Example</a></li>
<li class="toctree-l2"><a class="reference internal" href="#r-and-python">R and Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="#running-r-in-a-container">Running R in a container</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-cuda-aware-mpi.html">Using MPI and CUDA on Satori</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#getting-started">Getting started</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#compiling">Compiling</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#submiting-a-batch-script">Submiting a batch script</a><ul>
<li class="toctree-l3"><a class="reference internal" href="satori-cuda-aware-mpi.html#batch-script-header">Batch script header</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-cuda-aware-mpi.html#assigning-gpus-to-mpi-ranks">Assigning GPUs to MPI ranks</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-cuda-aware-mpi.html#running-the-mpi-program-within-the-batch-script">Running the MPI program within the batch script</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#a-complete-example-slurm-batch-script">A complete example SLURM batch script</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#using-alternate-mpi-builds">Using alternate MPI builds</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="lsf-templates/satori-lsf-ml-examples.html">Example machine learning LSF jobs</a><ul>
<li class="toctree-l2"><a class="reference internal" href="lsf-templates/satori-lsf-ml-examples.html#a-single-node-4-gpu-keras-example">A single node, 4 GPU Keras example</a></li>
<li class="toctree-l2"><a class="reference internal" href="lsf-templates/satori-lsf-ml-examples.html#a-single-node-4-gpu-caffe-example">A single node, 4 GPU Caffe example</a></li>
<li class="toctree-l2"><a class="reference internal" href="lsf-templates/satori-lsf-ml-examples.html#a-multi-node-pytorch-example">A multi-node, pytorch example</a></li>
<li class="toctree-l2"><a class="reference internal" href="lsf-templates/satori-lsf-ml-examples.html#a-multi-node-pytorch-example-with-the-horovod-conda-environment">A multi-node, pytorch example with the horovod conda environment</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-howto-videos.html">Satori Howto Video Sessions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-howto-videos.html#installing-wmcle-on-satori">Installing WMCLE on Satori</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-howto-videos.html#pytorch-with-ddl-on-satori">Pytorch with DDL on Satori</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-howto-videos.html#tensorflow-with-ddl-on-satori">Tensorflow with DDL on Satori</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-howto-videos.html#jupyterlab-with-ssh-tunnel-on-satori">Jupyterlab with SSH Tunnel on Satori</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-public-datasets.html">Satori Public Datasets</a></li>
<li class="toctree-l1"><a class="reference internal" href="singularity.html">Singularity for Satorians</a><ul>
<li class="toctree-l2"><a class="reference internal" href="singularity.html#fast-start">Fast start</a></li>
<li class="toctree-l2"><a class="reference internal" href="singularity.html#other-notes">Other notes</a></li>
<li class="toctree-l2"><a class="reference internal" href="singularity.html#interactive-allocation">Interactive Allocation:</a></li>
<li class="toctree-l2"><a class="reference internal" href="singularity.html#non-interactive-batch-mode">Non interactive / batch mode</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-relion-cryoem.html">Relion Cryoem for Satorians</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-relion-cryoem.html#prerequisites">Prerequisites</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-relion-cryoem.html#quick-start">Quick start</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-relion-cryoem.html#other-notes">Other notes</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-copy-large-filesets.html">Copying larger files and large file sets</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-copy-large-filesets.html#using-mrsync">Using mrsync</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-copy-large-filesets.html#using-aspera-for-remote-file-transfer-to-satori-cluster">Using Aspera for remote file transfer to Satori cluster</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-doc-examples-contributing.html">FAQ</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-doc-examples-contributing.html#tips-tricks-and-questions">Tips, tricks and questions</a><ul>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/storage/index.html">How can I see disk usage?</a></li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/storage/index.html#where-should-i-put-world-or-project-shared-datasets">Where should I put world or project shared datasets?</a></li>
<li class="toctree-l3"><a class="reference internal" href="portal-howto/customization.html">How can I create custom Jupyter kernels for the Satori web portal?</a><ul>
<li class="toctree-l4"><a class="reference internal" href="portal-howto/customization.html#steps-to-create-a-kernel">Steps to create a kernel</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/carlos-quick-start-commands/index.html">How do I set up a basic conda environment?</a></li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html">System software queries</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-linux-distribution-version-am-i-running">What Linux distribution version am I running?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-linux-kernel-level-am-i-running">What Linux kernel level am I running?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-software-levels-are-installed-on-the-system">What software levels are installed on the system?</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#system-hardware-queries">System hardware queries</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-is-my-cpu-configuration">What is my CPU configuration?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-much-ram-is-there-on-my-nodes">How much RAM is there on my nodes?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-smt-mode-are-my-nodes-in">What SMT mode are my nodes in?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-cpu-governor-is-in-effect-on-my-nodes">What CPU governor is in effect on my nodes?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-are-the-logical-ids-and-uuids-for-the-gpus-on-my-nodes">What are the logical IDs and UUIDs for the GPUs on my nodes?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-is-the-ibm-model-of-my-system">What is the IBM model of my system?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#which-logical-cpus-belong-to-which-socket">Which logical CPUs belong to which socket?</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#questions-about-my-jobs">Questions about my jobs</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-can-i-establish-which-logical-cpu-ids-my-process-is-bound-to">How can I establish which logical CPU IDs my process is bound to?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#can-i-see-the-output-of-my-job-before-it-completes">Can I see the output of my job before it completes?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#i-have-a-job-waiting-in-the-queue-and-i-want-to-modify-the-options-i-had-selected">I have a job waiting in the queue, and I want to modify the options I had selected</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#i-have-submitted-my-job-several-times-but-i-get-no-output">I have submitted my job several times, but I get no output</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-do-i-set-a-time-limit-on-my-job">How do I set a time limit on my job?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#can-i-make-a-jobs-startup-depend-on-the-completion-of-a-previous-one">Can I make a job’s startup depend on the completion of a previous one?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-do-i-select-a-specific-set-of-hosts-for-my-job">How do I select a specific set of hosts for my job?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-do-i-deselect-specific-nodes-for-my-job">How do I deselect specific nodes for my job?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#my-jobs-runtime-environment-is-different-from-what-i-expected">My job’s runtime environment is different from what I expected</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#i-want-to-know-precisely-what-my-jobs-runtime-environment-is">I want to know precisely what my job’s runtime environment is</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/ondemand_portal_queries/index.html">Portal queries</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/ondemand_portal_queries/index.html#i-see-no-active-sessions-in-my-interactive-sessions">I see no active sessions in My Interactive Sessions?</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html">How do I build a Singularity image from scratch?</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#set-up-to-run-docker-in-ppc64le-mode-on-an-x86-machine">Set up to run Docker in ppc64le mode on an x86 machine</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#run-docker-in-ppc64le-mode-on-an-x86-machine-to-generate-an-image-for-satori">Run Docker in ppc64le mode on an x86 machine to generate an image for Satori</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#import-new-docker-hub-image-into-singularity-on-satori">Import new Docker hub image into Singularity on Satori</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#using-singularity-instead-of-docker">Using Singularity instead of Docker</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-tutorial-examples.html">Green Up Hackathon IAP 2020</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial-examples/index.html">Tutorial Examples</a><ul>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/pytorch-style-transfer/index.html">Pytorch Style Transfer</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/pytorch-style-transfer/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/pytorch-style-transfer/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/pytorch-style-transfer/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/pytorch-style-transfer/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/neural-network-dna-demo/index.html">Neural network DNA</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/neural-network-dna-demo/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/neural-network-dna-demo/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/neural-network-dna-demo/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/neural-network-dna-demo/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/transfer-learning-pathology/index.html">Pathology Image Classification Transfer Learning</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/transfer-learning-pathology/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/transfer-learning-pathology/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/transfer-learning-pathology/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/transfer-learning-pathology/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html">Multi Node Multi GPU TensorFlow 2.0 Distributed Training Example</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#prerequisites-if-you-are-not-yet-running-tensorflow-2-0">Prerequisites if you are not yet running TensorFlow 2.0</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#what-s-going-on-here">What’s going on here?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/eric-fiala-wmlce-notebooks-master/index.html">WMLCE demonstration notebooks</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/eric-fiala-wmlce-notebooks-master/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/eric-fiala-wmlce-notebooks-master/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/eric-fiala-wmlce-notebooks-master/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/eric-fiala-wmlce-notebooks-master/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html">Finding clusters in high-dimensional data using tSNE and DB-SCAN</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html">BigGAN-PyTorch</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html#useful-references">Useful references</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="tutorial-examples/index.html#measuring-resource-use">Measuring Resource Use</a><ul>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/energy-profiling/index.html">Intergrated energy use profiling</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/energy-profiling/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/energy-profiling/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/energy-profiling/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/energy-profiling/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/nvprof-profiling/index.html">Profiling code with nvprof</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/nvprof-profiling/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/nvprof-profiling/index.html#commands-to-run-the-examples">Commands to run the examples</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/nvprof-profiling/index.html#useful-references">Useful references</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-getting-help.html">Getting help on Satori</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-help.html#email-help">Email help</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-help.html#slack">Slack</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-help.html#slack-or-satori-support-techsquare-com">Slack or satori-support@techsquare.com</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-help.html#satori-office-hours">Satori Office Hours</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-help.html#tips-and-tricks">Tips and Tricks</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="ause-coc.html">Acceptable Use and Code of Conduct</a><ul>
<li class="toctree-l2"><a class="reference internal" href="ause-coc.html#acceptable-use-guidelines">Acceptable Use Guidelines</a></li>
<li class="toctree-l2"><a class="reference internal" href="ause-coc.html#code-of-conduct">Code of Conduct</a></li>
</ul>
</li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">MIT Satori User Documentation</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content style-external-links">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html" class="icon icon-home"></a> »</li>
<li>R on Satori</li>
<li class="wy-breadcrumbs-aside">
<a href="https://github.com/mit-satori/getting-started/blob/master/satori-R.rst" class="fa fa-github"> Edit on GitHub</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="r-on-satori">
<h1>R on Satori<a class="headerlink" href="#r-on-satori" title="Permalink to this headline">¶</a></h1>
<p>R’s PowerPC support is currently limited, and there may be issues trying to install it from source. R can instead be run on Satori using either a Spack build or a container.</p>
<div class="section" id="getting-started-with-r">
<h2>Getting Started with R<a class="headerlink" href="#getting-started-with-r" title="Permalink to this headline">¶</a></h2>
<p>A fast way to get R running on Satori is to load the Spack build</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">module load spack-flat</span>
<span class="go">module load r</span>
<span class="go">R</span>
</pre></div>
</div>
</div>
<div class="section" id="installing-packages">
<h2>Installing Packages<a class="headerlink" href="#installing-packages" title="Permalink to this headline">¶</a></h2>
<p>To avoid R packages taking up space on home, you can consider setting the R library path inside <cite>/nobackup</cite>, e.g.</p>
<div class="highlight-R notranslate"><div class="highlight"><pre><span></span><span class="nf">.libPaths</span><span class="p">(</span><span class="s">"/nobackup/users/{username}/packages/R"</span><span class="p">)</span>
</pre></div>
</div>
<p>R packages can be installed as usual:</p>
<div class="highlight-R notranslate"><div class="highlight"><pre><span></span><span class="nf">install.packages</span><span class="p">(</span><span class="s">"ggplot2"</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="section" id="a-simple-batch-script-example">
<h2>A Simple Batch Script Example<a class="headerlink" href="#a-simple-batch-script-example" title="Permalink to this headline">¶</a></h2>
<p>Here is a simple example of a batch script for running a small R job.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/bash</span>
<span class="c1">#SBATCH -J my_r_job</span>
<span class="c1">#SBATCH -o my_r_job.out</span>
<span class="c1">#SBATCH -e my_r_job.err</span>
<span class="c1">#SBATCH [email protected]</span>
<span class="c1">#SBATCH --mail-type=ALL</span>
<span class="c1">#SBATCH --gres=gpu:1</span>
<span class="c1">#SBATCH --nodes=1</span>
<span class="c1">#SBATCH --mem=50G</span>
<span class="c1">#SBATCH --time=2:00:00</span>
module add spack-flat
module add r
Rscript script.R
</pre></div>
</div>
</div>
<div class="section" id="r-and-python">
<h2>R and Python<a class="headerlink" href="#r-and-python" title="Permalink to this headline">¶</a></h2>
<p>With the R Spack build, it is possible to interface between R and Python using <cite>rpy2</cite>. However, as this uses multiple environments, it may break things.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>module load spack-flat
module load r
conda activate <span class="o">{</span>env_name<span class="o">}</span>
<span class="o">{</span>env_dir<span class="o">}</span>/<span class="o">{</span>env_name<span class="o">}</span>/bin/python3 -m pip install rpy2
<span class="o">{</span>env_dir<span class="o">}</span>/<span class="o">{</span>env_name<span class="o">}</span>/bin/python3 -c <span class="s2">"import rpy2"</span>
</pre></div>
</div>
</div>
<div class="section" id="running-r-in-a-container">
<h2>Running R in a container<a class="headerlink" href="#running-r-in-a-container" title="Permalink to this headline">¶</a></h2>
<p>It is also possible to run R within a container, which has the advantage of letting you work with R in a more closed system. This involves pulling the <cite>docker://ppc64le/r-base</cite> container, which can be done by</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">cd /nobackup/users/$USER/containers</span>
<span class="go">singularity pull r-base.img docker://ppc64le/r-base</span>
</pre></div>
</div>
<p>For installation and other interactive tasks you can launch the container in interactive mode</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">cd /nobackup/users/$USER/containers</span>
<span class="go">singularity shell r-base.img</span>
<span class="go">R</span>
<span class="go">install.packages("ggplot2")</span>
</pre></div>
</div>
<p>You can also run R scripts by executing the container. The following example also binds a local folder <cite>/nobackup/users/{username}/project_folder</cite> to the container as <cite>/project_folder</cite> to allow for reading and writing data to disk.</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">cd /nobackup/users/$USER/containers</span>
<span class="go">singularity exec --bind /nobackup/users/$USER/project_folder:/project_folder r-base.img Rscript script.R</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="satori-cuda-aware-mpi.html" class="btn btn-neutral float-right" title="Using MPI and CUDA on Satori" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
<a href="satori-julia.html" class="btn btn-neutral float-left" title="Julia on Satori" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
</div>
<hr/>
<div role="contentinfo">
<p>
© Copyright 2021, MIT Satori Project.
</p>
</div>
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>