Wiki source code of Resources for Research

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1 {{toc/}}
2
3 = (% style="color: rgb(0,128,0);" %)1.0 Introduction(%%) =
4
5 IT for Science group provides resources and consulting services for the research community. This document provides an compendium of the free resources available for the research community. In short, we provide following services:
6
7 (% style="list-style-type: square;" %)
8 * Cubbli Linux distribution
9 * GPU capacity, up to 20 GPU's available for interactive and batch use.
10 * High Performance Computational capacity in three facilities for interactive and batch use.
11 * Fast I/O
12 * Consulting services and best practices.
13
14 (% style="margin-left: 30.0px;" %)
15 == 1.1 Can I buy my own servers? ==
16
17 (% style="margin-left: 30.0px;" %)
18 You may be considering procuring computational resources, whether they are GPU machines for Deep Learning, regular servers for computing, servers for heavy duty database use, or storage capacity and have checked that your requirement is something we do not yet offer. We have a good news. We can house servers that are used for computational tasks and incorporate them gladly to the existing pool of resources. These can be for example:(% style="letter-spacing: 0.0px;" %)
19
20 (% style="list-style-type: square;" %)
21 * \\
22 (% style="list-style-type: square;" %)
23 ** Dedicated to you alone, or...
24 ** Your research group could ask for pre-emption capability, or...
25 ** A standard addition to common pool without special privileges besides of becoming an **Investor User**.
26
27 (% style="margin-left: 30.0px;" %)
28 You can always opt to increase the **common pool** of resources at any time. Even ones that have been dedicated before.
29
30 (% style="margin-left: 30.0px;" %)
31 (Regardless of whether the server would be added into the cluster environment or remain a standalone machine, any purchases must be done through University's purchase contracts to ensure that legal aspects such as formal bidding contest are fulfilled properly.)
32
33 (% style="margin-left: 30.0px;" %)
34 === 1.1.1 We offer benefits ===
35
36 (% style="list-style-type: square;" %)
37 * \\
38 (% style="list-style-type: square;" %)
39 ** (% style="letter-spacing: 0.0px;" %)Standard, centrally managed Centos7 Linux environment.
40 ** (% style="letter-spacing: 0.0px;" %)All the software modules listed later in this document.
41 ** (% style="letter-spacing: 0.0px;" %) Very high throughput/low latency I/O (//$WRKDIR//).
42 ** (% style="letter-spacing: 0.0px;color: rgb(122,134,154);" %)Automated data migration from $WRKDIR to CEPH data lake - Planned 2019Q2.
43 ** (% style="letter-spacing: 0.0px;" %)Other resources in a same high-bandwidth interconnect fabric.
44 ** (% style="letter-spacing: 0.0px;" %)Resource Usage statistics.
45 ** (% style="letter-spacing: 0.0px;" %)You can utilize our procurement process and therefore get better deals.
46
47 (% style="margin-left: 30.0px;" %)
48 == (% style="letter-spacing: 0.0px;" %)1.2 If you still think you must choose yourself, we have something to say...(%%) ==
49
50 (% style="margin-left: 30.0px;" %)
51 In exchange for above benefits, we have a few requirements for servers that are not bought by us:
52
53 (% style="list-style-type: square;" %)
54 * \\
55 (% style="list-style-type: square;" %)
56 ** Rack mountable server, or chassis solution
57 ** Infiniband nic (//depending on the bandwidth requirement, this can be FDR (56Gb/s) and EDR (100Gb/s)//)
58 ** Associated IB cable
59
60 (% style="margin-left: 30.0px;" %)
61 (% style="letter-spacing: 0.0px;color: rgb(77,77,77);font-size: 20.0px;" %)1.3 Because
62
63 (% style="margin-left: 30.0px;" %)
64 === 1.3.1 Why should I become Investor User? ===
65
66 * \\
67 ** You will be granted higher percentage of the shares of the computational resources.
68 ** Being investor user is especially beneficial when your jobs are resource intensive.
69 ** Having more shares means that job priorities decay slower.
70
71 (% style="margin-left: 30.0px;" %)
72 === 1.3.2 Why not to use dedicated servers? ===
73
74 * \\
75 ** A history has shown that dedicated resources are often ill utilized. Utilization of less than 20% is very common.
76 ** Larger pool of common resources enables greater availability for everyone.
77 ** When resources are not dedicated, you can scale immediately upwards whenever you have temporary need.
78 ** Pooled resources are immediately available for use.
79 ** We are flexible, and if you know in advance, we can create resource reservations in advance.
80
81 (% style="margin-left: 30.0px;" %)
82 If you would need to have dedicated pool of $WRKDIR I/O resources which is only accessible by named research group, we can do this as well. In this case you should contact us and we will discuss the details.
83
84 (% style="margin-left: 30.0px;" %)
85 You can find additional details about access, restrictions etc and other topics in the User Guides.
86
87 (% style="margin-left: 30.0px;" %)
88 == 1.4 Other topics ==
89
90 (% style="margin-left: 30.0px;" %)
91 A brief information about general University wide terms and conditions can be found through the links listed below.
92
93 * \\
94 ** Terms for [[purchasing and using>>url:https://flamma.helsinki.fi/portal/home/sisalto?_nfpb=true&_windowLabel=contentviewer&contentId=HY294018&lang=en&_pageLabel=content_view||shape="rect"]] the scientific software at the university.
95 ** Availability and licensing of [[mathematical software>>url:https://flamma.helsinki.fi/portal/home/sisalto?_nfpb=true&_windowLabel=contentviewer&contentId=HY294026&lang=en&_pageLabel=content_view||shape="rect"]].
96
97 For any concerns, questions or comments you can reach us in person at Kumpula campus, or through the university helpdesk at [[helpdesk (at) helsinki (dot) fi>>mailto:helpdesk@helsinki.fi||shape="rect"]] . Resource requests, and bug reports should be addressed through [[helpdesk (at) helsinki (dot) fi>>mailto:helpdesk@helsinki.fi||shape="rect"]] .
98
99 = (% style="color: rgb(0,128,0);" %)2.0 Cubbli Linux(%%) =
100
101 Cubbli Linux distribution is fully supported by IT4SciFi. Please see the [[Cubbli Linux >>doc:Cubbli.User documentation.WebHome]] for additional information about availability and release notes. Cubbli Linux is available for servers, workstations and laptops.
102
103 Cubbli [[documentation also here (in Finnish)>>url:https://wiki.helsinki.fi/display/Cubbli/Cubbli||shape="rect"]].
104
105 = (% style="color: rgb(0,128,0);" %)3.0 HPC Environment(%%) =
106
107 If, and when the demand of computational resources exceed the capabilities of ordinary workstation, we invite you to utilize our HPC resources. We offer significant GPU, CPU and I/O resources, and fairly comprehensive - and constantly updated library of scientific software, compilers and programming environments. Should you have specific resource need not listed here, you can contact us through [[helpdesk (at) helsinki (dot) fi>>mailto:helpdesk@helsinki.fi||shape="rect"]]. If you know that your workload scales beyond our resources, you can take a look at the national supercomputing resources available at [[CSC>>url:http://www.csc.fi||shape="rect"]].
108
109 Below you can find a list of hardware resources available on the high performance computing platform. 'How to access example' refers to the use of [[batch scheduler>>doc:it4sci.IT for Science group.Internal Documentation.HPC Environment.Archive.OBSOLETE - Ukko2 User Guide.WebHome]] flags. Notes include special details of the components included. 'HT' indicates that [[CPU Hyperthreading>>url:https://www.howtogeek.com/194756/cpu-basics-multiple-cpus-cores-and-hyper-threading-explained/||shape="rect"]] is used on the nodes to increase the core count.
110
111 Note that sometimes Vendors have grants for certain resources as indicated on the list. Do check if you are eligible.
112
113 (% class="wrapped" %)
114 |=(((
115 Node Type
116 )))|=(% colspan="1" %)(% colspan="1" %)
117 (((
118 Node Qty
119 )))|=(% colspan="1" %)(% colspan="1" %)
120 (((
121 Sockets x Core (HT) per Node
122 )))|=(% colspan="1" %)(% colspan="1" %)
123 (((
124 Node Memory
125 )))|=(((
126 Where
127 )))|=(((
128 How to Use
129 )))|=(% colspan="1" %)(% colspan="1" %)
130 (((
131 Notes
132 )))
133 |(((
134 GPU, [[Tesla P100>>url:http://images.nvidia.com/content/tesla/pdf/NV-tesla-p100-pcie-PB-08248-001-v01.pdf||shape="rect"]]
135 )))|(% colspan="1" %)(% colspan="1" %)
136 (((
137 2
138 )))|(% colspan="1" %)(% colspan="1" %)
139 (((
140 2x 2.4GHz 14HT, 4xGPU
141 )))|(% colspan="1" %)(% colspan="1" %)
142 (((
143 512GB
144 )))|(((
145 Kale
146 )))|(((
147 -p ~-~-gres:gpu=1
148 )))|(% colspan="1" %)(% colspan="1" %)
149 (((
150 [[Academic Nvidia GPU Grant>>url:https://developer.nvidia.com/academic_gpu_seeding||shape="rect"]]
151 )))
152 |(((
153 GPU [[Tesla k80>>url:https://images.nvidia.com/content/pdf/kepler/Tesla-K80-BoardSpec-07317-001-v05.pdf||shape="rect"]]
154 )))|(% colspan="1" %)(% colspan="1" %)
155 (((
156 1
157 )))|(% colspan="1" %)(% colspan="1" %)
158 (((
159 2x 2.4GHz 12, 4xGPU
160 )))|(% colspan="1" %)(% colspan="1" %)
161 (((
162 \\
163 )))|(((
164 Kale
165 )))|(((
166 -p ~-~-gres:gpu=1
167 )))|(% colspan="1" %)(% colspan="1" %)
168 (((
169 [[Academic Nvidia GPU Grant>>url:https://developer.nvidia.com/academic_gpu_seeding||shape="rect"]]
170 )))
171 |(% colspan="1" %)(% colspan="1" %)
172 (((
173 Skylake
174 )))|(% colspan="1" %)(% colspan="1" %)
175 (((
176 23
177 )))|(% colspan="1" %)(% colspan="1" %)
178 (((
179 2x 20HT cores
180 )))|(% colspan="1" %)(% colspan="1" %)
181 (((
182 384GB
183 )))|(% colspan="1" %)(% colspan="1" %)
184 (((
185 Kale
186 )))|(% colspan="1" %)(% colspan="1" %)
187 (((
188 ~-~-constraint=avx
189 )))|(% colspan="1" %)(% colspan="1" %)
190 (((
191 [[AVX-512>>url:https://www.intel.com/content/www/us/en/architecture-and-technology/avx-512-overview.html||shape="rect"]]
192 )))
193 |(% colspan="1" %)(% colspan="1" %)
194 (((
195 Xeon E5
196 )))|(% colspan="1" %)(% colspan="1" %)
197 (((
198 31
199 )))|(% colspan="1" %)(% colspan="1" %)
200 (((
201 2x 2.4GHz 14HT cores
202 )))|(% colspan="1" %)(% colspan="1" %)
203 (((
204 256GB
205 )))|(% colspan="1" %)(% colspan="1" %)
206 (((
207 Ukko2
208 )))|(% colspan="1" %)(% colspan="1" %)
209 (((
210 Default
211 )))|(% colspan="1" %)(% colspan="1" %)
212 (((
213 \\
214 )))
215 |(% colspan="1" %)(% colspan="1" %)
216 (((
217 Xeon E7
218 )))|(% colspan="1" %)(% colspan="1" %)
219 (((
220 2
221 )))|(% colspan="1" %)(% colspan="1" %)
222 (((
223 4x 2.2GHz 24HT cores
224 )))|(% colspan="1" %)(% colspan="1" %)
225 (((
226 3TB
227 )))|(% colspan="1" %)(% colspan="1" %)
228 (((
229 Ukko2
230 )))|(% colspan="1" %)(% colspan="1" %)
231 (((
232 -p bigmem
233 )))|(% colspan="1" %)(% colspan="1" %)
234 (((
235 \\
236 )))
237 |(% colspan="1" %)(% colspan="1" %)
238 (((
239 Xeon
240 )))|(% colspan="1" %)(% colspan="1" %)
241 (((
242 19
243 )))|(% colspan="1" %)(% colspan="1" %)
244 (((
245 2x 2.4GHz 12 cores
246 )))|(% colspan="1" %)(% colspan="1" %)
247 (((
248 129GB
249 )))|(% colspan="1" %)(% colspan="1" %)
250 (((
251 Kale
252 )))|(% colspan="1" %)(% colspan="1" %)
253 (((
254 ~-~-constraint=smem, Default
255 )))|(% colspan="1" %)(% colspan="1" %)
256 (((
257 \\
258 )))
259 |(% colspan="1" %)(% colspan="1" %)
260 (((
261 Xeon
262 )))|(% colspan="1" %)(% colspan="1" %)
263 (((
264 13
265 )))|(% colspan="1" %)(% colspan="1" %)
266 (((
267 2x 2.4GHz 12 cores
268 )))|(% colspan="1" %)(% colspan="1" %)
269 (((
270 260GB
271 )))|(% colspan="1" %)(% colspan="1" %)
272 (((
273 Kale
274 )))|(% colspan="1" %)(% colspan="1" %)
275 (((
276 ~-~-constraint=mmem, Default
277 )))|(% colspan="1" %)(% colspan="1" %)
278 (((
279 \\
280 )))
281 |(% colspan="1" %)(% colspan="1" %)
282 (((
283 Xeon
284 )))|(% colspan="1" %)(% colspan="1" %)
285 (((
286 1
287 )))|(% colspan="1" %)(% colspan="1" %)
288 (((
289 4x 2.4GHz 12 cores
290 )))|(% colspan="1" %)(% colspan="1" %)
291 (((
292 1.57TB
293 )))|(% colspan="1" %)(% colspan="1" %)
294 (((
295 Kale
296 )))|(% colspan="1" %)(% colspan="1" %)
297 (((
298 ~-~-constraint=bmem
299 )))|(% colspan="1" %)(% colspan="1" %)
300 (((
301 \\
302 )))
303 |(% colspan="1" %)(% colspan="1" %)
304 (((
305 (% style="color: rgb(23,43,77);" %)GPU, V100
306 )))|(% colspan="1" %)(% colspan="1" %)
307 (((
308 (% style="color: rgb(23,43,77);" %)4
309 )))|(% colspan="1" %)(% colspan="1" %)
310 (((
311 (% style="color: rgb(23,43,77);" %)4x GPU
312 )))|(% colspan="1" %)(% colspan="1" %)
313 (((
314 (% style="color: rgb(23,43,77);" %)384GB
315 )))|(% colspan="1" %)(% colspan="1" %)
316 (((
317 Kale
318 )))|(% colspan="1" %)(% colspan="1" %)
319 (((
320 \\
321 )))|(% colspan="1" %)(% colspan="1" %)
322 (((
323 (% style="color: rgb(23,43,77);" %)800GB NVMe SSD. 12GPU's with 32GB, 4GPU's with 16GB
324
325 (% style="color: rgb(23,43,77);" %)[[Academic Nvidia GPU Grant>>url:https://developer.nvidia.com/academic_gpu_seeding||shape="rect"]]
326 )))
327 |(% colspan="1" %)(% colspan="1" %)
328 (((
329 Sandybridge
330 )))|(% colspan="1" %)(% colspan="1" %)
331 (((
332 180
333 )))|(% colspan="1" %)(% colspan="1" %)
334 (((
335 2x 2.66GHz 8HT (32 HT cores)
336 )))|(% colspan="1" %)(% colspan="1" %)
337 (((
338 64GB
339 )))|(% colspan="1" %)(% colspan="1" %)
340 (((
341 Vorna
342 )))|(% colspan="1" %)(% colspan="1" %)
343 (((
344 \\
345 )))|(% colspan="1" %)(% colspan="1" %)
346 (((
347 About 6000 cores
348 )))
349 |(% colspan="1" %)(% colspan="1" %)
350 (((
351 Sandybridge
352 )))|(% colspan="1" %)(% colspan="1" %)
353 (((
354 12
355 )))|(% colspan="1" %)(% colspan="1" %)
356 (((
357 2x 2.66GHz 8 cores
358 )))|(% colspan="1" %)(% colspan="1" %)
359 (((
360 64GB
361 )))|(% colspan="1" %)(% colspan="1" %)
362 (((
363 Vorna
364 )))|(% colspan="1" %)(% colspan="1" %)
365 (((
366 \\
367 )))|(% colspan="1" %)(% colspan="1" %)
368 (((
369 Service nodes
370 )))
371 |(% colspan="1" %)(% colspan="1" %)
372 (((
373 AMD Epyc
374 )))|(% colspan="1" %)(% colspan="1" %)
375 (((
376 10
377 )))|(% colspan="1" %)(% colspan="1" %)
378 (((
379 \\
380 )))|(% colspan="1" %)(% colspan="1" %)
381 (((
382 \\
383 )))|(% colspan="1" %)(% colspan="1" %)
384 (((
385 Carrington
386 )))|(% colspan="1" %)(% colspan="1" %)
387 (((
388 \\
389 )))|(% colspan="1" %)(% colspan="1" %)
390 (((
391 \\
392 )))
393 |(% colspan="1" %)(% colspan="1" %)
394 (((
395 AMD Epyc
396 )))|(% colspan="1" %)(% colspan="1" %)
397 (((
398 16
399 )))|(% colspan="1" %)(% colspan="1" %)
400 (((
401 \\
402 )))|(% colspan="1" %)(% colspan="1" %)
403 (((
404 \\
405 )))|(% colspan="1" %)(% colspan="1" %)
406 (((
407 ukko
408 )))|(% colspan="1" %)(% colspan="1" %)
409 (((
410 \\
411 )))|(% colspan="1" %)(% colspan="1" %)
412 (((
413 \\
414 )))
415
416 = (% style="color: rgb(0,128,0);" %)4.0 Storage and I/O(%%) =
417
418 List of available I/O resources for the users. If a I/O resource is missing from the list, or there are bugs/problems or other concerns, please do contact us through university helpdesk at [[helpdesk (at) helsinki (dot) fi>>mailto:helpdesk@helsinki.fi||shape="rect"]]. We are investing on high performance I/O, and additional computational resources at the moment, and expect a fresh capability to be in production 1Q2019.
419
420 (% class="relative-table wrapped" style="width: 78.8355%;" %)
421 |=(((
422 Actual Path
423 )))|=(% colspan="1" %)(% colspan="1" %)
424 (((
425 Nodes
426 )))|=(((
427 Where
428 )))|=(((
429 How to Access (examples)
430 )))|=(% colspan="1" %)(% colspan="1" %)
431 (((
432 Quota Limit
433 )))|=(% colspan="1" %)(% colspan="1" %)
434 (((
435 Notes
436 )))
437 |(% colspan="1" %)(% colspan="1" %)
438 (((
439 /home/$USER
440 )))|(% colspan="1" %)(% colspan="1" %)
441 (((
442 NFS
443 )))|(% colspan="1" %)(% colspan="1" %)
444 (((
445 ALL
446 )))|(% colspan="1" %)(% colspan="1" %)
447 (((
448 Home directories
449 )))|(% colspan="1" %)(% colspan="1" %)
450 (((
451 Very low
452 )))|(% colspan="1" %)(% colspan="1" %)
453 (((
454 \\
455 )))
456 |(% colspan="1" %)(% colspan="1" %)
457 (((
458 Data Lake
459 )))|(% colspan="1" %)(% colspan="1" %)
460 (((
461 [[Ceph>>url:https://ceph.com||shape="rect"]]
462 )))|(% colspan="1" %)(% colspan="1" %)
463 (((
464 ALL
465 )))|(% colspan="1" %)(% colspan="1" %)
466 (((
467 \\
468 )))|(% colspan="1" %)(% colspan="1" %)
469 (((
470 N/A
471 )))|(% colspan="1" %)(% colspan="1" %)
472 (((
473 \\
474 )))
475 |(% colspan="1" %)(% colspan="1" %)
476 (((
477 /wrk/users/$USER
478 )))|(% colspan="1" %)(% colspan="1" %)
479 (((
480 [[Lustre>>url:http://lustre.org||shape="rect"]]
481
482 (Vakka)
483 )))|(% colspan="1" %)(% colspan="1" %)
484 (((
485 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], (% style="letter-spacing: 0.0px;" %)pangolin, melkki, melkinkari, desktops
486
487 \\
488 )))|(% colspan="1" %)(% colspan="1" %)
489 (((
490 [[User Guide>>doc:it4sci.IT for Science group.HPC Environment User Guide.Lustre User Guide.WebHome]]
491
492 #SBATCH ~-~-workdir=/wrk/users/<username>
493
494 (% style="color: rgb(0,0,0);" %)**Samba desktops**: ukko2-smb.cs.helsinki.fi
495
496 (% style="color: rgb(0,0,0);" %)**pangolin, melkki and melkinkari**: /home/ad/ukko2-wrk/$USER
497 )))|(% colspan="1" %)(% colspan="1" %)
498 (((
499 User quota limit 50T
500 )))|(% colspan="1" %)(% colspan="1" %)
501 (((
502 $WRKDIR
503
504 Capacity: 1.2PB, redundant ZFS backend
505 )))
506 |(% colspan="1" %)(% colspan="1" %)
507 (((
508 /wrk/users/$USER
509 )))|(% colspan="1" %)(% colspan="1" %)
510 (((
511 [[Lustre>>url:http://lustre.org||shape="rect"]]
512
513 (Kappa)
514 )))|(% colspan="1" %)(% colspan="1" %)
515 (((
516 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
517 )))|(% colspan="1" %)(% colspan="1" %)
518 (((
519 Temp directory
520 )))|(% colspan="1" %)(% colspan="1" %)
521 (((
522 \\
523 )))|(% colspan="1" %)(% colspan="1" %)
524 (((
525 $WRKDIR
526
527 Capacity: 750TB, non-redundant, ZFS backend
528 )))
529 |(% colspan="1" %)(% colspan="1" %)
530 (((
531 /proj/$USER
532 )))|(% colspan="1" %)(% colspan="1" %)
533 (((
534 NFS
535 )))|(% colspan="1" %)(% colspan="1" %)
536 (((
537 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], pangolin, melkki, melkinkari, desktops
538 )))|(% colspan="1" %)(% colspan="1" %)
539 (((
540 User application directory for applications, source codes.
541
542 **pangolin, melkki and melkinkari**: /home/ad/turso-proj/$USER\\
543 )))|(% colspan="1" %)(% colspan="1" %)
544 (((
545 20GB
546 )))|(% colspan="1" %)(% colspan="1" %)
547 (((
548 $USERAPPL
549 )))
550 |(% colspan="1" %)(% colspan="1" %)
551 (((
552 /appl/
553 )))|(% colspan="1" %)(% colspan="1" %)
554 (((
555 NFS
556 )))|(% colspan="1" %)(% colspan="1" %)
557 (((
558 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
559 )))|(% colspan="1" %)(% colspan="1" %)
560 (((
561 Global software module repository (RHEL7, CentOS7)
562 )))|(% colspan="1" %)(% colspan="1" %)
563 (((
564 N/A
565 )))|(% colspan="1" %)(% colspan="1" %)
566 (((
567 Read Only
568 )))
569 |(% colspan="1" %)(% colspan="1" %)
570 (((
571 /proj/$USER
572 )))|(% colspan="1" %)(% colspan="1" %)
573 (((
574 NFS
575 )))|(% colspan="1" %)(% colspan="1" %)
576 (((
577 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], pangolin, melkki, melkinkari, desktops
578 )))|(% colspan="1" %)(% colspan="1" %)
579 (((
580 Longer term storage for datasets and results.
581
582 **pangolin, melkki and melkinkari**: /home/ad/turso-proj/$USER
583 )))|(% colspan="1" %)(% colspan="1" %)
584 (((
585 20GB
586 )))|(% colspan="1" %)(% colspan="1" %)
587 (((
588 $PROJ
589 )))
590
591 = (% style="color: rgb(0,128,0);" %)5.0 Licensed Software(%%) =
592
593 We provide licensed software, some which are available also for free for certain users, or user groups. It is advisable to check if you qualify for a free license, if the product information so implies. If the licensed program is not present and you would like it to be included, please do not hesitate to contact us through university helpdesk at [[helpdesk (at) helsinki (dot) fi>>mailto:helpdesk@helsinki.fi||shape="rect"]].
594
595 (% class="wrapped" %)
596 |=(((
597 Name
598 )))|=(((
599 Where
600 )))|=(((
601 How to Access
602 )))|=(% colspan="1" %)(% colspan="1" %)
603 (((
604 Licenses
605 )))
606 |(((
607 [[Comsol>>url:https://www.comsol.com/documentation||shape="rect"]]
608 )))|(((
609 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
610 )))|(((
611 Installed as a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]].
612 )))|(% colspan="1" %)(% colspan="1" %)
613 (((
614 \\
615 )))
616 |(% colspan="1" %)(% colspan="1" %)
617 (((
618 [[Intel C++ compiler>>url:https://software.intel.com/en-us/cpp-compiler-18.0-developer-guide-and-reference||shape="rect"]]
619 )))|(% colspan="1" %)(% colspan="1" %)
620 (((
621 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
622 )))|(% colspan="1" %)(% colspan="1" %)
623 (((
624 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]].
625 )))|(% colspan="1" %)(% colspan="1" %)
626 (((
627 2
628 )))
629 |(% colspan="1" %)(% colspan="1" %)
630 (((
631 [[Intel Fortran>>url:https://software.intel.com/en-us/intel-fortran-compiler-17.0-user-and-reference-guide||shape="rect"]]
632 )))|(% colspan="1" %)(% colspan="1" %)
633 (((
634 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
635 )))|(% colspan="1" %)(% colspan="1" %)
636 (((
637 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]] .
638 )))|(% colspan="1" %)(% colspan="1" %)
639 (((
640 2
641 )))
642 |(% colspan="1" %)(% colspan="1" %)
643 (((
644 [[Intel MKL>>url:https://software.intel.com/en-us/mkl/documentation||shape="rect"]]
645 )))|(% colspan="1" %)(% colspan="1" %)
646 (((
647 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
648 )))|(% colspan="1" %)(% colspan="1" %)
649 (((
650 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]] .
651 )))|(% colspan="1" %)(% colspan="1" %)
652 (((
653 2
654 )))
655 |(% colspan="1" %)(% colspan="1" %)
656 (((
657 [[Intel DAAL>>url:https://software.intel.com/en-us/intel-daal-support/documentation||shape="rect"]]
658 )))|(% colspan="1" %)(% colspan="1" %)
659 (((
660 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
661 )))|(% colspan="1" %)(% colspan="1" %)
662 (((
663 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]] .
664 )))|(% colspan="1" %)(% colspan="1" %)
665 (((
666 2
667 )))
668 |(% colspan="1" %)(% colspan="1" %)
669 (((
670 [[Intel IPP>>url:https://software.intel.com/en-us/intel-ipp/documentation||shape="rect"]]
671 )))|(% colspan="1" %)(% colspan="1" %)
672 (((
673 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
674 )))|(% colspan="1" %)(% colspan="1" %)
675 (((
676 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]] .
677 )))|(% colspan="1" %)(% colspan="1" %)
678 (((
679 2
680 )))
681 |(% colspan="1" %)(% colspan="1" %)
682 (((
683 [[Intel Advisor>>url:https://software.intel.com/en-us/advisor/documentation/get-started||shape="rect"]]
684 )))|(% colspan="1" %)(% colspan="1" %)
685 (((
686 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
687 )))|(% colspan="1" %)(% colspan="1" %)
688 (((
689 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]] .
690 )))|(% colspan="1" %)(% colspan="1" %)
691 (((
692 2
693 )))
694 |(% colspan="1" %)(% colspan="1" %)
695 (((
696 [[Intel Inspector>>url:https://software.intel.com/en-us/intel-inspector-xe-support/documentation||shape="rect"]]
697 )))|(% colspan="1" %)(% colspan="1" %)
698 (((
699 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
700 )))|(% colspan="1" %)(% colspan="1" %)
701 (((
702 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]] .
703 )))|(% colspan="1" %)(% colspan="1" %)
704 (((
705 2
706 )))
707 |(% colspan="1" %)(% colspan="1" %)
708 (((
709 [[Intel MPI>>url:https://software.intel.com/en-us/intel-mpi-library/documentation||shape="rect"]]
710 )))|(% colspan="1" %)(% colspan="1" %)
711 (((
712 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
713 )))|(% colspan="1" %)(% colspan="1" %)
714 (((
715 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]] .
716 )))|(% colspan="1" %)(% colspan="1" %)
717 (((
718 2
719 )))
720 |(% colspan="1" %)(% colspan="1" %)
721 (((
722 [[Intel VTune Amplifier>>url:https://software.intel.com/en-us/vtune-amplifier-help||shape="rect"]]
723 )))|(% colspan="1" %)(% colspan="1" %)
724 (((
725 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
726 )))|(% colspan="1" %)(% colspan="1" %)
727 (((
728 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]] .
729 )))|(% colspan="1" %)(% colspan="1" %)
730 (((
731 2
732 )))
733 |(% colspan="1" %)(% colspan="1" %)
734 (((
735 [[Intel Trace Analyzer>>url:https://software.intel.com/en-us/intel-trace-analyzer/documentation||shape="rect"]]
736 )))|(% colspan="1" %)(% colspan="1" %)
737 (((
738 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
739 )))|(% colspan="1" %)(% colspan="1" %)
740 (((
741 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]] .
742 )))|(% colspan="1" %)(% colspan="1" %)
743 (((
744 2
745 )))
746 |(% colspan="1" %)(% colspan="1" %)
747 (((
748 [[Intel Distribution for Python>>url:https://software.intel.com/en-us/distribution-for-python/documentation||shape="rect"]]
749 )))|(% colspan="1" %)(% colspan="1" %)
750 (((
751 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
752 )))|(% colspan="1" %)(% colspan="1" %)
753 (((
754 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]] .
755 )))|(% colspan="1" %)(% colspan="1" %)
756 (((
757 2
758 )))
759 |(% colspan="1" %)(% colspan="1" %)
760 (((
761 [[Intel Cluster Checker>>url:https://software.intel.com/en-us/intel-cluster-checker||shape="rect"]]
762 )))|(% colspan="1" %)(% colspan="1" %)
763 (((
764 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
765 )))|(% colspan="1" %)(% colspan="1" %)
766 (((
767 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters, [[Check eligibility for a free license>>url:https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries||shape="rect"]] .
768 )))|(% colspan="1" %)(% colspan="1" %)
769 (((
770 2
771 )))
772 |(((
773 [[Matlab>>url:https://se.mathworks.com/help/matlab/||shape="rect"]]
774 )))|(((
775 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[doc:Cubbli.User documentation.WebHome]], Desktop
776 )))|(((
777 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
778 )))|(% colspan="1" %)(% colspan="1" %)
779 (((
780 TAC
781 )))
782 |(% colspan="1" %)(% colspan="1" %)
783 (((
784 IBM ILOC CPEX
785 )))|(% colspan="1" %)(% colspan="1" %)
786 (((
787 \\
788 )))|(% colspan="1" %)(% colspan="1" %)
789 (((
790 [[Check eligibility for a free license>>url:https://www.ibm.com/developerworks/community/blogs/jfp/entry/CPLEX_Is_Free_For_Students||shape="rect"]]
791 )))|(% colspan="1" %)(% colspan="1" %)
792 (((
793 \\
794 )))
795 |(% colspan="1" %)(% colspan="1" %)
796 (((
797 [[Mathematica>>url:https://www.wolfram.com/mathematica/||shape="rect"]]
798 )))|(% colspan="1" %)(% colspan="1" %)
799 (((
800 [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
801 )))|(% colspan="1" %)(% colspan="1" %)
802 (((
803 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
804 )))|(% colspan="1" %)(% colspan="1" %)
805 (((
806 (% style="color: rgb(255,0,0);" %)Commercial?
807 )))
808 |(% colspan="1" %)(% colspan="1" %)
809 (((
810 [[ARCGIS>>url:https://www.arcgis.com/features/index.html||shape="rect"]]
811 )))|(% colspan="1" %)(% colspan="1" %)
812 (((
813 \\
814 )))|(% colspan="1" %)(% colspan="1" %)
815 (((
816 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
817 )))|(% colspan="1" %)(% colspan="1" %)
818 (((
819 (% style="color: rgb(255,0,0);" %)Commercial?
820 )))
821 |(% colspan="1" %)(% colspan="1" %)
822 (((
823 [[IDRISI>>url:https://clarklabs.org/terrset/idrisi-gis/||shape="rect"]]
824 )))|(% colspan="1" %)(% colspan="1" %)
825 (((
826 \\
827 )))|(% colspan="1" %)(% colspan="1" %)
828 (((
829 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
830 )))|(% colspan="1" %)(% colspan="1" %)
831 (((
832 (% style="color: rgb(255,0,0);" %)Commercial?
833 )))
834 |(% colspan="1" %)(% colspan="1" %)
835 (((
836 [[MAPINFO>>url:https://www.pitneybowes.com/us/location-intelligence/geographic-information-systems/mapinfo-pro.html||shape="rect"]]
837 )))|(% colspan="1" %)(% colspan="1" %)
838 (((
839 \\
840 )))|(% colspan="1" %)(% colspan="1" %)
841 (((
842 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
843 )))|(% colspan="1" %)(% colspan="1" %)
844 (((
845 (% style="color: rgb(255,0,0);" %)Commercial?
846 )))
847
848 = (% style="color: rgb(0, 128, 0); font-size: x-large; text-transform: uppercase" %)6.0 Open Source Software & Libraries(%%) =
849
850 This list includes most of the special scientific software packages, tools and specialized libraries made available by IT4SciFi. Items on this list have multiple versions available on the clusters and different versions cam be managed with [[Modules>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]]. If the utility, tool, library or program, or specific version is not present and you would like it to be included, please do not hesitate to contact us through university helpdesk at [[helpdesk (at) helsinki (dot) fi>>mailto:helpdesk@helsinki.fi||shape="rect"]].
851
852 You can also create modules for of your own software and then share it conveniently within the research group if you like. We have [[brief instructions here>>url:https://wiki.helsinki.fi/display/it4sci/Module+System#ModuleSystem-1.2Creatingmodulesforyourownsoftware||shape="rect"]].
853
854 All system and development libraries are present on the computational environment by default, and therefore not included in the list - except where tools are installed as modules in the HPC environment.
855
856 === Aalto software modules ===
857
858 You are also eligible to use software module from Aalto univerisity. However these are not defaulted because the module list would be very long. To have Aalto modules included, please add modules:
859
860 \\
861
862 {{{module use /cvmfs/fgi.csc.fi/apps/el7/aalto/spack/lmod/linux-centos7-x86_64/allmodule use /cvmfs/fgi.csc.fi/apps/el7/aalto/spack/lmod/linux-centos7-westmere/all/}}}
863
864 === Local software modules ===
865
866 (% class="relative-table wrapped" style="width: 70.72691%;" %)
867 |=(((
868 Name
869 )))|=(((
870 Where Available
871 )))|=(((
872 How to Access
873 )))|=(% colspan="1" %)(% colspan="1" %)
874 (((
875 Tutorials & Use Cases
876 )))
877 |(% colspan="1" %)(% colspan="1" %)
878 (((
879 AOCC
880 )))|(% colspan="1" %)(% colspan="1" %)
881 (((
882 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
883 )))|(% colspan="1" %)(% colspan="1" %)
884 (((
885 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
886 )))|(% colspan="1" %)(% colspan="1" %)
887 (((
888 AMD Compiler Suite
889 )))
890 |(((
891 [[TensorFlow>>url:https://www.tensorflow.org||shape="rect"]]
892 )))|(((
893 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
894 )))|(((
895 Through [[Python Virtualenv>>doc:it4sci.IT for Science group.Internal Documentation.HPC Environment.Archive.OBSOLETE - Ukko2 User Guide.OBSOLETE - Scientific Software FAQ.WebHome]]
896 )))|(% colspan="1" %)(% colspan="1" %)
897 (((
898 [[Basic Tutorials>>url:https://www.datacamp.com/community/tutorials/tensorflow-tutorial#basics||shape="rect"]]
899 )))
900 |(% colspan="1" %)(% colspan="1" %)
901 (((
902 [[Keras>>url:https://keras.io||shape="rect"]]
903 )))|(% colspan="1" %)(% colspan="1" %)
904 (((
905 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
906 )))|(% colspan="1" %)(% colspan="1" %)
907 (((
908 Through [[Python Virtualenv>>doc:it4sci.IT for Science group.Internal Documentation.HPC Environment.Archive.OBSOLETE - Ukko2 User Guide.OBSOLETE - Scientific Software FAQ.WebHome]]
909 )))|(% colspan="1" %)(% colspan="1" %)
910 (((
911 [[Tutorial>>url:https://elitedatascience.com/keras-tutorial-deep-learning-in-python||shape="rect"]]
912
913 [[Keras model into Tensorflow>>url:https://js.tensorflow.org/tutorials/import-keras.html||shape="rect"]]
914
915 [[Practical use case>>url:https://www.kdnuggets.com/2017/11/understanding-deep-convolutional-neural-networks-tensorflow-keras.html||style="text-decoration: underline;" shape="rect"]]
916 )))
917 |(((
918 [[CUDA>>url:https://developer.nvidia.com/cuda-zone||shape="rect"]]
919 )))|(((
920 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
921 )))|(((
922 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
923
924 Cubbli default\\
925 )))|(% colspan="1" %)(% colspan="1" %)
926 (((
927 [[GPU Tutorials>>url:https://devblogs.nvidia.com/even-easier-introduction-cuda/||shape="rect"]]
928 )))
929 |(((
930 [[CudNN>>url:https://developer.nvidia.com/cudnn||style="text-decoration: underline;" shape="rect"]]
931 )))|(((
932 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
933 )))|(((
934 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
935 )))|(% colspan="1" %)(% colspan="1" %)
936 (((
937 [[Convolutions tutorial>>url:http://www.goldsborough.me/cuda/ml/cudnn/c++/2017/10/01/14-37-23-convolutions_with_cudnn/||shape="rect"]]
938 )))
939 |(% colspan="1" %)(% colspan="1" %)
940 (((
941 [[AMBER>>url:http://ambermd.org||shape="rect"]]
942 )))|(% colspan="1" %)(% colspan="1" %)
943 (((
944 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
945 )))|(% colspan="1" %)(% colspan="1" %)
946 (((
947 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
948 )))|(% colspan="1" %)(% colspan="1" %)
949 (((
950 Molecular simulation toolkit
951 )))
952 |(% colspan="1" %)(% colspan="1" %)
953 (((
954 [[GROMACS>>url:http://manual.gromacs.org/documentation/||shape="rect"]]
955 )))|(% colspan="1" %)(% colspan="1" %)
956 (((
957 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
958 )))|(% colspan="1" %)(% colspan="1" %)
959 (((
960 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
961 )))|(% colspan="1" %)(% colspan="1" %)
962 (((
963 [[G>>url:http://www.mdtutorials.com/gmx/||shape="rect"]] [[romacs tutorials>>url:http://www.mdtutorials.com/gmx/||shape="rect"]], (% style="color: rgb(33,33,33);" %)GROMACS/2018.3-fosscuda-2018b with GPU support.
964 )))
965 |(% colspan="1" %)(% colspan="1" %)
966 (((
967 [[OpenBLAS>>url:https://github.com/xianyi/OpenBLAS/wiki/User-Manual||shape="rect"]]
968 )))|(% colspan="1" %)(% colspan="1" %)
969 (((
970 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
971 )))|(% colspan="1" %)(% colspan="1" %)
972 (((
973 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
974 )))|(% colspan="1" %)(% colspan="1" %)
975 (((
976 \\
977 )))
978 |(% colspan="1" %)(% colspan="1" %)
979 (((
980 [[OpenMPI>>url:https://www.open-mpi.org/doc/||shape="rect"]]
981 )))|(% colspan="1" %)(% colspan="1" %)
982 (((
983 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
984 )))|(% colspan="1" %)(% colspan="1" %)
985 (((
986 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
987 )))|(% colspan="1" %)(% colspan="1" %)
988 (((
989 [[Tutorial>>url:https://www.open-mpi.org/papers/sc-2009/jjhursey-iu-booth.pdf||shape="rect"]]
990
991 [[Tutorial>>url:https://computing.llnl.gov/tutorials/mpi/||shape="rect"]]
992 )))
993 |(% colspan="1" %)(% colspan="1" %)
994 (((
995 [[OpenFOAM>>url:https://www.openfoam.com||shape="rect"]]
996 )))|(% colspan="1" %)(% colspan="1" %)
997 (((
998 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
999 )))|(% colspan="1" %)(% colspan="1" %)
1000 (((
1001 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1002 )))|(% colspan="1" %)(% colspan="1" %)
1003 (((
1004 [[Tutorial>>url:https://www.researchgate.net/publication/282272911_OpenFOAM_step_by_step_tutorial_%27beginners%27_version||shape="rect"]]
1005 )))
1006 |(% colspan="1" %)(% colspan="1" %)
1007 (((
1008 [[Python>>url:https://www.python.org/doc/||shape="rect"]]
1009 )))|(% colspan="1" %)(% colspan="1" %)
1010 (((
1011 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1012 )))|(% colspan="1" %)(% colspan="1" %)
1013 (((
1014 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1015 )))|(% colspan="1" %)(% colspan="1" %)
1016 (((
1017 \\
1018 )))
1019 |(% colspan="1" %)(% colspan="1" %)
1020 (((
1021 [[GCC>>url:https://gcc.gnu.org/||shape="rect"]]
1022 )))|(% colspan="1" %)(% colspan="1" %)
1023 (((
1024 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
1025 )))|(% colspan="1" %)(% colspan="1" %)
1026 (((
1027 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1028
1029 Cubbli default\\
1030 )))|(% colspan="1" %)(% colspan="1" %)
1031 (((
1032 GNU Compiler Collection
1033 )))
1034 |(% colspan="1" %)(% colspan="1" %)
1035 (((
1036 Java
1037 )))|(% colspan="1" %)(% colspan="1" %)
1038 (((
1039 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
1040 )))|(% colspan="1" %)(% colspan="1" %)
1041 (((
1042 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1043
1044 Cubbli default\\
1045 )))|(% colspan="1" %)(% colspan="1" %)
1046 (((
1047 \\
1048 )))
1049 |(% colspan="1" %)(% colspan="1" %)
1050 (((
1051 [[Bison>>url:https://www.gnu.org/software/bison/manual/||shape="rect"]]
1052 )))|(% colspan="1" %)(% colspan="1" %)
1053 (((
1054 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1055 )))|(% colspan="1" %)(% colspan="1" %)
1056 (((
1057 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1058 )))|(% colspan="1" %)(% colspan="1" %)
1059 (((
1060 \\
1061 )))
1062 |(% colspan="1" %)(% colspan="1" %)
1063 (((
1064 [[Dalton>>url:http://daltonprogram.org/documentation/||shape="rect"]]
1065 )))|(% colspan="1" %)(% colspan="1" %)
1066 (((
1067 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1068 )))|(% colspan="1" %)(% colspan="1" %)
1069 (((
1070 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1071 )))|(% colspan="1" %)(% colspan="1" %)
1072 (((
1073 \\
1074 )))
1075 |(% colspan="1" %)(% colspan="1" %)
1076 (((
1077 [[MVAPICH>>url:http://mvapich.cse.ohio-state.edu/||shape="rect"]]
1078 )))|(% colspan="1" %)(% colspan="1" %)
1079 (((
1080 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1081 )))|(% colspan="1" %)(% colspan="1" %)
1082 (((
1083 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1084 )))|(% colspan="1" %)(% colspan="1" %)
1085 (((
1086 [[MVAPICH tutorials>>url:https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=5&ved=0ahUKEwjd8p-d-qDbAhWjQpoKHTztCc0QFghRMAQ&url=https%3A%2F%2Fcomputing.llnl.gov%2Ftutorials%2Flinux_clusters%2Fmvapich_user_guide_1.2.pdf&usg=AOvVaw3gv3FRh0ox-WHPozhoNiiU||shape="rect"]]
1087 )))
1088 |(% colspan="1" %)(% colspan="1" %)
1089 (((
1090 [[Molden>>url:http://www.cmbi.ru.nl/molden/||shape="rect"]]
1091 )))|(% colspan="1" %)(% colspan="1" %)
1092 (((
1093 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1094 )))|(% colspan="1" %)(% colspan="1" %)
1095 (((
1096 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1097 )))|(% colspan="1" %)(% colspan="1" %)
1098 (((
1099 Molecular Structure Analysis
1100 )))
1101 |(% colspan="1" %)(% colspan="1" %)
1102 (((
1103 [[ORCA>>url:https://orcaforum.cec.mpg.de/||shape="rect"]]
1104 )))|(% colspan="1" %)(% colspan="1" %)
1105 (((
1106 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1107 )))|(% colspan="1" %)(% colspan="1" %)
1108 (((
1109 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1110 )))|(% colspan="1" %)(% colspan="1" %)
1111 (((
1112 Quantum Chemistry
1113 )))
1114 |(% colspan="1" %)(% colspan="1" %)
1115 (((
1116 [[Perl>>url:https://perldoc.perl.org||shape="rect"]]
1117 )))|(% colspan="1" %)(% colspan="1" %)
1118 (((
1119 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]], [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
1120 )))|(% colspan="1" %)(% colspan="1" %)
1121 (((
1122 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1123
1124 Cubbli default\\
1125 )))|(% colspan="1" %)(% colspan="1" %)
1126 (((
1127 \\
1128 )))
1129 |(% colspan="1" %)(% colspan="1" %)
1130 (((
1131 [[ScaLAPACK>>url:http://www.netlib.org/scalapack/#_documentation||shape="rect"]]
1132 )))|(% colspan="1" %)(% colspan="1" %)
1133 (((
1134 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1135 )))|(% colspan="1" %)(% colspan="1" %)
1136 (((
1137 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1138 )))|(% colspan="1" %)(% colspan="1" %)
1139 (((
1140 \\
1141 )))
1142 |(% colspan="1" %)(% colspan="1" %)
1143 (((
1144 GMP
1145 )))|(% colspan="1" %)(% colspan="1" %)
1146 (((
1147 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1148 )))|(% colspan="1" %)(% colspan="1" %)
1149 (((
1150 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1151 )))|(% colspan="1" %)(% colspan="1" %)
1152 (((
1153 \\
1154 )))
1155 |(% colspan="1" %)(% colspan="1" %)
1156 (((
1157 [[NASM>>url:https://www.nasm.us/index.php||shape="rect"]]
1158 )))|(% colspan="1" %)(% colspan="1" %)
1159 (((
1160 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1161 )))|(% colspan="1" %)(% colspan="1" %)
1162 (((
1163 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1164 )))|(% colspan="1" %)(% colspan="1" %)
1165 (((
1166 \\
1167 )))
1168 |(% colspan="1" %)(% colspan="1" %)
1169 (((
1170 [[Mesa>>url:https://github.com/projectmesa/mesa||shape="rect"]]
1171 )))|(% colspan="1" %)(% colspan="1" %)
1172 (((
1173 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1174 )))|(% colspan="1" %)(% colspan="1" %)
1175 (((
1176 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1177 )))|(% colspan="1" %)(% colspan="1" %)
1178 (((
1179 \\
1180 )))
1181 |(% colspan="1" %)(% colspan="1" %)
1182 (((
1183 Mako
1184 )))|(% colspan="1" %)(% colspan="1" %)
1185 (((
1186 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1187 )))|(% colspan="1" %)(% colspan="1" %)
1188 (((
1189 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1190 )))|(% colspan="1" %)(% colspan="1" %)
1191 (((
1192 \\
1193 )))
1194 |(% colspan="1" %)(% colspan="1" %)
1195 (((
1196 [[R>>url:https://cran.r-project.org/manuals.html||shape="rect"]]
1197 )))|(% colspan="1" %)(% colspan="1" %)
1198 (((
1199 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1200 )))|(% colspan="1" %)(% colspan="1" %)
1201 (((
1202 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1203 )))|(% colspan="1" %)(% colspan="1" %)
1204 (((
1205 [[R Tutorials>>url:https://www.statmethods.net/r-tutorial/index.html||shape="rect"]]
1206 )))
1207 |(% colspan="1" %)(% colspan="1" %)
1208 (((
1209 [[R-Studio>>url:https://www.rstudio.com/||shape="rect"]]
1210 )))|(% colspan="1" %)(% colspan="1" %)
1211 (((
1212 [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
1213 )))|(% colspan="1" %)(% colspan="1" %)
1214 (((
1215 Cubbli default
1216 )))|(% colspan="1" %)(% colspan="1" %)
1217 (((
1218 \\
1219 )))
1220 |(% colspan="1" %)(% colspan="1" %)
1221 (((
1222 [[GNU Octave>>url:https://www.gnu.org/software/octave/||shape="rect"]]
1223 )))|(% colspan="1" %)(% colspan="1" %)
1224 (((
1225 [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
1226 )))|(% colspan="1" %)(% colspan="1" %)
1227 (((
1228 Cubbli default
1229 )))|(% colspan="1" %)(% colspan="1" %)
1230 (((
1231 \\
1232 )))
1233 |(% colspan="1" %)(% colspan="1" %)
1234 (((
1235 [[FreeSurfer>>url:https://surfer.nmr.mgh.harvard.edu/||shape="rect"]]
1236 )))|(% colspan="1" %)(% colspan="1" %)
1237 (((
1238 [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
1239 )))|(% colspan="1" %)(% colspan="1" %)
1240 (((
1241 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
1242 )))|(% colspan="1" %)(% colspan="1" %)
1243 (((
1244 MRI Imaging
1245 )))
1246 |(% colspan="1" %)(% colspan="1" %)
1247 (((
1248 [[NoMachine client>>url:https://www.nomachine.com/||shape="rect"]]
1249 )))|(% colspan="1" %)(% colspan="1" %)
1250 (((
1251 [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
1252 )))|(% colspan="1" %)(% colspan="1" %)
1253 (((
1254 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
1255 )))|(% colspan="1" %)(% colspan="1" %)
1256 (((
1257 \\
1258 )))
1259 |(% colspan="1" %)(% colspan="1" %)
1260 (((
1261 [[VMD>>url:http://www.ks.uiuc.edu/Research/vmd/||shape="rect"]]
1262 )))|(% colspan="1" %)(% colspan="1" %)
1263 (((
1264 [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
1265 )))|(% colspan="1" %)(% colspan="1" %)
1266 (((
1267 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
1268 )))|(% colspan="1" %)(% colspan="1" %)
1269 (((
1270 Molecular Dynamics
1271 )))
1272 |(% colspan="1" %)(% colspan="1" %)
1273 (((
1274 [[PCRE>>url:https://www.pcre.org/||shape="rect"]]
1275 )))|(% colspan="1" %)(% colspan="1" %)
1276 (((
1277 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1278 )))|(% colspan="1" %)(% colspan="1" %)
1279 (((
1280 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1281 )))|(% colspan="1" %)(% colspan="1" %)
1282 (((
1283 \\
1284 )))
1285 |(% colspan="1" %)(% colspan="1" %)
1286 (((
1287 OpenPGM
1288 )))|(% colspan="1" %)(% colspan="1" %)
1289 (((
1290 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1291 )))|(% colspan="1" %)(% colspan="1" %)
1292 (((
1293 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1294 )))|(% colspan="1" %)(% colspan="1" %)
1295 (((
1296 \\
1297 )))
1298 |(% colspan="1" %)(% colspan="1" %)
1299 (((
1300 [[PyZMQ>>url:https://pyzmq.readthedocs.io/en/latest/||shape="rect"]]
1301 )))|(% colspan="1" %)(% colspan="1" %)
1302 (((
1303 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1304 )))|(% colspan="1" %)(% colspan="1" %)
1305 (((
1306 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1307 )))|(% colspan="1" %)(% colspan="1" %)
1308 (((
1309 \\
1310 )))
1311 |(% colspan="1" %)(% colspan="1" %)
1312 (((
1313 [[IPython>>url:https://ipython.org/ipython-doc/3/index.html||shape="rect"]]
1314 )))|(% colspan="1" %)(% colspan="1" %)
1315 (((
1316 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1317 )))|(% colspan="1" %)(% colspan="1" %)
1318 (((
1319 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1320 )))|(% colspan="1" %)(% colspan="1" %)
1321 (((
1322 [[Jupyter Notebook>>doc:it4sci.IT for Science group.HPC Environment User Guide.Jupyter Hub User Guide.WebHome]]
1323 )))
1324 |(% colspan="1" %)(% colspan="1" %)
1325 (((
1326 [[ZeroMQ>>url:http://zeromq.org/intro:read-the-manual||shape="rect"]]
1327 )))|(% colspan="1" %)(% colspan="1" %)
1328 (((
1329 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1330 )))|(% colspan="1" %)(% colspan="1" %)
1331 (((
1332 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1333 )))|(% colspan="1" %)(% colspan="1" %)
1334 (((
1335 \\
1336 )))
1337 |(% colspan="1" %)(% colspan="1" %)
1338 (((
1339 XZ
1340 )))|(% colspan="1" %)(% colspan="1" %)
1341 (((
1342 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1343 )))|(% colspan="1" %)(% colspan="1" %)
1344 (((
1345 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1346 )))|(% colspan="1" %)(% colspan="1" %)
1347 (((
1348 \\
1349 )))
1350 |(% colspan="1" %)(% colspan="1" %)
1351 (((
1352 [[Valgrind>>url:http://valgrind.org||shape="rect"]]
1353 )))|(% colspan="1" %)(% colspan="1" %)
1354 (((
1355 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1356 )))|(% colspan="1" %)(% colspan="1" %)
1357 (((
1358 System Package
1359 )))|(% colspan="1" %)(% colspan="1" %)
1360 (((
1361 [[Small tutorial>>url:http://www.st.ewi.tudelft.nl/koen/ti2725-c/valgrind.pdf||shape="rect"]]
1362 )))
1363 |(% colspan="1" %)(% colspan="1" %)
1364 (((
1365 Valgrind-openmpi
1366 )))|(% colspan="1" %)(% colspan="1" %)
1367 (((
1368 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1369 )))|(% colspan="1" %)(% colspan="1" %)
1370 (((
1371 System Package
1372 )))|(% colspan="1" %)(% colspan="1" %)
1373 (((
1374 [[Resources for OpenMPI debugging>>url:https://www.open-mpi.org/faq/?category=debugging||shape="rect"]]
1375 )))
1376 |(% colspan="1" %)(% colspan="1" %)
1377 (((
1378 [[v8>>url:https://www.r-bloggers.com/introducing-v8-an-embedded-javascript-engine-for-r/||shape="rect"]]
1379 )))|(% colspan="1" %)(% colspan="1" %)
1380 (((
1381 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1382 )))|(% colspan="1" %)(% colspan="1" %)
1383 (((
1384 System Package
1385 )))|(% colspan="1" %)(% colspan="1" %)
1386 (((
1387 v8 Development Library
1388 )))
1389 |(% colspan="1" %)(% colspan="1" %)
1390 (((
1391 [[LLVM>>url:https://llvm.org/||shape="rect"]]
1392 )))|(% colspan="1" %)(% colspan="1" %)
1393 (((
1394 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1395 )))|(% colspan="1" %)(% colspan="1" %)
1396 (((
1397 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1398 )))|(% colspan="1" %)(% colspan="1" %)
1399 (((
1400 \\
1401 )))
1402 |(% colspan="1" %)(% colspan="1" %)
1403 (((
1404 [[NLopt>>url:https://nlopt.readthedocs.io/en/latest/||shape="rect"]]
1405 )))|(% colspan="1" %)(% colspan="1" %)
1406 (((
1407 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1408 )))|(% colspan="1" %)(% colspan="1" %)
1409 (((
1410 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1411 )))|(% colspan="1" %)(% colspan="1" %)
1412 (((
1413 \\
1414 )))
1415 |(% colspan="1" %)(% colspan="1" %)
1416 (((
1417 [[M4>>url:http://www.gnu.org/software/m4/m4.html||shape="rect"]]
1418 )))|(% colspan="1" %)(% colspan="1" %)
1419 (((
1420 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1421 )))|(% colspan="1" %)(% colspan="1" %)
1422 (((
1423 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1424 )))|(% colspan="1" %)(% colspan="1" %)
1425 (((
1426 \\
1427 )))
1428 |(% colspan="1" %)(% colspan="1" %)
1429 (((
1430 [[GDAL>>url:http://www.gdal.org/||shape="rect"]]
1431 )))|(% colspan="1" %)(% colspan="1" %)
1432 (((
1433 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1434 )))|(% colspan="1" %)(% colspan="1" %)
1435 (((
1436 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1437 )))|(% colspan="1" %)(% colspan="1" %)
1438 (((
1439 (% style="color: rgb(0,0,0);" %)Geospatial Data Abstraction Library
1440 )))
1441 |(% colspan="1" %)(% colspan="1" %)
1442 (((
1443 [[HDF5>>url:https://support.hdfgroup.org/HDF5/doc/||shape="rect"]]
1444 )))|(% colspan="1" %)(% colspan="1" %)
1445 (((
1446 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1447 )))|(% colspan="1" %)(% colspan="1" %)
1448 (((
1449 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1450 )))|(% colspan="1" %)(% colspan="1" %)
1451 (((
1452 \\
1453 )))
1454 |(% colspan="1" %)(% colspan="1" %)
1455 (((
1456 [[H5py>>url:https://www.h5py.org||shape="rect"]]
1457 )))|(% colspan="1" %)(% colspan="1" %)
1458 (((
1459 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1460 )))|(% colspan="1" %)(% colspan="1" %)
1461 (((
1462 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1463 )))|(% colspan="1" %)(% colspan="1" %)
1464 (((
1465 \\
1466 )))
1467 |(% colspan="1" %)(% colspan="1" %)
1468 (((
1469 [[FFTW>>url:http://www.fftw.org/#documentation||shape="rect"]]
1470 )))|(% colspan="1" %)(% colspan="1" %)
1471 (((
1472 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1473 )))|(% colspan="1" %)(% colspan="1" %)
1474 (((
1475 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1476 )))|(% colspan="1" %)(% colspan="1" %)
1477 (((
1478 C subroutine library for discrete Fourier transform
1479 )))
1480 |(% colspan="1" %)(% colspan="1" %)
1481 (((
1482 [[Spark>>url:https://spark.apache.org/documentation.html||shape="rect"]]
1483 )))|(% colspan="1" %)(% colspan="1" %)
1484 (((
1485 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1486 )))|(% colspan="1" %)(% colspan="1" %)
1487 (((
1488 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1489 )))|(% colspan="1" %)(% colspan="1" %)
1490 (((
1491 [[HY User Guide>>doc:it4sci.IT for Science group.Internal Documentation.HPC Environment.Archive.OBSOLETE - Ukko2 User Guide.OBSOLETE - Spark User Guide.WebHome]]
1492 )))
1493 |(% colspan="1" %)(% colspan="1" %)
1494 (((
1495 [[Fortran>>url:http://www.fortran90.org||shape="rect"]]
1496 )))|(% colspan="1" %)(% colspan="1" %)
1497 (((
1498 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1499 )))|(% colspan="1" %)(% colspan="1" %)
1500 (((
1501 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1502 )))|(% colspan="1" %)(% colspan="1" %)
1503 (((
1504 \\
1505 )))
1506 |(% colspan="1" %)(% colspan="1" %)
1507 (((
1508 [[Julia>>url:https://julialang.org/||shape="rect"]]
1509 )))|(% colspan="1" %)(% colspan="1" %)
1510 (((
1511 [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
1512 )))|(% colspan="1" %)(% colspan="1" %)
1513 (((
1514 Cubbli default
1515 )))|(% colspan="1" %)(% colspan="1" %)
1516 (((
1517 [[Data science tutorial>>url:https://www.analyticsvidhya.com/blog/2017/10/comprehensive-tutorial-learn-data-science-julia-from-scratch/||shape="rect"]]
1518
1519 [[Julia on HPC environment>>url:http://www.stochasticlifestyle.com/multi-node-parallelism-in-julia-on-an-hpc/||shape="rect"]]
1520 )))
1521 |(% colspan="1" %)(% colspan="1" %)
1522 (((
1523 [[Haskell>>url:https://www.haskell.org/||shape="rect"]]
1524 )))|(% colspan="1" %)(% colspan="1" %)
1525 (((
1526 [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
1527 )))|(% colspan="1" %)(% colspan="1" %)
1528 (((
1529 Cubbli default
1530 )))|(% colspan="1" %)(% colspan="1" %)
1531 (((
1532 \\
1533 )))
1534 |(% colspan="1" %)(% colspan="1" %)
1535 (((
1536 Oracle JDK
1537 )))|(% colspan="1" %)(% colspan="1" %)
1538 (((
1539 [[Cubbli>>doc:Cubbli.User documentation.WebHome]]
1540 )))|(% colspan="1" %)(% colspan="1" %)
1541 (((
1542 Cubbli default
1543 )))|(% colspan="1" %)(% colspan="1" %)
1544 (((
1545 \\
1546 )))
1547 |(% colspan="1" %)(% colspan="1" %)
1548 (((
1549 [[Tcl/tk>>url:https://www.tcl.tk/doc/||shape="rect"]]
1550 )))|(% colspan="1" %)(% colspan="1" %)
1551 (((
1552 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1553 )))|(% colspan="1" %)(% colspan="1" %)
1554 (((
1555 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1556 )))|(% colspan="1" %)(% colspan="1" %)
1557 (((
1558 \\
1559 )))
1560 |(% colspan="1" %)(% colspan="1" %)
1561 (((
1562 [[SHRiMP>>url:http://compbio.cs.toronto.edu/shrimp/||shape="rect"]]
1563 )))|(% colspan="1" %)(% colspan="1" %)
1564 (((
1565 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1566 )))|(% colspan="1" %)(% colspan="1" %)
1567 (((
1568 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1569 )))|(% colspan="1" %)(% colspan="1" %)
1570 (((
1571 \\
1572 )))
1573 |(% colspan="1" %)(% colspan="1" %)
1574 (((
1575 [[GPAW>>url:https://wiki.fysik.dtu.dk/gpaw/||shape="rect"]]
1576 )))|(% colspan="1" %)(% colspan="1" %)
1577 (((
1578 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1579 )))|(% colspan="1" %)(% colspan="1" %)
1580 (((
1581 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1582 )))|(% colspan="1" %)(% colspan="1" %)
1583 (((
1584 \\
1585 )))
1586 |(% colspan="1" %)(% colspan="1" %)
1587 (((
1588 [[BLAST+>>url:https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download||shape="rect"]]
1589 )))|(% colspan="1" %)(% colspan="1" %)
1590 (((
1591 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1592 )))|(% colspan="1" %)(% colspan="1" %)
1593 (((
1594 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1595 )))|(% colspan="1" %)(% colspan="1" %)
1596 (((
1597 \\
1598 )))
1599 |(% colspan="1" %)(% colspan="1" %)
1600 (((
1601 [[ASE>>url:https://wiki.fysik.dtu.dk/ase/||shape="rect"]]
1602 )))|(% colspan="1" %)(% colspan="1" %)
1603 (((
1604 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1605 )))|(% colspan="1" %)(% colspan="1" %)
1606 (((
1607 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1608 )))|(% colspan="1" %)(% colspan="1" %)
1609 (((
1610 \\
1611 )))
1612 |(% colspan="1" %)(% colspan="1" %)
1613 (((
1614 [[LAMMPS>>url:http://lammps.sandia.gov||shape="rect"]]
1615 )))|(% colspan="1" %)(% colspan="1" %)
1616 (((
1617 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1618 )))|(% colspan="1" %)(% colspan="1" %)
1619 (((
1620 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1621 )))|(% colspan="1" %)(% colspan="1" %)
1622 (((
1623 \\
1624 )))
1625 |(% colspan="1" %)(% colspan="1" %)
1626 (((
1627 [[Geant4>>url:https://www.sciencedirect.com/science/article/pii/S0168900203013688||shape="rect"]]
1628 )))|(% colspan="1" %)(% colspan="1" %)
1629 (((
1630 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1631 )))|(% colspan="1" %)(% colspan="1" %)
1632 (((
1633 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1634 )))|(% colspan="1" %)(% colspan="1" %)
1635 (((
1636 \\
1637 )))
1638 |(% colspan="1" %)(% colspan="1" %)
1639 (((
1640 SQLite
1641 )))|(% colspan="1" %)(% colspan="1" %)
1642 (((
1643 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1644 )))|(% colspan="1" %)(% colspan="1" %)
1645 (((
1646 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1647 )))|(% colspan="1" %)(% colspan="1" %)
1648 (((
1649 \\
1650 )))
1651 |(% colspan="1" %)(% colspan="1" %)
1652 (((
1653 [[NumPy>>url:http://www.numpy.org||shape="rect"]]
1654 )))|(% colspan="1" %)(% colspan="1" %)
1655 (((
1656 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1657 )))|(% colspan="1" %)(% colspan="1" %)
1658 (((
1659 As a [[module>>doc:it4sci.IT for Science group.HPC Environment User Guide.Module System.WebHome]] in clusters.
1660 )))|(% colspan="1" %)(% colspan="1" %)
1661 (((
1662 [[Julia vs. Python performance>>url:https://www.ibm.com/developerworks/community/blogs/jfp/entry/A_Comparison_Of_C_Julia_Python_Numba_Cython_Scipy_and_BLAS_on_LU_Factorization?lang=en||shape="rect"]]
1663 )))
1664 |(% colspan="1" %)(% colspan="1" %)
1665 (((
1666 [[Scilab>>url:https://www.scilab.org||shape="rect"]]
1667 )))|(% colspan="1" %)(% colspan="1" %)
1668 (((
1669 [[Cubbli>>doc:Cubbli.User documentation.WebHome]]?
1670 )))|(% colspan="1" %)(% colspan="1" %)
1671 (((
1672 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
1673 )))|(% colspan="1" %)(% colspan="1" %)
1674 (((
1675 (% style="color: rgb(255,0,0);" %)Commercial?
1676 )))
1677 |(% colspan="1" %)(% colspan="1" %)
1678 (((
1679 [[Cernlib>>url:https://cernlib.web.cern.ch/cernlib/||shape="rect"]]
1680 )))|(% colspan="1" %)(% colspan="1" %)
1681 (((
1682 [[Cubbli>>doc:Cubbli.User documentation.WebHome]] ?
1683 )))|(% colspan="1" %)(% colspan="1" %)
1684 (((
1685 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
1686 )))|(% colspan="1" %)(% colspan="1" %)
1687 (((
1688 \\
1689 )))
1690 |(% colspan="1" %)(% colspan="1" %)
1691 (((
1692 [[GSL>>url:https://www.gnu.org/software/gsl/doc/html/index.html||shape="rect"]]
1693 )))|(% colspan="1" %)(% colspan="1" %)
1694 (((
1695 [[Cubbli>>doc:Cubbli.User documentation.WebHome]] ?, [[Mutteri>>url:https://flamma.helsinki.fi/fi/mutteri||shape="rect"]], [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1696 )))|(% colspan="1" %)(% colspan="1" %)
1697 (((
1698 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
1699 )))|(% colspan="1" %)(% colspan="1" %)
1700 (((
1701 \\
1702 )))
1703 |(% colspan="1" %)(% colspan="1" %)
1704 (((
1705 [[SLATEC>>url:http://people.sc.fsu.edu/~~jburkardt/f_src/slatec/slatec.html||shape="rect"]]
1706 )))|(% colspan="1" %)(% colspan="1" %)
1707 (((
1708 [[Cubbli>>doc:Cubbli.User documentation.WebHome]] ?
1709 )))|(% colspan="1" %)(% colspan="1" %)
1710 (((
1711 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
1712 )))|(% colspan="1" %)(% colspan="1" %)
1713 (((
1714 (% style="color: rgb(255,0,0);" %)Commercial?
1715 )))
1716 |(% colspan="1" %)(% colspan="1" %)
1717 (((
1718 [[Maple>>url:https://www.maplesoft.com/products/Maple/||shape="rect"]]
1719 )))|(% colspan="1" %)(% colspan="1" %)
1720 (((
1721 [[Cubbli>>doc:Cubbli.User documentation.WebHome]] ?
1722 )))|(% colspan="1" %)(% colspan="1" %)
1723 (((
1724 [[Software Distribution>>url:https://ohjelmistojakelu.helsinki.fi/index/index||shape="rect"]]
1725 )))|(% colspan="1" %)(% colspan="1" %)
1726 (((
1727 (% style="color: rgb(255,0,0);" %)Commercial?
1728 )))
1729 |(% colspan="1" %)(% colspan="1" %)
1730 (((
1731 [[Singularity>>url:https://singularity.lbl.gov||shape="rect"]]
1732 )))|(% colspan="1" %)(% colspan="1" %)
1733 (((
1734 [[Turso>>doc:it4sci.IT for Science group.HPC Environment User Guide.WebHome]]
1735 )))|(% colspan="1" %)(% colspan="1" %)
1736 (((
1737 System package on a compute nodes
1738 )))|(% colspan="1" %)(% colspan="1" %)
1739 (((
1740 Container system
1741 )))
1742
1743 = (% style="color: rgb(0,128,0);font-size: 24.0px;text-transform: uppercase;" %)7.0 VDI(%%) =
1744
1745 Please see the [[Cubbli>>doc:Cubbli.User documentation.WebHome]] and[[ VDI>>url:https://helpdesk.it.helsinki.fi/en/instructions/computer-and-printing/workstation-service/virtual-desktops-vdi-and-vmware||shape="rect"]] for additional information.
1746
1747 **Note:** that VDI is not an environment to be used for computationally intensive tasks, such as Tensorflow over GPU. You will get far better performance if you use [[these resources instead>>url:https://wiki.helsinki.fi/display/it4sci/Resources+for+Research#ResourcesforResearch-3.0HPCEnvironment||shape="rect"]].
1748
1749 = (% style="color: rgb(0,128,0);" %)8.0 GitLab Server(%%) =
1750
1751 IT4SciFi offers and manages [[GitLab>>url:https://docs.gitlab.com||shape="rect"]] server at [[version.helsinki.fi>>url:http://version.helsinki.fi||shape="rect"]]. Please see the [[User Guide>>doc:it4sci.IT for Science group.OLD AND OBSOLETE.Version\.helsinki\.fi GitLab server.WebHome]] for further details and usage policies.
1752
1753 = (% style="color: rgb(0,128,0);" %)9.0 Infrastructure(%%) =
1754
1755 (% style="margin-left: 30.0px;" %)
1756 == (% style="color: rgb(51,51,51);" %)9.1 Geoinformatics(%%) ==
1757
1758 (% style="margin-left: 30.0px;" %)
1759 (% style="color: rgb(0, 128, 0); color: rgb(20, 20, 20)" %)The university of Helsinki uses the (% style="color: rgb(0,128,0);" %) (% style="color: rgb(0, 128, 0); color: rgb(20, 20, 20)" %)[[CSC GIS services>>url:http://www.csc.fi/english/research/sciences/geo/gis/index_html||shape="rect"]] (% style="color: rgb(0,128,0);" %) (% style="color: rgb(0, 128, 0); color: rgb(20, 20, 20)" %)as a central source for GIS data.
1760
1761
1762 (% style="margin-left: 30.0px;" %)
1763 == (% style="color: rgb(51,51,51);" %)9.2 VMWare Virtual Servers(%%) ==
1764
1765 (% style="margin-left: 30.0px;" %)
1766 What to say?
1767
1768 = (% style="color: rgb(0,128,0);" %)10.0 Consulting Services(%%) =
1769
1770 IT4SciFi offers consulting services. Wether the question is about virtual machines, hardware, software or computational, or storage etc. resource requirements, project servers or any other topic, feel free to contact us through university helpdesk at [[helpdesk (at) helsinki (dot) fi>>mailto:helpdesk@helsinki.fi||shape="rect"]].
1771
1772 = 11.0 ePouta =
1773
1774 A cloud computing environment designed for processing and / or storing sensitive data. Service provided by csc but server administration handled by IT department. Request resources via [[helpdesk@helsinki.fi>>mailto:helpdesk@helsinki.fi||shape="rect"]]. See [[https:~~/~~/research.csc.fi/epouta>>url:https://research.csc.fi/epouta||shape="rect"]] for further details.
1775
1776 \\
1777
1778 \\