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
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head> <link rel="canonical" href="http://www.mcs.anl.gov/petsc/petsc-current/docs/installation.html" />
<meta http-equiv="content-type" content="text/html;charset=utf-8">
<title>Documentation: Installation</title>
</head>
<body bgcolor="#ffffff">
<div id="version" align=right><b>petsc-3.4.2 2013-07-02</b></div>
<h1>Documentation: Installation</h1>
<style type="text/css">
.code, code, #details li > ul {
color: red;
}
.code, #details li > ul:not([style]) {
font-size: .9em;
font-family: Pragmata, Menlo, 'DejaVu LGC Sans Mono', 'DejaVu Sans Mono', Consolas, 'Everson Mono', 'Lucida Console', 'Andale Mono', 'Nimbus Mono L', 'Liberation Mono', FreeMono, 'Osaka Monospaced', Courier, 'New Courier', monospace;
}
.code, #details li > ul {
padding: .7em;
padding-left: 2em;
}
.def, #details h3, #details h4 {
color: #551a8b;
font-weight: bold;
}
</style>
<div id="main">
<!-- This is here for the grepping between begin / end, weaksauce! -->
<h3>Quick Instructions:</h3>
Invoke the following commands from the top level PETSc directory: <br>
<ul class="code">
<li>./configure --with-cc=gcc --with-fc=gfortran --download-f-blas-lapack --download-mpich</li>
<li>make all test</li>
</ul>
<a style="color: rgb(204,102,0);" href="#windows"><b>Check here for MS Windows Installation</b></a>
<h3>Encounter problems?</h3>
<ul>
<li><b>Read the error message from ./configure!</b></li>
<li>If you get the message 'No such file or directory' try: <code style="color: red">python ./configure</code></li>
<li><a href="installation.html#blas-lapack">BLAS and LAPACK problems</a></li>
<li><a href="installation.html#mpi">MPI problems</a>. I <a href="installation.html#i-dont-want-to-use-mpi">don't want MPI</a></li>
<li><i><b>make</i></b> problems? Just copy/paste <i><b>make</i></b> command printed by configure including PETSC_DIR and PETSC_ARCH options</li>
<li>Do not have fortran compiler? check <a href=#exampleusage>examples</a> below
<li> Check the <a href="http://www.mcs.anl.gov/petsc/documentation/bugreporting.html">bug-reporting</a> section</li>
</ul>
<h3>Notes:</h3>
<ul>
<li>Please <a href="../download/index.html">download</a> the <b>latest</b> patched tarball
<li>For most users we recommend installing PETSc as a <b>regular/non-root user</b>, perhaps in <b>/home/username/soft</b></li>
<li>To extract the sources use: <code>gunzip -c petsc-3.4.0.tar.gz | tar -xof -</code></li>
<li>Please check: <code>./configure --help</code></li>
<li>Please check <a href="#exampleusage">example usages</a></li>
<li>To install in <a href="#root">system directories</a> and for <a href="#packagemanagers">package managers.</a></li>
<li><a href="#pkgconfig">Pkgconfig</a> and <a href="#pkgconfig">module files.</a></li>
</ul>
</div>
<hr>
<div id="details">
<div>
<h3><a name="exampleusage">Example Usages:</a></h3>
<ul>
<li>
Examples are at <b>config/examples/*.py</b>. We use some of these scripts
locally for testing - for example one can update these files and run as:
<ul>
<li>./config/examples/arch-osx-10.6.py</li>
</ul>
</li>
<li>
Assuming BLAS, LAPACK, MPICH are not currently
installed <code>./configure</code> will download & install BLAS,
LAPACK, MPICH if they are not already installed on the system):
<ul>
<li>./configure --with-cc=gcc --with-fc=gfortran --download-f-blas-lapack --download-mpich</li>
</ul>
</li>
<li>
Same as above - but do not have a fortran compiler [and want to use PETSc from C].
<ul>
<li>./configure --with-cc=gcc --with-fc=0 --download-f2cblaslapack --download-mpich</li>
</ul>
</li>
<li>
If BLAS, LAPACK, MPI are already installed in default system/compiler locations and mpicc,
mpif90, mpiexec are available via PATH - configure does not require any additional options.
<ul>
<li>./configure</li>
</ul>
</li>
<li>
If BLAS, LAPACK, MPI are already installed in known user location use:<br>
[Note: Do not specify --with-cc --with-fc etc when using --with-mpi-dir -
so that mpicc/mpif90 can be picked up from mpi-dir]
<ul>
<li>./configure --with-blas-lapack-dir=/usr/local/blaslapack --with-mpi-dir=/usr/local/mpich</li>
</ul>
or
<ul>
<li>./configure --with-blas-lapack-dir=/usr/local/blaslapack --with-cc=/usr/local/mpich/bin/mpicc --with-mpi-f90=/usr/local/mpich/bin/mpif90 --with-mpiexec=/usr/local/mpich/bin/mpiexec</li>
</ul>
</li>
<li>
Build Complex version of PETSc [using c++ compiler]
(add the option <code>--with-fortran-kernels=generic</code> to get
possibly faster complex number performance on some systems):
<ul>
<li>./configure --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --download-f-blas-lapack --download-mpich --with-scalar-type=complex --with-clanguage=cxx</li>
</ul>
</li>
<li>
Install 2 variants of PETSc, one with gnu, the other with intel compilers. Specify different PETSC_ARCH for each build.
<ul>
<li>./configure PETSC_ARCH=linux-gnu --with-cc=gcc --with-fc=gfortran --download-mpich</li>
<li>make PETSC_ARCH=linux-gnu all test</li>
<li>./configure PETSC_ARCH=linux-gnu-intel --with-cc=icc --with-fc=ifort --download-mpich --with-blas-lapack-dir=/usr/local/mkl</li>
<li>make PETSC_ARCH=linux-gnu-intel all test</li>
</ul>
</li>
</ul>
</div><!-- #exampleusage -->
<hr>
<div id="vars">
PETSC_DIR and PETSC_ARCH are a couple of variables that control the
configuration and build process of PETSc. These variables can be set as
envirnment variables or specified on the command line [to both configure and make]
<ul>
<li>
specify enviornment variable for csh/tcsh [can be specified in ~/.cshrc]
<ul>
<li>setenv PETSC_DIR /home/balay/petsc-3.4.0</li>
<li>setenv PETSC_ARCH linux-gnu-c-debug</li>
</ul>
</li>
<li>
specify enviornment variable for bash [can be specified in ~/.bashrc]
<ul>
<li>export PETSC_DIR=/home/balay/petsc-3.4.0</li>
<li>export PETSC_ARCH=linux-gnu-c-debug</li>
</ul>
</li>
<li>
specify variable on commandline to configure
<ul>
<li>./configure PETSC_DIR=/home/balay/petsc-3.4.0 PETSC_ARCH=linux-gnu-c-debug [other configure options]</li>
</ul>
</li>
<li>
specify variables on command line to make
<ul>
<li>make PETSC_DIR=/home/balay/petsc-3.4.0 PETSC_ARCH=linux-gnu-c-debug [other make options]</li>
</ul>
</li>
</ul>
<p>
<a class="def" name="PETSC_DIR">PETSC_DIR:</a>
this variable should point to the location of the PETSc
installation that is used. Multiple PETSc versions can
coexist on the same file-system. By changing PETSC_DIR
value, one can switch between these installed versions of
PETSc.
</p>
<p>
<span class="def">PETSC_ARCH:</span>
this variable gives a name to a configuration/build.
Configure uses this value to stores the generated config
makefiles in ${PETSC_DIR}/${PETSC_ARCH}/conf. And make
uses this value to determine this location of these
makefiles [which intern help in locating the correct
include and library files].
</p>
<p>
Thus one can install multiple variants of PETSc libraries
- by providing different PETSC_ARCH values to each
configure build. Then one can switch between using these
variants of libraries [from make] by switching the
PETSC_ARCH value used.<br>
</p>
<p>
If configure doesn't find a PETSC_ARCH value [either in
env variable or command line option], it automatically
generates a default value and uses it. Also - if make
doesn't find a PETSC_ARCH env variable - it defaults to
the value used by last successful invocation of previous
configure.
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div><!-- #vars -->
<hr>
<div>
<h3><a name="compilers">Compilers:</a></h3>
<p>Specify compilers and compiler options used to build PETSc [and perhaps external packages]</p>
<ul>
<li>
Specify compilers using the options <code>--with-cc --with-fc --with-cxx</code> for c, c++, and fortran compilers
<ul>
<li>--with-cc=mpicc --with-fc=mpif90</li>
<li>--with-cc=gcc --with-fc=gfortran</li>
<li>--with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-clanguage=cxx</li>
</ul>
</li>
<li>
If fortran compiler is not available - then disabling using fortran
<ul>
<li>--with-fc=0</li>
</ul>
</li>
<li>
If no compilers are specified - configure will
automatically look for available MPI or regular
compilers in the user's PATH
<ul>
<li>mpicc/mpiCC/mpif90 or mpif77</li>
<li>gcc/g++/gfortran or g77</li>
<li>cc/CC/f77 etc..</li>
</ul>
</li>
<li>
It's best to use <a href="MPICompilers">MPI compilers</a>
as this will avoid the situation where MPI is compiled
with one set of compilers [like gcc/g77] and user
specified incompatible compilers to PETSc [perhaps
icc/ifort]. This can be done by either specifying
--with-cc=mpicc or --with-mpi-dir [and not
--with-cc=gcc]
<ul>
<li>--with-cc=mpicc --with-fc=mpif90</li>
<li>--with-mpi-dir=/opt/mpich2-1.1 [but <b>*no*</b> --with-cc=gcc]</li>
</ul>
</li>
<li>
Configure defaults to building PETSc in debug mode.
One can switch to using optimzed mode with the toggle
option --with-debugging [defaults to debug enabled].
Additionally one can specify more suitable optimization
flags with the options COPTFLAGS, FOPTFLAGS,
CXXOPTFLAGS.
<ul>
<li>./configure --with-cc=gcc --with-fc=gfortran --with-debugging=0 COPTFLAGS='-O3 -march=p4 -mtune=p4' FOPTFLAGS='-O3 -qarch=p4 -qtune=p4'</li>
</ul>
</li>
<li>
Configure cannot detect compiler libraries for certain
set of compilers. In this case one can specify
additional system/compiler libraries using the LIBS option
<ul>
<li>./configure --LIBS='-ldl /usr/lib/libm.a' </li>
</ul>
</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #compilers -->
<hr>
<div id="externalpackages">
<h3><a name="external">External Packages:</a></h3>
<p>
PETSc provides interfaces to various <a href="../miscellaneous/external.html">external packages</a>.
Blas/Lapack is a required package, MPI is not required if running sequentially. One can optionally use
<a href="linearsolvertable.html">external solvers</a> like Hypre, MUMPS, etc. from within PETSc aplications.
</p>
<p>
PETSc configure has the ability to download and install these external packages. Alternatively if these packages
are already installed, then configure can detect and use them.
</p>
<p>The following modes can be used to install/use external packages with configure.</p>
<ul>
<li>
<span class="def">--download-PACKAGENAME</span>: Download specified
package and install it. Then configure PETSc to use this package.
<ul>
<li>--download-f-blas-lapack --download-mpich</li>
<li>--download-scalapack --download-mumps</li>
</ul>
</li>
<li>
<span class="def">--download-PACKAGENAME=/PATH/TO/package.tar.gz</span>:
If ./configure cannot automatically download the package
[due to network/firewall issues], one can download the
package by alternaive means [perhaps wget or scp via some
other machine]. Once the tarfile is downloaded, the path
to this file can be specified to configure with this
option. Configure will proceed to install this package and
then configure PETSc with it.
<ul>
<li>--download-mpich=/home/petsc/mpich2-1.0.4p1.tar.gz</li>
</ul>
</li>
<li>
<span class="def">--with-PACKAGENAME-dir=PATH</span>:
If the external package is already installed - specify
its location to configure [it will attempt to detect,
include, library files from this location.] Normally this
corresponds to the top-level installation dir for the
package.
<ul>
<li>--with-mpi-dir=/home/petsc/software/mpich2-1.0.4p1</li>
</ul>
</li>
<li>
<span class="def">--with-PACKAGENAME-include=INCLUDEPATH --with-PACKAGENAME-lib=LIBRARYLIST</span>:
Usually a package is defined completely by its include file location -
and library list. [If the package is already installed] - then one can use
these two options to specify the package to configure. For eg:
<ul>
<li>
--with-superlu-include=/home/petsc/software/suerplu/include
--with-superlu-lib=/home/petsc/software/superlu/lib/libsuperlu.a
</li>
<li>
--with-parmetis-include=/sandbox/balay/parmetis/include
--with-parmetis-lib="-L/sandbox/balay/parmetis/lib -lparmetis -lmetis"
</li>
<li>
--with-parmetis-include=/sandbox/balay/parmetis/include
--with-parmetis-lib=[/sandbox/balay/parmetis/lib/libparmetis.a,libmetis.a]
</li>
</ul>
</li>
</ul>
<b>Notes:</b>
<ul>
<li>
Run <code>./configure --help</code> to get the list of external
packages and corresponding additional options [for example
<code>--with-mpiexec</code> for mpich]
</li>
<li>
Generally one would use either one of the above 4 modes for any given
package - and not mix these. [i.e mixing <code>--with-mpi-dir</code> and
<code>--with-mpi-include</code> etc.. should be avoided]
</li>
<li>
Some packages might not support certain options like
<code>--download-PACKAGENAME</code> or
<code>--with-PACKAGENAME-dir</code>. Architectures like Microsoft
Windows might have issues with these options. In these cases,
<code>--with-PACKAGENAME-include --with-PACKAGENAME-lib</code>
options should be prefered.
</li>
<li>
It's best to install some external packages like SuperLU_DIST, MUMPS,
Hypre, METIS, and ParMETIS with the option <code>--download-PACKAGENAME</code>. [the
correct options for these packages are <code>--download-superlu_dist
--download-mumps --download-hypre</code>]
<ul style="color: black">
<li>
This will install the COMPATIBLE version of the external package.
A generic install of this package might not be compatible with
PETSc [perhaps due to version differences - or perhaps due to the
requirement of additional patches for it to work with PETSc]
</li>
<li>
Some packages have bug fixes, portability patches, and upgrades
for dependent packages that have not yet been included in an
upstream release.
</li>
<li>
All packages will be installed with the same set of compilers
- this avoids problems [for example weird link time errors] with
mixing code compiled with multiple compilers [for example mixing
gfortran and ifort compiled code].
</li>
</ul>
</li>
<li>
If you want to download a compatible external package manually, then
the URL for this package is listed in configure source for this
package. For example, check
<code>config/PETSc/packages/SuperLU.py</code> for the url for
download this package.
</li>
</ul>
<b>Additional options</b>:
<ul>
<li>
<span class="def">--with-external-packages-dir=PATH</span>: By default,
external packages will be unpacked in <code>${PETSC_DIR}/externalpackages</code>.
However one can choose a different location where these packages are unpacked.
</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #externalpackages -->
<hr>
<div>
<h3><a name="blas-lapack">BLAS/LAPACK</a></h3>
<p>These packages provide some basic numeric kernels used by PETSc.</p>
<ul>
<li>
Configure will automatically look for blas/lapack in certain standard
locations, on most systems you should not need to provide any
information about BLAS/LAPACK in the ./configure command.
</li>
<li>
One can use the following options to let configure download/install blas/lapack automatically.
<ul>
<li>--download-f-blas-lapack [when fortran compiler is present]</li>
<li>--download-f2cblaslapack [when configuring without a fortran compiler - i.e --with-fc=0]</li>
</ul>
</li>
<li>
Alternatively one can use other options like one of the following.
<ul>
<li>--with-blas-lapack-lib=libsunperf.a</li>
<li>--with-blas-lib=libblas.a --with-lapack-lib=liblapack.a</li>
<li>--with-blas-lapack-dir=/soft/com/packages/intel/13/079/mkl</li>
</ul>
</li>
</ul>
<b>Notes:</b>
<ul>
<li> <h4> Intel MKL</h4>
Intel provides blas/lapack via <a href="http://software.intel.com/en-us/intel-mkl">MKL</a> library.
It usually works from GNU/Intel compilers on linux and MS/Intel compilers on Windows.
One can specify it to PETSc configure with for eg: <code>--with-blas-lapack-dir=/soft/com/packages/intel/13/079/mkl</code>
<br>
If the above option does not work - one could determine the correct library list for your compilers using
<a href="http://software.intel.com/sites/products/mkl/">Intel MKL Link Line Advisor</a>
and specify with the configure option <code>--with-blas-lapack-lib</code>
</li>
<li> <h4>IBM ESSL</h4>
Sadly, IBM's ESSL does not have all the routines of BLAS and LAPACK
that some packages, such as SuperLU expect; in particular slamch,
dlamch and xerbla. In this case instead of using ESSL we suggest
<code>--download-f-blas-lapack</code>. If you really want to use ESSL,
see <a href="http://www.pdc.kth.se/resources/computers/bluegene/LAPACK-CBLAS/LAPACK-CBLAS-build">http://www.pdc.kth.se/resources/computers/bluegene/LAPACK-CBLAS/LAPACK-CBLAS-build</a>.
</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #blas -->
<hr>
<div id="mpi">
<h3><a name="mpi">MPI</a></h3>
<p>This software provides the parallel functionality for PETSc.</p>
<ul>
<li>Configure will automatically look for MPI compilers mpicc/mpif77 etc and use them if found in your PATH.</li>
<li>
One can use the following options to let configure download/install MPI automatically
<ul>
<li>--download-mpich [install and use MPICH]</li>
<li>--download-openmpi [Install and use Open MPI]</li>
</ul>
</li>
<li>See <a href="installation.html#external">externalpackages</a> for other installation options.</li>
</ul>
<h4><a name="mpicompilers">Using MPI Compilers:</a></h4>
<ul>
<li>
It's best to install PETSc with MPI compiler wrappers (often called
mpicc, mpicxx, mpif90) - this way, the SAME compilers used to build
MPI are used to build PETSc [this avoids incompatibilities which
might crop up - when using libraries compiled with different c or
fortran compilers.]. This can be achieved with the following
modes.
<ul style="color: black">
<li>
Vendor provided MPI might already be installed. IBM, SGI, Cray etc provide their own:<br>
<code>./config/confiure.py --with-cc=mpcc --with-fc=mpf77</code>
</li>
<li>
If using MPICH which is already installed [perhaps using
myrinet/gm] then use [without specifying --with-cc=gcc etc.so
that configure picks up mpicc from mpi-dir]:<br>
<code>./configure --with-mpi-dir=/path-to-mpich-install</code>
</li>
</ul>
</li>
</ul>
<h4><a name="i-dont-want-to-use-mpi">Installing without MPI:</a></h4>
<ul>
<li>
You can build (sequential) PETSc without an MPI. This is useful for
quickly installing PETSc [if MPI is not available - for whatever
reason]. However - if there is any MPI code in user application, then
its best to install a full MPI - even if the usage is currently
limited to uniprocessor mode.
<ul>
<li>./configure --with-mpi=0</li>
</ul>
</li>
</ul>
<h4>Installing with Open MPI with shared MPI libraries:</h4>
<p>
OpenMPI defaults to building shared libraries for MPI. However, the
binaries generated by MPI wrappers mpicc/mpif77 etc require
LD_LIBRARY_PATH to be set to the location of these libraries.
</p>
<p>
Due to this OpenMPI restriction one has to set
<code>LD_LIBRARY_PATH</code> correctly [per OpenMPI installation
instructions], before running PETSc configure. If you do not set this
environmental variables you will get messages when running
<code>./configure</code> such as
</p>
<pre>
UNABLE to EXECUTE BINARIES for config/configure.py
-------------------------------------------------------------------------------
Cannot run executables created with C. If this machine uses a batch system
to submit jobs you will need to configure using/configure.py with the additional option --with-batch.
Otherwise there is problem with the compilers. Can you compile and run code with your C/C++ (and maybe Fortran) compilers?
</pre>
<p>or when running a code compiled with OpenMPI</p>
<p>
<code>
-bash-3.3$ ./conftest <br>
./conftest: error while loading shared libraries: libmpi.so.0: cannot open shared object file: No such file or directory
</code>
</p>
<h4>Notes:</h4>
<ul>
<li>
Avoid specifing compilers [with options <code>--with-cc</code> or
<code>--with-fc</code>] when using the option
<code>--with-mpi-dir</code>. [Option<code>--with-mpi-dir</code>
specifies using MPI compilers - so its best to use them - and not
overwride them with user specified <code>--with-cc</code>].
</li>
<li>
One can specify mpiexec or mpiexec with the options <code>--with-mpiexec</code>
</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #mpi -->
<hr>
<div>
<h3><a name="windows">Microsoft Windows Installation With MS/Intel/Compaq Compilers:</a></h3>
<p>
Microsoft Windows OS does not provide the same unix shell enviornment
as the other OSes. Also the default MS/Intel/Compaq compilers behave
differently than other unix compilers. So to install PETSc on Microsoft
Windows - one has to install <a href="http://www.cygwin.com">cygwin</a>
[for the unix enviornment] and use <a href="#win32fe">win32fe</a> [part
of PETSc sources,to interface to MS/Intel/Compaq compilers].
</p>
<p>
<span class="def">Install Cygwin: </span>Please download and install
cygwin package from <a href="http://www.cygwin.com">http://www.cygwin.com</a>.
Make sure the following cygwin components are installed.
</p>
<ul>
<li>python</li>
<li>make</li>
<li>[default selection should already have <code>diff</code> and other tools]</li>
</ul>
<p>
<span class="def">Remove Cygwin link.exe: </span>Cygwin link.exe can
conflict with Intel ifort and Comapq F90 compilers. If you are using
these compilers - please do [from cygwin terminal/bash-shell]:
</p>
<ul>
<li><code>mv /usr/bin/link.exe /usr/bin/link-cygwin.exe</code></li>
</ul>
<p>
<span class="def">Setup cygwin terminal/bash-shell with Working Compilers:
</span>We require the compilers to be setup properly in a cygwin bash
command shell, so that "<code>cl foo.c</code>" or "<code>ifort
foo.f</code>" works from this shell. For example - if using VS2005
C and Intel 10 Fortran one can do:
</p>
<ul>
<li>
Start -> Programs -> Intel Software Development Tools ->
Intel Fortran Compiler 10 -> Visual Fortran Build Enviornment
[32bit or 64bit depending on your usage]. This should start a 'dos
cmd' shell.
</li>
<li>
Within this shell - run cygwin terminal/bash-shell mintty.exe as:
<code>c:\cygwin\bin\mintty.exe</code>
</li>
<li>verify if the compilers are useable [by running cl, ifort in this cygwin terminal/bash-shell]</li>
<li>Now run configure with win32fe and then build the libraries with make [as per the usual instructions]</li>
</ul>
<h4>Example Configure usage with Windows Compilers:</h4>
<p>
Use configure with VC2005 C and Intel Fortran 10 [With MPICH2 installed].
</p>
<ul>
<li><code>./configure --with-cc='win32fe cl' --with-fc='win32fe ifort' --with-cxx='win32fe cl' --download-f-blas-lapack</code></li>
</ul>
<p>If fortran usage is not required, use:</p>
<ul>
<li><code>./configure --with-cc='win32fe cl' --with-fc=0 --download-f2cblaslapack</code></li>
</ul>
<h4>Using Compaq F90:</h4>
<p>Using Microsoft C/C++ 6.0 & Compaq Fortran 6.0 with MPICH2 configure command to use:</p>
<ul>
<li><code>./configure --with-cc='win32fe cl' --with-fc='win32fe f90' --download-f-blas-lapack</code></li>
</ul>
<p>
<b>Note</b>: MPICH2 mpif.h needs a fix for it to work with Compaq F90
[specifically remove line with MPI_DISPLACEMENT_CURRENT - which uses
'integer*8' - which is unsupported by Compaq F90]
</p>
<p>
<span class="def">ExternalPackages</span>: The <code>--download-package
</code> option does not work with many external packages on Microsoft
Windows.
</p>
<p>
<span class="def">Project Files:</span> We cannot provide Microsoft
Visual Studio project files for users as they are specific to the
configure options, location of external packages, compiler versions
etc. used for any given build of PETSc, so they are potentially
different for each build of PETSc. So if you need a project file for
use with PETSc - please do the following.
</p>
<ul>
<li>
create an empty project file with one of the examples say
<code>src/ksp/ksp/examples/tutorials/ex2.c</code>
</li>
<li>
try compiling the example from cygwin bash shell - using makefile - for eg:
<ul>
<li>cd src/ksp/ksp/examples/tutorials</li>
<li>make ex2</li>
</ul>
</li>
<li>
if the above works - then make sure all the compiler/linker options
used by make are also present in the project file in the correct
notation.
</li>
<li>
if errors - redo the above step. [if all the options are correctly
specified - then the example should compile from MSDev.
</li>
</ul>
<p>
<span class="def">Debugger:</span> Running PETSc probrams with
-start_in_debugger is not supported on this platform, so debuggers will
need to be initiated manually. Make sure your environment is properly
configured to use the appropriate debugger for your compiler. The
debuggers can be initiated using Microsoft Visual Studio 6: <code>msdev
ex1.exe</code>, Microsoft Visual Studio .NET: <code>devenv
ex1.exe</code>, Intel Enhanced Debugger: <code>edb ex1.exe</code>, or
GNU Debugger <code>gdb ex1.exe</code>.
</p>
<p>
<span class="def">Using Cygwin gcc/g++/gfortran:</span> One can install
and use PETSc with gcc/gfortran compilers from cygwin. In this case
follow the regular Unix instructions.
</p>
<p>
<span class="def"><a name="win32fe">PETSc Win32 front end - win32fe</a>:</span>
This tool is used as a wrapper to Microsoft/ Borland/ Intel compilers
and associated tools - to enable building PETSc libraries using cygwin
make and other UNIX tools. For additional info, run
<code>${PETSC_DIR}/bin/win32/win32fe</code> without any options.
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #windows -->
<hr>
<div>
<h3><a name="root">Installing PETSc in /usr/local or /opt where sudo or root privileges are required:</a></h3>
<p>
If one wants to install PETSc [with sources] in a common system
location like /usr/local or /opt, then we suggest creating a dir for
PETSc in the required location with user privileges, and then do the
PETSc install [as a <b>regular/non-root user</b>]. i.e.
</p>
<ul class="code">
<li>sudo mkdir /opt/petsc</li>
<li>sudo chown user:group /opt/petsc</li>
<li>cd /opt/petsc</li>
<li>tar -xzf petsc-3.4.0.tar.gz</li>
<li>cd petsc-3.4.0</li>
<li>./configure</li>
<li>make</li>
</ul>
<h4>Installing with --prefix:</h4>
<p>One can also use the GNU <b>--prefix</b> install mode.</p>
<ul class="code">
<li>./configure --prefix=/opt/petsc/petsc-3.4.0 [other configure options]</li>
<li>make</li>
<li>[sudo] make install</li>
<li>[user can now use this PETSc install with:] make PETSC_DIR=/opt/petsc/petsc-3.4.0 ex1</li>
</ul>
<p>
Note: one has to switch to using <code>PETSC_DIR=/opt/petsc/petsc-3.4.0</code> after
install is done - and <b>NOT</b> use PETSC_ARCH anymore.
</p>
<h4><a name="packagemanagers">Using DESTDIR with prefix install:</h4>
<p>
One can also use the GNU <b>DESTDIR</b> with a prefix install. This mode is generally
used by binary packagers. For example
</p>
<ul class="code">
<li>./configure --prefix=/opt/petsc/petsc-3.4.0</li>
<li>make</li>
<li>make install DESTDIR=/tmp/petsc-pkg</li>
<li>[package up /tmp/petsc-pkg The package should then be installed at /opt/petsc/petsc-3.4.0]</li>
<li>[user can now use this PETSc install with:] make PETSC_DIR=/opt/petsc/petsc-3.4.0 ex1</li>
</ul>
<h4>Multiple installs using --prefix and DESTDIR:</h4>
Sepcify a different --prefix location/option for each build - at configure time. For eg:
<ul class="code">
<li>untar petsc tar ball</li>
<li>./configure --prefix=/opt/petsc/petsc-3.4.0-mpich --with-mpi-dir=/opt/mpich</li>
<li>make</li>
<li>make install DESTDIR=/tmp/petsc-pkg</li>
<li>untar petsc tar ball</li>
<li>./configure --prefix=/opt/petsc/petsc-3.4.0-openmpi --with-mpi-dir=/opt/openmpi</li>
<li>make</li>
<li>make install DESTDIR=/tmp/petsc-pkg</li>
</ul>
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #root -->
<hr>
<div>
<h3><a name="pkgconfig">PETSc ./configure automatically generates Pkgconfig and module files for each install</a></h3>
These can be found in ${PETSC_DIR}/${PETSC_ARCH}/lib/pkgconfig/PETSc.pc and ${PETSC_DIR}/${PETSC_ARCH}/lib/modules/${PETSC_VERSION}-${PETSC_ARCH}.
The module file may need to be edited for your particular system. Note that if --prefix is used then $PETSC_ARCH is not included in the above directories
nor is -${PETSC_ARCH} included in the module file name.
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #root -->
<hr>
<div id="cross">
<h3><a name="SP">Installing on machine requiring cross compiler or a job scheduler, such as IBM SP or IBM Blue Gene:</a></h3>
<p>
If one has to use a cross compiler - or go through the job scheduler to
use MPI on a given machine - use the configure option
<code>--with-batch</code> as follows:
</p>
<ul>
<li>
run configure with the additional option <code>--with-batch</code> on
the <b>frontend node</b> (compiler server) [perhaps with the
additional option <code>--known-mpi-shared-libraries=0</code>]
</li>
<li>
the above configure run will create a binary <code>conftest</code>.
Run this binary <code>conftest</code> on <b>one compute node</b>
using the job scheduler.
</li>
<li>
The above run of conftest will create a new python script
<code>reconfigure</code>. Run <code>python reconfigure</code> again
on the <b>frontend node</b> (compiler server) to complete the
configuration process
</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #cross -->
<hr>
<div id="tau">
<h3><a name="usingtau">Installing with TAU Instrumentation package:</a></h3>
<p>
<a href="http://www.cs.uoregon.edu/research/paracomp/tau/tautools/">TAU</a>
package and the prerequisite <a href="http://www.cs.uoregon.edu/research/paracomp/pdtoolkit/">PDT</a>
packages need to be installed separately [perhaps with MPI].
Now use tau_cc.sh as compiler to PETSc configure.
</p>
<ul class="code">
<li>export TAU_MAKEFILE=/home/balay/soft/linux64/tau-2.20.3/x86_64/lib/Makefile.tau-mpi-pdt</li>
<li>./configure CC=/home/balay/soft/linux64/tau-2.20.3/x86_64/bin/tau_cc.sh --with-fc=0 PETSC_ARCH=arch-tau</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #tau -->
<hr>
<div>
<h3><a name="cuda">Installing PETSc to use NVidia GPUs (aka CUDA)</a></h3>
<ul>
<li>
Requires <a href="http://developer.nvidia.com/cuda-downloads"> CUDA</a>,
<a href="https://code.google.com/p/thrust"> Thrust</a> and
<a href="https://code.google.com/p/cusp-library/"> Cusp </a>.
Thrust has been included in CUDA since the 4.0 release - so a separate install is not needed.
</li>
<li>Currently using CUDA-4.1 or CUDA-4.2 with Cusp-v0.3.1</li>
<li>
On Linux - make sure you have compatible <a href="http://developer.nvidia.com/cuda-downloads"> NVidia driver</a>
installed.
</li>
<li>check <code>config/examples/arch-cuda-double.py</code> for example usage.</li>
</ul>
<p>
Cuda build of PETSc curently works on Apple OSX, Linux [Ubuntu 10.04], Microsoft Windows [Server 2003].
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #cuda -->
<hr>
<div id="threads">
<h3><a name="threads">Installing PETSc to use Threads</a></h3>
<p>
<b>petsc-dev</b>
</p>
<ul>
<li>
Configure and build PETSc with the additional configure options
<ul>
<li> --with-threadcomm --with-pthreadclasses and/or --with-openmp </li>
</ul>
</li>
<li>
Run a sample example with:
<ul>
<li>cd src/snes/examples/tutorials</li>
<li>make ex19</li>
<li>
./ex19 -threadcomm_type pthread -threadcomm_nthreads 2 -pc_type none
-da_grid_x 100 -da_grid_y 100 -log_summary
-mat_no_inode -preload off
</li>
</ul>
</li>
</ul>
</div> <!-- #threads -->
<a href="#" target="_top">Return to Installation Instructions</a>
</div>
</body>
</html>
|
