-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path2016-neurohackweek-chrisg-docker-for-scientists.html
554 lines (272 loc) · 17.6 KB
/
2016-neurohackweek-chrisg-docker-for-scientists.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
545
546
547
548
549
550
551
552
553
554
<!DOCTYPE html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content=" Chris Gorgolweski - Neurohackweek - Docker for scientists Sep 6, 2016 / In this presentation, Chris describes using Docker for reproducible science and then how to convert to Singularity when you want to run it on an HPC resource (because Docker is not supported on traiditional HPC). Please enable JavaScript to view the comments powered by Disqus. Site last generated: Jul 26, 2017 ">
<meta name="keywords" content="presentations">
<meta name="name" content="Chris Gorgolweski - Neurohackweek - Docker for scientists">
<meta name="thumbnail" content="http://singularity.lbl.gov/images/logo/logo.svg">
<title>Chris Gorgolweski - Neurohackweek - Docker for scientists | Singularity</title>
<link rel="stylesheet" href="assets/css/syntax.css">
<link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css">
<link href="https://fonts.googleapis.com/css?family=Open+Sans" rel="stylesheet">
<!--<link rel="stylesheet" type="text/css" href="css/bootstrap.min.css">-->
<link rel="stylesheet" href="assets/css/modern-business.css">
<link rel="stylesheet" href="assets/css/lavish-bootstrap.css">
<link rel="stylesheet" href="assets/css/customstyles.css">
<link rel="stylesheet" href="assets/css/theme-blue.css">
<link rel="stylesheet" type="text/css" href="assets/css/asciinema-player.css" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.4/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery-cookie/1.4.1/jquery.cookie.min.js"></script>
<script src="assets/js/jquery.navgoco.min.js"></script>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/anchor-js/2.0.0/anchor.min.js"></script>
<script src="assets/js/toc.js"></script>
<script src="assets/js/customscripts.js"></script>
<link rel="shortcut icon" href="images/favicon/favicon.ico">
<!-- HTML5 Shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!-- WARNING: Respond.js doesn't work if you view the page via file:// -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
<script src="https://oss.maxcdn.com/libs/respond.js/1.4.2/respond.min.js"></script>
<![endif]-->
<link rel="alternate" type="application/rss+xml" title="" href="http://localhost:4005feed.xml">
<script>
$(document).ready(function() {
// Initialize navgoco with default options
$("#mysidebar").navgoco({
caretHtml: '',
accordion: true,
openClass: 'active', // open
save: false, // leave false or nav highlighting doesn't work right
cookie: {
name: 'navgoco',
expires: false,
path: '/'
},
slide: {
duration: 400,
easing: 'swing'
}
});
$("#collapseAll").click(function(e) {
e.preventDefault();
$("#mysidebar").navgoco('toggle', false);
});
$("#expandAll").click(function(e) {
e.preventDefault();
$("#mysidebar").navgoco('toggle', true);
});
});
</script>
<script>
$(function () {
$('[data-toggle="tooltip"]').tooltip()
})
</script>
</head>
<body>
<!-- asciinema player -->
<script src="assets/js/asciinema-player.js"></script>
<!-- Show or hide players on button clicks-->
<script>
$( document ).ready(function() {
$(".asciinema-button").click(function(){
var asciinemaVideo = "#asciinema-" + $(this).attr('id');
if ($(asciinemaVideo).hasClass('hidden')){
$(asciinemaVideo).removeClass('hidden');
$(this).text('Hide Tutorial')
} else {
$(asciinemaVideo).addClass('hidden');
$(this).text('Show Tutorial')
}
});
});
</script>
<!-- Navigation -->
<nav class="navbar navbar-inverse navbar-fixed-top">
<div class="container topnavlinks">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html"> <span class="projectTitle"> Singularity</span></a>
</div>
<div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
<ul class="nav navbar-nav navbar-right">
<!-- entries without drop-downs appear here -->
<li><a href="blog">News</a></li>
<!-- entries with drop-downs appear here -->
<!-- conditional logic to control which topnav appears for the audience defined in the configuration file.-->
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Docs<b class="caret"></b></a>
<ul class="dropdown-menu">
<li><a href="admin-guide">Admin Guide</a></li>
<li><a href="user-guide">User Guide</a></li>
<li><a href="links">Contributed Content</a></li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Quick Links<b class="caret"></b></a>
<ul class="dropdown-menu">
<li><a href="https://github.com/singularityware/singularity" target="_blank">Github Repo</a></li>
<li><a href="https://groups.google.com/a/lbl.gov/forum/#!forum/singularity" target="_blank">Google Group</a></li>
<li><a href="http://stackoverflow.com/questions/tagged/singularity" target="_blank">Singularity on Stack Overflow</a></li>
<li><a href="https://singularity-hub.org/faq" target="_blank">Singularity Hub</a></li>
<li><a href="https://singularity-container.slack.com" target="_blank">Slack</a></li>
<li><a href="faq#troubleshooting">Troubleshooting</a></li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">People<b class="caret"></b></a>
<ul class="dropdown-menu">
<li><a href="https://github.com/gmkurtzer" target="_blank">Gregory M. Kurtzer</a></li>
<li><a href="https://github.com/vsoch" target="_blank">Vanessa Sochat</a></li>
<li><a href="https://github.com/bauerm97" target="_blank">Michael Bauer</a></li>
<li><a href="https://github.com/bbockelm" target="_blank">Brian Bockelman</a></li>
<li><a href="https://github.com/singularityware/singularity/blob/master/AUTHORS" target="_blank">Complete Authors List</a></li>
</ul>
</li>
<li><a href="/search"><i class="fa fa-search"></i></li>
<!-- jekyll search hidden in favor of google
<li>
<div id="search-demo-container">
<input type="text" id="search-input" placeholder="search...">
<ul id="results-container"></ul>
</div>
<script src="assets/js/jekyll-search.js" type="text/javascript"></script>
<script type="text/javascript">
SimpleJekyllSearch.init({
searchInput: document.getElementById('search-input'),
resultsContainer: document.getElementById('results-container'),
dataSource: 'search.json',
searchResultTemplate: '<li><a href="{url}" title="Chris Gorgolweski - Neurohackweek - Docker for scientists">{title}</a></li>',
noResultsText: 'No results found.',
limit: 10,
fuzzy: true,
})
</script>
end search-->
</li>
</ul>
</div>
</div>
<!-- /.container -->
</nav>
<!-- Page Content -->
<div class="container">
<div class="col-lg-12"> </div>
<!-- Content Row -->
<div class="row">
<!-- Sidebar Column -->
<div class="col-md-3">
<div class="shiny"><a href="\"><figure><img src="/images/logo/logo.svg" class="sidebar-logo"/></figure></a></div>
<ul id="mysidebar" class="nav">
<li class="sidebarTitle">Singularity</li>
<li>
<a href="#">Information</a>
<ul>
<li><a href="blog">News</a></li>
<li><a href="about">About Singularity</a></li>
<li><a href="presentations">Presentations</a></li>
<li><a href="citation-registration">Registry: Citations and Installations</a></li>
</ul>
<li>
<a href="#">Download / Installation</a>
<ul>
<li><a href="all-releases">All Releases</a></li>
<li><a href="install-linux">Install Singularity on Linux</a></li>
<li><a href="install-mac">Install Singularity on Mac</a></li>
<li><a href="install-windows">Install Singularity on Windows</a></li>
</ul>
<li>
<a href="#">Contributing</a>
<ul>
<li><a href="contributing-support">User Support</a></li>
<li><a href="contributing-code">Code Development</a></li>
<li><a href="contributing-docs">Writing Documentation</a></li>
</ul>
<li>
<a href="#">Getting Help</a>
<ul>
<li><a href="faq">FAQ</a></li>
<li><a href="support">Support</a></li>
<li><a href="faq#troubleshooting">Troubleshooting</a></li>
</ul>
<li>
<a href="#">Documentation</a>
<ul>
<li><a href="quickstart">Quick Start</a></li>
<li><a href="tutorials">Recipes and Tutorials</a></li>
<li><a href="links">Contributed Content Links</a></li>
<li><a href="user-guide">User Documentation</a></li>
<li><a href="admin-guide">Admin Documentation</a></li>
</ul>
<!-- if you aren't using the accordion, uncomment this block:
<p class="external">
<a href="#" id="collapseAll">Collapse All</a> | <a href="#" id="expandAll">Expand All</a>
</p>
-->
</li>
</ul>
</div>
<!-- this highlights the active parent class in the navgoco sidebar. this is critical so that the parent expands when you're viewing a page. This must appear below the sidebar code above. Otherwise, if placed inside customscripts.js, the script runs before the sidebar code runs and the class never gets inserted.-->
<script>$("li.active").parents('li').toggleClass("active");</script>
<!-- Content Column -->
<div class="col-md-9">
<article class="post" itemscope itemtype="http://schema.org/BlogPosting">
<header class="post-header">
<h1 class="post-title" itemprop="name headline">Chris Gorgolweski - Neurohackweek - Docker for scientists</h1>
<p class="post-meta"><time datetime="2016-09-06T00:00:00-04:00" itemprop="datePublished">Sep 6, 2016</time> /
</p>
</header>
<div class="post-content" itemprop="articleBody">
<p>In this presentation, Chris describes using Docker for reproducible science and then how to convert to Singularity when you want to run it on an HPC resource (because Docker is not supported on traiditional HPC).</p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/wAATYzn8O54?start=3720" frameborder="0" allowfullscreen=""></iframe>
</div>
<!--links to download are under archive before version 2.2-->
<!--links to download changed at version 2.2-->
</article>
<div id="disqus_thread" style="margin-top:30px"></div>
<script type="text/javascript">
/* * * CONFIGURATION VARIABLES: EDIT BEFORE PASTING INTO YOUR WEBPAGE * * */
var disqus_shortname = 'singularityware'; // required: replace example with your forum shortname
/* * * DON'T EDIT BELOW THIS LINE * * */
(function() {
var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true;
dsq.src = '//' + disqus_shortname + '.disqus.com/embed.js';
(document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq);
})();
</script>
<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
<hr class="shaded"/>
<footer>
<div class="row">
<!-- Social Media links, etc -->
<div class="col-lg-6 footer">
<a class="no-after social-icon" href="https://twitter.com/SingularityApp">
<i class="fa fa-4x fa-twitter no-after"></i>
</a>
<a class="no-after social-icon" href="https://github.com/singularityware">
<i class="fa fa-4x fa-github no-after"></i>
</a>
</div>
<div class="col-lg-6 footer">
<p><img src="images/logo/logo.png" alt="Company logo" style="width:40px;padding-bottom:10px"/></p>
Site last generated: Jul 26, 2017 <br />
</div>
</div>
</footer>
</div>
<!-- /.row -->
</div>
<!-- /.container -->
</div>
</body>
<!-- the google_analytics_id gets auto inserted from the config file -->
<script>(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)})(window,document,'script','//www.google-analytics.com/analytics.js','ga');ga('create','UA-84672381-1','auto');ga('require','displayfeatures');ga('send','pageview');</script>
</html>