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
|
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE guide SYSTEM "/dtd/guide.dtd">
<!-- $Header: $ -->
<guide link="/proj/en/science/linalg.xml">
<title>Linear Algebra on Gentoo</title>
<author title="Author">
<mail link="bicatali@gentoo.org">Sébastien Fabbro</mail>
</author>
<abstract>
This guide explains the use of linear algebra libraries and focus on
how to use the different implementations of BLAS and LAPACK available on Gentoo.
</abstract>
<!-- The content of this document is licensed under the CC-BY-SA license -->
<!-- See http://creativecommons.org/licenses/by-sa/2.5 -->
<license/>
<version>1.0</version>
<date>2010-12-22</date>
<chapter>
<title>Introduction</title>
<section>
<body>
<p>
There are <uri link="http://en.wikipedia.org/wiki/List_of_numerical_libraries">many</uri>
performant numerical libraries available.
The Basic Linear Algebra Subprograms (BLAS) and the Linear Algebra PACKage (LAPACK)
are well designed linear algebra libraries developed by the
High Performance Computing (HPC) community. BLAS is an API of dense
matrix and vectors products, while LAPACK provides routines for
solving systems of linear equations. Both are widely used in
many scientific applications and it is, therefore, important to
have efficient implementations available.
</p>
<p>
BLAS and LAPACK were originally written in FORTRAN 77. Since then, a
number of additional language wrappers have been developed for
languages like C, C++, FORTRAN 95, Java, Python, etc...
Netlib offers exact implementations of the APIs and they are called
"reference" libraries. There is also some parallel implementations
for
</p>
<ul>
<li>
<uri link="http://www.netlib.org/blas/">BLAS</uri>: FORTRAN 77 and C
(CBLAS) implementations of BLAS
</li>
<li>
<uri link="http://www.netlib.org/lapack/">LAPACK</uri>: FORTRAN 77 and
C (LAPACKE) implementations of LAPACK
</li>
</ul>
<p>
</p>
<ul>
<li>
<uri link="http://www.netlib.org/blacs/">BLACS</uri>: FORTRAN 77 and C
implementations of BLACS
</li>
<li>
<uri link="http://www.netlib.org/scalapack/">ScaLAPACK</uri>: FORTRAN 77 and
C implementations of PBLAS and ScaLAPACK
</li>
</ul>
<p>
In addition, Gentoo provides a number of optimized implementations
of the above linear algebra libraries that will be described
below. You can switch between implementations with the
Gentoo's <c>eselect</c> system and the widely used <c>pkg-config</c>
tool.
</p>
<p>
It is important to note that if you require, e.g., a well performing
BLAS implementation, simply emerging X over Y often is not enough. Rather, you will have
to carefully benchmark your applications since performance may depend
on many factors,
such as hardware or network.
If you are simply looking for a well performing and well tested
implementation, the reference ebuilds will likely be your best choice.
</p>
</body>
</section>
</chapter>
<chapter>
<title>For Users</title>
<section>
<title>Installing</title>
<body>
<p>
If best possible performance is not of paramount importance for you
and you simply need BLAS and/or LAPACK, just emerge the virtual
package:
</p>
<pre caption="Installing">
# <i>emerge lapack</i>
</pre>
<p>
This will install both <><> and <><> the reference packages from
<uri>http://www.netlib.org/</uri> . They are well tested, easy to debug
implementations. They should satisfy most users; if they're all you need, you're
done reading.
</p>
<p>
However, if:
</p>
<ul>
<li>linear algebra libraries are critical for the speed of your applications</li>
<li>you absolutely need to build the fastest computer</li>
<li>you want to help Gentoo sci project to improve their packages</li>
</ul>
<p>
... then read on, and be sure to file bugs both to Gentoo and upstream.
</p>
<p>
There is a number of optimized implementations of these libraries in the Portage
tree:
</p>
<ul>
<li>
<uri link="http://math-atlas.sourceforge.net">ATLAS</uri>: Automatically
Tuned Linear Algebra Software is an open-source package that empirically
tunes the library to the machine it is being compiled on. It provides BLAS
(FORTRAN 77 and C), and LAPACK implementations on various architectures.
</li>
<li>
<uri
link="http://www.tacc.utexas.edu/tacc-projects/gotoblas2/">GotoBLAS</uri>:
Goto BLAS provides open-source, free for academic use, hand-coded
machine language, processor optimized versions of the FORTRAN 77
and C BLAS routines. Still claims to be the fastest BLAS.
</li>
<li>
<uri link="http://developer.amd.com/cpu/libraries/acml/Pages/default.aspx">ACML</uri>:
AMD Core Math Library is a closed-source but free package containing BLAS (FORTRAN 77
only) and LAPACK for x86 and x86_64 architectures, but also other math tools
such as statistical libraries and FFTs.
</li>
<li>
<uri link="http://software.intel.com/en-us/articles/intel-mkl/">MKL</uri>:
Intel® Math Kernel Library is a closed-source but free package for
non-commercial use on Linux systems containing implementations of all the linear
algebra libraries mentioned here.
</li>
</ul>
<p>
Usually performance gain is noticeable mainly with BLAS, since LAPACK routines
depend on BLAS kernels.
</p>
</body>
</section>
<section>
<title>Developping with the installed linear algebra libraries</title>
<body>
<p>
We took great care to make sure that each package provides
consistent pkg-config files generated by us.
Compiling and linking becomes straightforward:
</p>
<pre caption="Compiling and linking linear algebra libraries">
# <i>pkg-config --libs blas</i> <comment>(To link with FORTRAN 77 BLAS library)</comment>
# <i>pkg-config --cflags cblas</i> <comment>(To compile against C BLAS library)</comment>
# <i>pkg-config --libs cblas</i> <comment>(To link with C BLAS library)</comment>
# <i>pkg-config --libs scalapack</i> <comment>(To link with the ScaLAPACK library)</comment>
</pre>
<p>
<c>pkg-config</c> files are available for all implementations and
various alternatives within implementations. The default names of
the implementations are: blas, cblas, lapack, lapacke, blacs and
scalapack, and they can be chosen with <c>eselect</c>. You can also always compile or link
with an library not selected for the
More information on using <c>pkg-config</c> can be obtained with <c>man pkg-config</c>.
</p>
</body>
</section>
<section>
<title>Selecting libraries</title>
<body>
<p>
You can switch BLAS, CBLAS and LAPACK implementations with
<c>eselect</c>. you can view which implementations of CBLAS
are available.
</p>
<pre caption="Viewing available implementations of CBLAS">
# <i>eselect cblas list</i>
Installed CBLAS for library directory lib64
[1] atlas
[2] atlas-threads
[3] gsl
[4] mkl-threads *
[5] reference
</pre>
<p>
The implementation marked with an asterisk (*) is the currently
selected implementation. To switch implementations, run:
</p>
<pre caption="Switching to the threaded ATLAS implementation of BLAS">
# <i>eselect blas set atlas-threads</i>
</pre>
<p>
To learn more about the <c>eselect</c> tool, visit the
<uri link="http://www.gentoo.org/proj/en/eselect/user-guide.xml">eselect guide</uri>
</p>
<p>
When selecting your linear algebra profiles try to avoid mixing
different implementations since we don't have any mechanism to enforce
reasonable profiles. However, here is a list of well performing
profile combinations that have been used successfully in the past:
</p>
<ul>
<li> performant on most CPUs:
<ul>
<li>blas, cblas: atlas (or atlas-threads with multi-processor)</li>
<li>lapack, lapacke: atlas</li>
</ul>
</li>
<li> performant on most CPUs:
<ul>
<li>blas, cblas: goto2 </li>
<li>lapack, lapacke: reference</li>
</ul>
</li>
<li> performant on AMD based CPUs:
<ul>
<li>blas, lapack: acml-gfortran (or acml-gfortran-openmp with
multi-processors) </li>
<li>cblas: reference</li>
</ul>
</li>
<li> performant on Intel based CPUs:
<ul>
<li>blas,cblas,lapack: mkl-threads</li>
</ul>
</li>
</ul>
</body>
</section>
<section>
<title>Choosing a compiler</title>
<body>
<p>
All the above libraries have been tested with the GNU compiler
collections (gcc, gfortran).
There are many available C compilers and a few FORTRAN (ifort,
Open64) compilers on Gentoo and many other FORTRAN compilers outside
of Gentoo ().
</p>
<pre caption="Installing BLAS with the Intel FORTRAN compiler">
# <i>F77=ifort FFLAGS="-O2 -mp1" emerge blas-reference</i>
</pre>
<p>
Depending on your hardware, a small performance gain can be noticed thanks to
vectorization. The <c>-mp</c> flag maintains floating-point precision, since by
default ifort is pretty aggressive on floating point arithmetic, and we are
actually compiling a math package. Try <c>man ifort</c> to see additional flags
to fit your hardware.
</p>
<p>
Some of the implementations let you specify the Intel® C compiler as
well. Please beware that not all libraries compile with all
combinations. You should receive an error during the emerge in case you have
chosen an incompatible combination.
</p>
<p>
As usual for Gentoo, there are many combinations of USE flags and
compilers with which you could compile a package. Unfortunately
switching compilers between BLAS and LAPACK might not be always
compatible. For example:
</p>
<pre caption="Looking for trouble combinations">
# <i>USE=ifort emerge acml</i>
# <i>eselect blas set acml-ifort-openmp</i>
# <i>FC=gfortran FFLAGS="-O2" emerge lapack-reference</i>
</pre>
<p>
This will most likely break things or not even compile.
</p>
<p>
Try to be consistent in your choice. Stay with the GCC most of the time will
avoid you some trouble, unless you want to use the MKL, in which case the Intel
compilers make a good combination.
</p>
</body>
</section>
<section>
<title>Documentation</title>
<body>
<p>
If you need BLAS or LAPACK to develop your own programs, the documentation
becomes pretty handy. Setting the USE="doc" flag for the corresponding BLAS or
LAPACK package will install man pages and quick reference sheets from the
<c>app-doc/blas-docs</c> and <c>app-doc/lapack-docs</c> packages. They are
standard and valid for all implementations. For optimized packages, the
USE="doc" flags will usually install extra doc in PDF or HTML format.
</p>
</body>
</section>
</chapter>
<chapter>
<title>For ebuild developers</title>
<section>
<section>
<title>Packages with BLAS/LAPACK dependencies</title>
<body>
<p>
You need two things:
set [R]DEPEND to <c>virtual/<imp></c>. To build some
packages, you m need to use the pkg-config tool. If you are lucky, the
package uses autotools together with the autoconf <>AX_BLAS and <>AX_LAPACK M4
macros. In this case, the configuration step becomes simple. For example:
</p>
<pre caption="Sample package configuration with autotools">
<keyword>econf</keyword> --with-blas="<var>$(pkg-config --libs blas)</var>"
</pre>
</body>
</section>
<title>Providing new implementations</title>
<body>
<p>
The Portage tree contains many ebuilds that depend on the
BLAS/CBLAS/LAPACK/BLACS/ScaLAPACK libraries. As there is more than
one possible implementation, the Gentoo Science Project
reorganized all the packages to provide <c>virtual</c>. All ebuilds using
should depend on this virtual package, unless it is explicitly
known to break with a specific implementation.
</p>
<p>
To work with Gentoo's configuration tools
<c>app-admin/eselect-{blas,cblas,lapack}</c>, and the virtual, every ebuild that
installs a BLAS implementation must fulfill following requirements:
</p>
<ol>
<li>
The ebuild must install an eselect file for each profile it provides. The
libraries should link to the ones in <path>/usr/$(get_libdir)</path>
directories and the include files in <path>/usr/include</path>:
<ul>
<li>
<path>libblas.so[.0]</path> - Shared object for FORTRAN BLAS
applications
</li>
<li>
<path>libblas.a</path> - Static library for FORTRAN BLAS applications
</li>
<li>
<path>libcblas.so[.0]</path> - Shared object for C/C++ CBLAS applications
</li>
<li>
<path>libcblas.a</path> - Static library for C/C++ CBLAS applications
</li>
<li><path>cblas.h</path> - Include header for C/C++ applications</li>
<li>
<path>liblapack.so[.0]</path> - Shared object for FORTRAN LAPACK
applications
</li>
<li>
<path>liblapack.a</path> - Static library for FORTRAN LAPACK applications
</li>
</ul>
</li>
<li>
The ebuild must install a <path>blas.pc</path>, <path>cblas.pc</path> and/or
<path>lapack.pc</path> pkg-config file and therefore RDEPEND on
<c>dev-util/pkgconfig</c>. They should also be included in the eselect
files, and link to the <path>/usr/$(get_libdir)/pkgconfig</path> directory:
<ul>
<li><path>blas.pc</path> - BLAS pkg-config file</li>
<li><path>cblas.pc</path> - CBLAS pkg-config file</li>
<li><path>lapack.pc</path> - LAPACK pkg-config file</li>
</ul>
</li>
<li>Be included in the virtual package as a possible provider:
<ul>
<li><c>virtual/blas</c> - BLAS virtual package</li>
<li><c>virtual/cblas</c> - CBLAS virtual package</li>
<li><c>virtual/lapack</c> - LAPACK virtual package</li>
</ul>
</li>
</ol>
<p>
The easiest way of understanding all this is probably getting inspiration from
one of the available packages. Currently the Portage tree provide the following
virtual packages:
</p>
<table>
<tr>
<th>Package name</th>
<th>virtual/blas</th>
<th>virtual/cblas</th>
<th>virtual/lapack</th>
<th>virtual/lapacke</th>
<th>virtual/blacs</th>
<th>virtual/scalapack</th>
</tr>
<tr>
<ti><c>sci-libs/acml</c></ti>
<ti>*</ti>
<ti></ti>
<ti>*</ti>
<ti></ti>
<ti></ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/atlas</c></ti>
<ti>*</ti>
<ti>*</ti>
<ti>*</ti>
<ti>*</ti>
<ti></ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/gotoblas2</c></ti>
<ti>*</ti>
<ti>*</ti>
<ti></ti>
<ti></ti>
<ti></ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/blas-reference</c></ti>
<ti>*</ti>
<ti></ti>
<ti></ti>
<ti></ti>
<ti></ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/cblas-reference</c></ti>
<ti></ti>
<ti>*</ti>
<ti></ti>
<ti></ti>
<ti></ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/gsl</c></ti>
<ti></ti>
<ti>*</ti>
<ti></ti>
<ti></ti>
<ti></ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/lapack-reference</c></ti>
<ti></ti>
<ti></ti>
<ti>*</ti>
<ti></ti>
<ti></ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/mkl</c></ti>
<ti>*</ti>
<ti>*</ti>
<ti>*</ti>
<ti>*</ti>
<ti>*</ti>
<ti>*</ti>
</tr>
</table>
</body>
</section>
</chapter>
<chapter>
<title>Benchmarks</title>
<section>
<body>
<p>
If you feel inclined to write an ebuild for these, you
are more than welcomed to file it on our <uri
link="http://bugs.gentoo.org">Bugzilla</uri>.
</p>
</body>
</section>
</chapter>
</guide>
|