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
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
|
.. _basic-usage:
Basic usage
=====================
The ``spack`` command has many *subcommands*. You'll only need a
small subset of them for typical usage.
Listing available packages
------------------------------
To install software with Spack, you need to know what software is
available. You can see a list of available package names at the
:ref:`package-list` webpage, or using the ``spack list`` command.
.. _spack-list:
``spack list``
~~~~~~~~~~~~~~~~
The ``spack list`` command prints out a list of all of the packages
Spack can install:
.. command-output:: spack list
The packages are listed by name in alphabetical order. You can also
do wildcats searches using ``*``:
.. command-output:: spack list m*
.. command-output:: spack list *util*
.. _spack-info:
``spack info``
~~~~~~~~~~~~~~~~
To get more information on a particular package from `spack list`, use
`spack info`. Just supply the name of a package:
.. command-output:: spack info mpich
Most of the information is self-explanatory. The *safe versions* are
versions that Spack knows the checksum for, and it will use the
checksum to verify that these versions download without errors or
viruses.
:ref:`Dependencies <sec-specs>` and :ref:`virtual dependencies
<sec-virtual-dependencies>` are described in more detail later.
.. _spack-versions:
``spack versions``
~~~~~~~~~~~~~~~~~~~~~~~~
To see *more* available versions of a package, run ``spack versions``.
For example:
.. command-output:: spack versions libelf
There are two sections in the output. *Safe versions* are versions
for which Spack has a checksum on file. It can verify that these
versions are downloaded correctly.
In many cases, Spack can also show you what versions are available out
on the web---these are *remote versions*. Spack gets this information
by scraping it directly from package web pages. Depending on the
package and how its releases are organized, Spack may or may not be
able to find remote versions.
Installing and uninstalling
------------------------------
.. _spack-install:
``spack install``
~~~~~~~~~~~~~~~~~~~~~
``spack install`` will install any package shown by ``spack list``.
For example, To install the latest version of the ``mpileaks``
package, you might type this:
.. code-block:: sh
$ spack install mpileaks
If `mpileaks` depends on other packages, Spack will install the
dependencies first. It then fetches the ``mpileaks`` tarball, expands
it, verifies that it was downloaded without errors, builds it, and
installs it in its own directory under ``$SPACK_ROOT/opt``. You'll see
a number of messages from spack, a lot of build output, and a message
that the packages is installed:
.. code-block:: sh
$ spack install mpileaks
==> Installing mpileaks
==> mpich is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpich@3.0.4.
==> callpath is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/callpath@1.0.2-5dce4318.
==> adept-utils is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da.
==> Trying to fetch from https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
######################################################################## 100.0%
==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7=chaos_5_x86_64_ib-59f6ad23/mpileaks-1.0.tar.gz
==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7=chaos_5_x86_64_ib-59f6ad23.
==> No patches needed for mpileaks.
==> Building mpileaks.
... build output ...
==> Successfully installed mpileaks.
Fetch: 2.16s. Build: 9.82s. Total: 11.98s.
[+] /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpileaks@1.0-59f6ad23
The last line, with the ``[+]``, indicates where the package is
installed.
Building a specific version
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Spack can also build *specific versions* of a package. To do this,
just add ``@`` after the package name, followed by a version:
.. code-block:: sh
$ spack install mpich@3.0.4
Any number of versions of the same package can be installed at once
without interfering with each other. This is good for multi-user
sites, as installing a version that one user needs will not disrupt
existing installations for other users.
In addition to different versions, Spack can customize the compiler,
compile-time options (variants), and platform (for cross compiles) of
an installation. Spack is unique in that it can also configure the
*dependencies* a package is built with. For example, two
configurations of the same version of a package, one built with boost
1.39.0, and the other version built with version 1.43.0, can coexist.
This can all be done on the command line using the *spec* syntax.
Spack calls the descriptor used to refer to a particular package
configuration a **spec**. In the commands above, ``mpileaks`` and
``mpileaks@3.0.4``. We'll talk more about how you can use them to
customize an installation in :ref:`sec-specs`.
.. _spack-uninstall:
``spack uninstall``
~~~~~~~~~~~~~~~~~~~~~
To uninstall a package, type ``spack uninstall <package>``. This will ask the user for
confirmation, and in case will completely remove the directory in which the package was installed.
.. code-block:: sh
spack uninstall mpich
If there are still installed packages that depend on the package to be
uninstalled, spack will refuse to uninstall it.
To uninstall a package and every package that depends on it, you may give the
`--dependents` option.
.. code-block:: sh
spack uninstall --dependents mpich
will display a list of all the packages that depends on `mpich` and, upon confirmation,
will uninstall them in the right order.
A line like
.. code-block:: sh
spack uninstall mpich
may be ambiguous, if multiple ``mpich`` configurations are installed. For example, if both
``mpich@3.0.2`` and ``mpich@3.1`` are installed, ``mpich`` could refer
to either one. Because it cannot determine which one to uninstall,
Spack will ask you either to provide a version number to remove the
ambiguity or use the ``--all`` option to uninstall all of the matching packages.
You may force uninstall a package with the `--force` option
.. code-block:: sh
spack uninstall --force mpich
but you risk breaking other installed packages. In general, it is safer to remove dependent
packages *before* removing their dependencies or use the `--dependents` option.
Seeing installed packages
-----------------------------------
We know that ``spack list`` shows you the names of available packages,
but how do you figure out which are installed?
.. _spack-find:
``spack find``
~~~~~~~~~~~~~~~~~~~~~~
``spack find`` shows the *specs* of installed packages. A spec is
like a name, but it has a version, compiler, architecture, and build
options associated with it. In spack, you can have many installations
of the same package with different specs.
Running ``spack find`` with no arguments lists installed packages:
.. code-block:: sh
$ spack find
==> 74 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
ImageMagick@6.8.9-10 libdwarf@20130729 py-dateutil@2.4.0
adept-utils@1.0 libdwarf@20130729 py-ipython@2.3.1
atk@2.14.0 libelf@0.8.12 py-matplotlib@1.4.2
boost@1.55.0 libelf@0.8.13 py-nose@1.3.4
bzip2@1.0.6 libffi@3.1 py-numpy@1.9.1
cairo@1.14.0 libmng@2.0.2 py-pygments@2.0.1
callpath@1.0.2 libpng@1.6.16 py-pyparsing@2.0.3
cmake@3.0.2 libtiff@4.0.3 py-pyside@1.2.2
dbus@1.8.6 libtool@2.4.2 py-pytz@2014.10
dbus@1.9.0 libxcb@1.11 py-setuptools@11.3.1
dyninst@8.1.2 libxml2@2.9.2 py-six@1.9.0
fontconfig@2.11.1 libxml2@2.9.2 python@2.7.8
freetype@2.5.3 llvm@3.0 qhull@1.0
gdk-pixbuf@2.31.2 memaxes@0.5 qt@4.8.6
glib@2.42.1 mesa@8.0.5 qt@5.4.0
graphlib@2.0.0 mpich@3.0.4 readline@6.3
gtkplus@2.24.25 mpileaks@1.0 sqlite@3.8.5
harfbuzz@0.9.37 mrnet@4.1.0 stat@2.1.0
hdf5@1.8.13 ncurses@5.9 tcl@8.6.3
icu@54.1 netcdf@4.3.3 tk@src
jpeg@9a openssl@1.0.1h vtk@6.1.0
launchmon@1.0.1 pango@1.36.8 xcb-proto@1.11
lcms@2.6 pixman@0.32.6 xz@5.2.0
libdrm@2.4.33 py-dateutil@2.4.0 zlib@1.2.8
-- chaos_5_x86_64_ib / gcc@4.9.2 --------------------------------
libelf@0.8.10 mpich@3.0.4
Packages are divided into groups according to their architecture and
compiler. Within each group, Spack tries to keep the view simple, and
only shows the version of installed packages.
``spack find`` can filter the package list based on the package name, spec, or
a number of properties of their installation status. For example, missing
dependencies of a spec can be shown with ``-m``, packages which were
explicitly installed with ``spack install <package>`` can be singled out with
``-e`` and those which have been pulled in only as dependencies with ``-E``.
In some cases, there may be different configurations of the *same*
version of a package installed. For example, there are two
installations of of ``libdwarf@20130729`` above. We can look at them
in more detail using ``spack find -d``, and by asking only to show
``libdwarf`` packages:
.. code-block:: sh
$ spack find --deps libdwarf
==> 2 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
libdwarf@20130729-d9b90962
^libelf@0.8.12
libdwarf@20130729-b52fac98
^libelf@0.8.13
Now we see that the two instances of ``libdwarf`` depend on
*different* versions of ``libelf``: 0.8.12 and 0.8.13. This view can
become complicated for packages with many dependencies. If you just
want to know whether two packages' dependencies differ, you can use
``spack find -l``:
.. code-block:: sh
$ spack find -l libdwarf
==> 2 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
libdwarf@20130729-d9b90962 libdwarf@20130729-b52fac98
Now the ``libwarf`` installs have hashes after their names. These are
hashes over all of the dependencies of each package. If the hashes
are the same, then the packages have the same dependency configuration.
If you want to know the path where each package is installed, you can
use ``spack find -p``:
.. code-block:: sh
$ spack find -p
==> 74 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
ImageMagick@6.8.9-10 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/ImageMagick@6.8.9-10-4df950dd
adept-utils@1.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da
atk@2.14.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/atk@2.14.0-3d09ac09
boost@1.55.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/boost@1.55.0
bzip2@1.0.6 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/bzip2@1.0.6
cairo@1.14.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/cairo@1.14.0-fcc2ab44
callpath@1.0.2 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/callpath@1.0.2-5dce4318
...
And, finally, you can restrict your search to a particular package
by supplying its name:
.. code-block:: sh
$ spack find -p libelf
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
libelf@0.8.11 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.11
libelf@0.8.12 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.12
libelf@0.8.13 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.13
``spack find`` actually does a lot more than this. You can use
*specs* to query for specific configurations and builds of each
package. If you want to find only libelf versions greater than version
0.8.12, you could say:
.. code-block:: sh
$ spack find libelf@0.8.12:
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
libelf@0.8.12 libelf@0.8.13
Finding just the versions of libdwarf built with a particular version
of libelf would look like this:
.. code-block:: sh
$ spack find -l libdwarf ^libelf@0.8.12
==> 1 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
libdwarf@20130729-d9b90962
The full spec syntax is discussed in detail in :ref:`sec-specs`.
Compiler configuration
-----------------------------------
Spack has the ability to build packages with multiple compilers and
compiler versions. Spack searches for compilers on your machine
automatically the first time it is run. It does this by inspecting
your path.
.. _spack-compilers:
``spack compilers``
~~~~~~~~~~~~~~~~~~~~~~~
You can see which compilers spack has found by running ``spack
compilers`` or ``spack compiler list``::
$ spack compilers
==> Available compilers
-- gcc ---------------------------------------------------------
gcc@4.9.0 gcc@4.8.0 gcc@4.7.0 gcc@4.6.2 gcc@4.4.7
gcc@4.8.2 gcc@4.7.1 gcc@4.6.3 gcc@4.6.1 gcc@4.1.2
-- intel -------------------------------------------------------
intel@15.0.0 intel@14.0.0 intel@13.0.0 intel@12.1.0 intel@10.0
intel@14.0.3 intel@13.1.1 intel@12.1.5 intel@12.0.4 intel@9.1
intel@14.0.2 intel@13.1.0 intel@12.1.3 intel@11.1
intel@14.0.1 intel@13.0.1 intel@12.1.2 intel@10.1
-- clang -------------------------------------------------------
clang@3.4 clang@3.3 clang@3.2 clang@3.1
-- pgi ---------------------------------------------------------
pgi@14.3-0 pgi@13.2-0 pgi@12.1-0 pgi@10.9-0 pgi@8.0-1
pgi@13.10-0 pgi@13.1-1 pgi@11.10-0 pgi@10.2-0 pgi@7.1-3
pgi@13.6-0 pgi@12.8-0 pgi@11.1-0 pgi@9.0-4 pgi@7.0-6
Any of these compilers can be used to build Spack packages. More on
how this is done is in :ref:`sec-specs`.
.. _spack-compiler-add:
``spack compiler add``
~~~~~~~~~~~~~~~~~~~~~~~
An alias for ``spack compiler find``.
.. _spack-compiler-find:
``spack compiler find``
~~~~~~~~~~~~~~~~~~~~~~~
If you do not see a compiler in this list, but you want to use it with
Spack, you can simply run ``spack compiler find`` with the path to
where the compiler is installed. For example::
$ spack compiler find /usr/local/tools/ic-13.0.079
==> Added 1 new compiler to /Users/gamblin2/.spack/compilers.yaml
intel@13.0.079
Or you can run ``spack compiler find`` with no arguments to force
auto-detection. This is useful if you do not know where compilers are
installed, but you know that new compilers have been added to your
``PATH``. For example, using dotkit, you might do this::
$ module load gcc-4.9.0
$ spack compiler find
==> Added 1 new compiler to /Users/gamblin2/.spack/compilers.yaml
gcc@4.9.0
This loads the environment module for gcc-4.9.0 to add it to
``PATH``, and then it adds the compiler to Spack.
.. _spack-compiler-info:
``spack compiler info``
~~~~~~~~~~~~~~~~~~~~~~~
If you want to see specifics on a particular compiler, you can run
``spack compiler info`` on it::
$ spack compiler info intel@15
intel@15.0.0:
cc = /usr/local/bin/icc-15.0.090
cxx = /usr/local/bin/icpc-15.0.090
f77 = /usr/local/bin/ifort-15.0.090
fc = /usr/local/bin/ifort-15.0.090
This shows which C, C++, and Fortran compilers were detected by Spack.
Notice also that we didn't have to be too specific about the
version. We just said ``intel@15``, and information about the only
matching Intel compiler was displayed.
Manual compiler configuration
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If auto-detection fails, you can manually configure a compiler by
editing your ``~/.spack/compilers.yaml`` file. You can do this by running
``spack config edit compilers``, which will open the file in your ``$EDITOR``.
Each compiler configuration in the file looks like this::
...
chaos_5_x86_64_ib:
...
intel@15.0.0:
cc: /usr/local/bin/icc-15.0.024-beta
cxx: /usr/local/bin/icpc-15.0.024-beta
f77: /usr/local/bin/ifort-15.0.024-beta
fc: /usr/local/bin/ifort-15.0.024-beta
...
The chaos_5_x86_64_ib string is an architecture string, and multiple
compilers can be listed underneath an architecture. The architecture
string may be replaced with the string 'all' to signify compilers that
work on all architectures.
For compilers, like ``clang``, that do not support Fortran, put
``None`` for ``f77`` and ``fc``::
clang@3.3svn:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: None
fc: None
Once you save the file, the configured compilers will show up in the
list displayed by ``spack compilers``.
.. _sec-specs:
Specs & dependencies
-------------------------
We know that ``spack install``, ``spack uninstall``, and other
commands take a package name with an optional version specifier. In
Spack, that descriptor is called a *spec*. Spack uses specs to refer
to a particular build configuration (or configurations) of a package.
Specs are more than a package name and a version; you can use them to
specify the compiler, compiler version, architecture, compile options,
and dependency options for a build. In this section, we'll go over
the full syntax of specs.
Here is an example of a much longer spec than we've seen thus far::
mpileaks @1.2:1.4 %gcc@4.7.5 +debug -qt =bgqos_0 ^callpath @1.1 %gcc@4.7.2
If provided to ``spack install``, this will install the ``mpileaks``
library at some version between ``1.2`` and ``1.4`` (inclusive),
built using ``gcc`` at version 4.7.5 for the Blue Gene/Q architecture,
with debug options enabled, and without Qt support. Additionally, it
says to link it with the ``callpath`` library (which it depends on),
and to build callpath with ``gcc`` 4.7.2. Most specs will not be as
complicated as this one, but this is a good example of what is
possible with specs.
More formally, a spec consists of the following pieces:
* Package name identifier (``mpileaks`` above)
* ``@`` Optional version specifier (``@1.2:1.4``)
* ``%`` Optional compiler specifier, with an optional compiler version
(``gcc`` or ``gcc@4.7.3``)
* ``+`` or ``-`` or ``~`` Optional variant specifiers (``+debug``,
``-qt``, or ``~qt``)
* ``=`` Optional architecture specifier (``bgqos_0``)
* ``^`` Dependency specs (``^callpath@1.1``)
There are two things to notice here. The first is that specs are
recursively defined. That is, each dependency after ``^`` is a spec
itself. The second is that everything is optional *except* for the
initial package name identifier. Users can be as vague or as specific
as they want about the details of building packages, and this makes
spack good for beginners and experts alike.
To really understand what's going on above, we need to think about how
software is structured. An executable or a library (these are
generally the artifacts produced by building software) depends on
other libraries in order to run. We can represent the relationship
between a package and its dependencies as a graph. Here is the full
dependency graph for ``mpileaks``:
.. graphviz::
digraph {
mpileaks -> mpich
mpileaks -> callpath -> mpich
callpath -> dyninst
dyninst -> libdwarf -> libelf
dyninst -> libelf
}
Each box above is a package and each arrow represents a dependency on
some other package. For example, we say that the package ``mpileaks``
*depends on* ``callpath`` and ``mpich``. ``mpileaks`` also depends
*indirectly* on ``dyninst``, ``libdwarf``, and ``libelf``, in that
these libraries are dependencies of ``callpath``. To install
``mpileaks``, Spack has to build all of these packages. Dependency
graphs in Spack have to be acyclic, and the *depends on* relationship
is directional, so this is a *directed, acyclic graph* or *DAG*.
The package name identifier in the spec is the root of some dependency
DAG, and the DAG itself is implicit. Spack knows the precise
dependencies among packages, but users do not need to know the full
DAG structure. Each ``^`` in the full spec refers to some dependency
of the root package. Spack will raise an error if you supply a name
after ``^`` that the root does not actually depend on (e.g. ``mpileaks
^emacs@23.3``).
Spack further simplifies things by only allowing one configuration of
each package within any single build. Above, both ``mpileaks`` and
``callpath`` depend on ``mpich``, but ``mpich`` appears only once in
the DAG. You cannot build an ``mpileaks`` version that depends on one
version of ``mpich`` *and* on a ``callpath`` version that depends on
some *other* version of ``mpich``. In general, such a configuration
would likely behave unexpectedly at runtime, and Spack enforces this
to ensure a consistent runtime environment.
The point of specs is to abstract this full DAG from Spack users. If
a user does not care about the DAG at all, she can refer to mpileaks
by simply writing ``mpileaks``. If she knows that ``mpileaks``
indirectly uses ``dyninst`` and she wants a particular version of
``dyninst``, then she can refer to ``mpileaks ^dyninst@8.1``. Spack
will fill in the rest when it parses the spec; the user only needs to
know package names and minimal details about their relationship.
When spack prints out specs, it sorts package names alphabetically to
normalize the way they are displayed, but users do not need to worry
about this when they write specs. The only restriction on the order
of dependencies within a spec is that they appear *after* the root
package. For example, these two specs represent exactly the same
configuration:
.. code-block:: sh
mpileaks ^callpath@1.0 ^libelf@0.8.3
mpileaks ^libelf@0.8.3 ^callpath@1.0
You can put all the same modifiers on dependency specs that you would
put on the root spec. That is, you can specify their versions,
compilers, variants, and architectures just like any other spec.
Specifiers are associated with the nearest package name to their left.
For example, above, ``@1.1`` and ``%gcc@4.7.2`` associates with the
``callpath`` package, while ``@1.2:1.4``, ``%gcc@4.7.5``, ``+debug``,
``-qt``, and ``=bgqos_0`` all associate with the ``mpileaks`` package.
In the diagram above, ``mpileaks`` depends on ``mpich`` with an
unspecified version, but packages can depend on other packages with
*constraints* by adding more specifiers. For example, ``mpileaks``
could depend on ``mpich@1.2:`` if it can only build with version
``1.2`` or higher of ``mpich``.
Below are more details about the specifiers that you can add to specs.
Version specifier
~~~~~~~~~~~~~~~~~~~~~~~
A version specifier comes somewhere after a package name and starts
with ``@``. It can be a single version, e.g. ``@1.0``, ``@3``, or
``@1.2a7``. Or, it can be a range of versions, such as ``@1.0:1.5``
(all versions between ``1.0`` and ``1.5``, inclusive). Version ranges
can be open, e.g. ``:3`` means any version up to and including ``3``.
This would include ``3.4`` and ``3.4.2``. ``4.2:`` means any version
above and including ``4.2``. Finally, a version specifier can be a
set of arbitrary versions, such as ``@1.0,1.5,1.7`` (``1.0``, ``1.5``,
or ``1.7``). When you supply such a specifier to ``spack install``,
it constrains the set of versions that Spack will install.
If the version spec is not provided, then Spack will choose one
according to policies set for the particular spack installation. If
the spec is ambiguous, i.e. it could match multiple versions, Spack
will choose a version within the spec's constraints according to
policies set for the particular Spack installation.
Details about how versions are compared and how Spack determines if
one version is less than another are discussed in the developer guide.
Compiler specifier
~~~~~~~~~~~~~~~~~~~~~~~
A compiler specifier comes somewhere after a package name and starts
with ``%``. It tells Spack what compiler(s) a particular package
should be built with. After the ``%`` should come the name of some
registered Spack compiler. This might include ``gcc``, or ``intel``,
but the specific compilers available depend on the site. You can run
``spack compilers`` to get a list; more on this below.
The compiler spec can be followed by an optional *compiler version*.
A compiler version specifier looks exactly like a package version
specifier. Version specifiers will associate with the nearest package
name or compiler specifier to their left in the spec.
If the compiler spec is omitted, Spack will choose a default compiler
based on site policies.
Variants
~~~~~~~~~~~~~~~~~~~~~~~
.. Note::
Variants are not yet supported, but will be in the next Spack
release (0.9), due in Q2 2015.
Variants are named options associated with a particular package, and
they can be turned on or off. For example, above, supplying
``+debug`` causes ``mpileaks`` to be built with debug flags. The
names of particular variants available for a package depend on what
was provided by the package author. ``spack info <package>`` will
provide information on what build variants are available.
Depending on the package a variant may be on or off by default. For
``mpileaks`` here, ``debug`` is off by default, and we turned it on
with ``+debug``. If a package is on by default you can turn it off by
either adding ``-name`` or ``~name`` to the spec.
There are two syntaxes here because, depending on context, ``~`` and
``-`` may mean different things. In most shells, the following will
result in the shell performing home directory substitution:
.. code-block:: sh
mpileaks ~debug # shell may try to substitute this!
mpileaks~debug # use this instead
If there is a user called ``debug``, the ``~`` will be incorrectly
expanded. In this situation, you would want to write ``mpileaks
-debug``. However, ``-`` can be ambiguous when included after a
package name without spaces:
.. code-block:: sh
mpileaks-debug # wrong!
mpileaks -debug # right
Spack allows the ``-`` character to be part of package names, so the
above will be interpreted as a request for the ``mpileaks-debug``
package, not a request for ``mpileaks`` built without ``debug``
options. In this scenario, you should write ``mpileaks~debug`` to
avoid ambiguity.
When spack normalizes specs, it prints them out with no spaces and
uses only ``~`` for disabled variants. We allow ``-`` and spaces on
the command line is provided for convenience and legibility.
Architecture specifier
~~~~~~~~~~~~~~~~~~~~~~~
.. Note::
Architecture specifiers are part of specs but are not yet
functional. They will be in Spack version 1.0, due in Q3 2015.
The architecture specifier starts with a ``=`` and also comes after
some package name within a spec. It allows a user to specify a
particular architecture for the package to be built. This is mostly
used for architectures that need cross-compilation, and in most cases,
users will not need to specify the architecture when they install a
package.
.. _sec-virtual-dependencies:
Virtual dependencies
-------------------------
The dependence graph for ``mpileaks`` we saw above wasn't *quite*
accurate. ``mpileaks`` uses MPI, which is an interface that has many
different implementations. Above, we showed ``mpileaks`` and
``callpath`` depending on ``mpich``, which is one *particular*
implementation of MPI. However, we could build either with another
implementation, such as ``openmpi`` or ``mvapich``.
Spack represents interfaces like this using *virtual dependencies*.
The real dependency DAG for ``mpileaks`` looks like this:
.. graphviz::
digraph {
mpi [color=red]
mpileaks -> mpi
mpileaks -> callpath -> mpi
callpath -> dyninst
dyninst -> libdwarf -> libelf
dyninst -> libelf
}
Notice that ``mpich`` has now been replaced with ``mpi``. There is no
*real* MPI package, but some packages *provide* the MPI interface, and
these packages can be substituted in for ``mpi`` when ``mpileaks`` is
built.
You can see what virtual packages a particular package provides by
getting info on it:
.. command-output:: spack info mpich
Spack is unique in that its virtual packages can be versioned, just
like regular packages. A particular version of a package may provide
a particular version of a virtual package, and we can see above that
``mpich`` versions ``1`` and above provide all ``mpi`` interface
versions up to ``1``, and ``mpich`` versions ``3`` and above provide
``mpi`` versions up to ``3``. A package can *depend on* a particular
version of a virtual package, e.g. if an application needs MPI-2
functions, it can depend on ``mpi@2:`` to indicate that it needs some
implementation that provides MPI-2 functions.
Constraining virtual packages
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When installing a package that depends on a virtual package, you can
opt to specify the particular provider you want to use, or you can let
Spack pick. For example, if you just type this::
spack install mpileaks
Then spack will pick a provider for you according to site policies.
If you really want a particular version, say mpich, then you could
run this instead::
spack install mpileaks ^mpich
This forces spack to use some version of ``mpich`` for its
implementation. As always, you can be even more specific and require
a particular ``mpich`` version::
spack install mpileaks ^mpich@3
The ``mpileaks`` package in particular only needs MPI-1 commands, so
any MPI implementation will do. If another package depends on
``mpi@2`` and you try to give it an insufficient MPI implementation
(e.g., one that provides only ``mpi@:1``), then Spack will raise an
error. Likewise, if you try to plug in some package that doesn't
provide MPI, Spack will raise an error.
.. _spack-providers:
``spack providers``
~~~~~~~~~~~~~~~~~~~~~~~~~~
You can see what packages provide a particular virtual package using
``spack providers``. If you wanted to see what packages provide
``mpi``, you would just run:
.. command-output:: spack providers mpi
And if you *only* wanted to see packages that provide MPI-2, you would
add a version specifier to the spec:
.. command-output:: spack providers mpi@2
Notice that the package versions that provide insufficient MPI
versions are now filtered out.
.. _shell-support:
Integration with module systems
-------------------------------
.. note::
Environment module support is currently experimental and should not
be considered a stable feature of Spack. In particular, the
interface and/or generated module names may change in future
versions.
Spack provides some integration with
`Environment Modules <http://modules.sourceforge.net/>`_
and `Dotkit <https://computing.llnl.gov/?set=jobs&page=dotkit>`_ to make
it easier to use the packages it installed.
Installing Environment Modules
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In order to use Spack's generated environment modules, you must have
installed the *Environment Modules* package. On many Linux
distributions, this can be installed from the vendor's repository:
.. code-block:: sh
yum install environment-modules # (Fedora/RHEL/CentOS)
apt-get install environment-modules # (Ubuntu/Debian)
If your Linux distribution does not have
Environment Modules, you can get it with Spack:
.. code-block:: sh
spack install environment-modules
In this case to activate it automatically you need to add the following two
lines to your ``.bashrc`` profile (or similar):
.. code-block:: sh
MODULES_HOME=`spack location -i environment-modules`
source ${MODULES_HOME}/Modules/init/bash
If you use a Unix shell other than ``bash``, modify the commands above
accordingly and source the appropriate file in
``${MODULES_HOME}/Modules/init/``.
.. TODO : Add a similar section on how to install dotkit ?
Spack and module systems
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
You can enable shell support by sourcing some files in the
``/share/spack`` directory.
For ``bash`` or ``ksh``, run:
.. code-block:: sh
. ${SPACK_ROOT}/share/spack/setup-env.sh
For ``csh`` and ``tcsh`` run:
.. code-block:: csh
setenv SPACK_ROOT /path/to/spack
source $SPACK_ROOT/share/spack/setup-env.csh
You can put the above code in your ``.bashrc`` or ``.cshrc``, and
Spack's shell support will be available on the command line.
When you install a package with Spack, it automatically generates a module file
that lets you add the package to your environment.
Currently, Spack supports the generation of `Environment Modules
<http://wiki.tcl.tk/12999>`_ and `Dotkit
<https://computing.llnl.gov/?set=jobs&page=dotkit>`_. Generated
module files for each of these systems can be found in these
directories:
.. code-block:: sh
${SPACK_ROOT}/share/spack/modules
${SPACK_ROOT}/share/spack/dotkit
The directories are automatically added to your ``MODULEPATH`` and
``DK_NODE`` environment variables when you enable Spack's `shell
support <shell-support_>`_.
Using Modules & Dotkits
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If you have shell support enabled you should be able to run either
``module avail`` or ``use -l spack`` to see what modules/dotkits have
been installed. Here is sample output of those programs, showing lots
of installed packages.
.. code-block:: sh
$ module avail
------- /home/gamblin2/spack/share/spack/modules/chaos_5_x86_64_ib --------
adept-utils@1.0%gcc@4.4.7-5adef8da libelf@0.8.13%gcc@4.4.7
automaded@1.0%gcc@4.4.7-d9691bb0 libelf@0.8.13%intel@15.0.0
boost@1.55.0%gcc@4.4.7 mpc@1.0.2%gcc@4.4.7-559607f5
callpath@1.0.1%gcc@4.4.7-5dce4318 mpfr@3.1.2%gcc@4.4.7
dyninst@8.1.2%gcc@4.4.7-b040c20e mpich@3.0.4%gcc@4.4.7
gcc@4.9.1%gcc@4.4.7-93ab98c5 mpich@3.0.4%gcc@4.9.0
gmp@6.0.0a%gcc@4.4.7 mrnet@4.1.0%gcc@4.4.7-72b7881d
graphlib@2.0.0%gcc@4.4.7 netgauge@2.4.6%gcc@4.9.0-27912b7b
launchmon@1.0.1%gcc@4.4.7 stat@2.1.0%gcc@4.4.7-51101207
libNBC@1.1.1%gcc@4.9.0-27912b7b sundials@2.5.0%gcc@4.9.0-27912b7b
libdwarf@20130729%gcc@4.4.7-b52fac98
.. code-block:: sh
$ use -l spack
spack ----------
adept-utils@1.0%gcc@4.4.7-5adef8da - adept-utils @1.0
automaded@1.0%gcc@4.4.7-d9691bb0 - automaded @1.0
boost@1.55.0%gcc@4.4.7 - boost @1.55.0
callpath@1.0.1%gcc@4.4.7-5dce4318 - callpath @1.0.1
dyninst@8.1.2%gcc@4.4.7-b040c20e - dyninst @8.1.2
gmp@6.0.0a%gcc@4.4.7 - gmp @6.0.0a
libNBC@1.1.1%gcc@4.9.0-27912b7b - libNBC @1.1.1
libdwarf@20130729%gcc@4.4.7-b52fac98 - libdwarf @20130729
libelf@0.8.13%gcc@4.4.7 - libelf @0.8.13
libelf@0.8.13%intel@15.0.0 - libelf @0.8.13
mpc@1.0.2%gcc@4.4.7-559607f5 - mpc @1.0.2
mpfr@3.1.2%gcc@4.4.7 - mpfr @3.1.2
mpich@3.0.4%gcc@4.4.7 - mpich @3.0.4
mpich@3.0.4%gcc@4.9.0 - mpich @3.0.4
netgauge@2.4.6%gcc@4.9.0-27912b7b - netgauge @2.4.6
sundials@2.5.0%gcc@4.9.0-27912b7b - sundials @2.5.0
The names here should look familiar, they're the same ones from
``spack find``. You *can* use the names here directly. For example,
you could type either of these commands to load the callpath module:
.. code-block:: sh
use callpath@1.0.1%gcc@4.4.7-5dce4318
.. code-block:: sh
module load callpath@1.0.1%gcc@4.4.7-5dce4318
Neither of these is particularly pretty, easy to remember, or
easy to type. Luckily, Spack has its own interface for using modules
and dotkits. You can use the same spec syntax you're used to:
========================= ==========================
Environment Modules Dotkit
========================= ==========================
``spack load <spec>`` ``spack use <spec>``
``spack unload <spec>`` ``spack unuse <spec>``
========================= ==========================
And you can use the same shortened names you use everywhere else in
Spack. For example, this will add the ``mpich`` package built with
``gcc`` to your path:
.. code-block:: sh
$ spack install mpich %gcc@4.4.7
# ... wait for install ...
$ spack use mpich %gcc@4.4.7
Prepending: mpich@3.0.4%gcc@4.4.7 (ok)
$ which mpicc
~/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpich@3.0.4/bin/mpicc
Or, similarly with modules, you could type:
.. code-block:: sh
$ spack load mpich %gcc@4.4.7
These commands will add appropriate directories to your ``PATH``,
``MANPATH``, ``CPATH``, and ``LD_LIBRARY_PATH``. When you no longer want to use
a package, you can type unload or unuse similarly:
.. code-block:: sh
$ spack unload mpich %gcc@4.4.7 # modules
$ spack unuse mpich %gcc@4.4.7 # dotkit
.. note::
These ``use``, ``unuse``, ``load``, and ``unload`` subcommands are
only available if you have enabled Spack's shell support *and* you
have dotkit or modules installed on your machine.
Ambiguous module names
~~~~~~~~~~~~~~~~~~~~~~~~
If a spec used with load/unload or use/unuse is ambiguous (i.e. more
than one installed package matches it), then Spack will warn you:
.. code-block:: sh
$ spack load libelf
==> Error: Multiple matches for spec libelf. Choose one:
libelf@0.8.13%gcc@4.4.7=chaos_5_x86_64_ib
libelf@0.8.13%intel@15.0.0=chaos_5_x86_64_ib
You can either type the ``spack load`` command again with a fully
qualified argument, or you can add just enough extra constraints to
identify one package. For example, above, the key differentiator is
that one ``libelf`` is built with the Intel compiler, while the other
used ``gcc``. You could therefore just type:
.. code-block:: sh
$ spack load libelf %intel
To identify just the one built with the Intel compiler.
Module files generation and customization
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Environment Modules and Dotkit files are generated when packages are installed,
and are placed in the following directories under the Spack root:
.. code-block:: sh
${SPACK_ROOT}/share/spack/modules
${SPACK_ROOT}/share/spack/dotkit
The content that gets written in each module file can be customized in two ways:
1. overriding part of the ``spack.Package`` API within a ``package.py``
2. writing dedicated configuration files
Override ``Package`` API
^^^^^^^^^^^^^^^^^^^^^^^^
There are currently two methods in ``spack.Package`` that may affect the content
of module files:
.. code-block:: python
def setup_environment(self, spack_env, run_env):
"""Set up the compile and runtime environments for a package."""
pass
.. code-block:: python
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
"""Set up the environment of packages that depend on this one"""
pass
As briefly stated in the comments, the first method lets you customize the
module file content for the package you are currently writing, the second
allows for modifications to your dependees module file. In both cases one
needs to fill ``run_env`` with the desired list of environment modifications.
Example : ``builtin/packages/python/package.py``
""""""""""""""""""""""""""""""""""""""""""""""""
The ``python`` package that comes with the ``builtin`` Spack repository
overrides ``setup_dependent_environment`` in the following way:
.. code-block:: python
def setup_dependent_environment(self, spack_env, run_env, extension_spec):
# ...
if extension_spec.package.extends(self.spec):
run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
to insert the appropriate ``PYTHONPATH`` modifications in the module
files of python packages.
Configuration files
^^^^^^^^^^^^^^^^^^^
Another way of modifying the content of module files is writing a
``modules.yaml`` configuration file. Following usual Spack conventions, this
file can be placed either at *site* or *user* scope.
The default site configuration reads:
.. literalinclude:: ../../../etc/spack/modules.yaml
:language: yaml
It basically inspects the installation prefixes for the
existence of a few folders and, if they exist, it prepends a path to a given
list of environment variables.
For each module system that can be enabled a finer configuration is possible:
.. code-block:: yaml
modules:
tcl:
# contains environment modules specific customizations
dotkit:
# contains dotkit specific customizations
The structure under the ``tcl`` and ``dotkit`` keys is almost equal, and will
be showcased in the following by some examples.
Select module files by spec constraints
"""""""""""""""""""""""""""""""""""""""
Using spec syntax it's possible to have different customizations for different
groups of module files.
Considering :
.. code-block:: yaml
modules:
tcl:
all: # Default addition for every package
environment:
set:
BAR: 'bar'
^openmpi:: # A double ':' overrides previous rules
environment:
set:
BAR: 'baz'
zlib:
environment:
prepend_path:
LD_LIBRARY_PATH: 'foo'
zlib%gcc@4.8:
environment:
unset:
- FOOBAR
what will happen is that:
- every module file will set ``BAR=bar``
- unless the associated spec satisfies ``^openmpi`` in which case ``BAR=baz``
- any spec that satisfies ``zlib`` will additionally prepend ``foo`` to ``LD_LIBRARY_PATH``
- any spec that satisfies ``zlib%gcc@4.8`` will additionally unset ``FOOBAR``
.. note::
Order does matter
The modifications associated with the ``all`` keyword are always evaluated
first, no matter where they appear in the configuration file. All the other
spec constraints are instead evaluated top to bottom.
Filter modifications out of module files
""""""""""""""""""""""""""""""""""""""""
Modifications to certain environment variables in module files are generated by
default. Suppose you would like to avoid having ``CPATH`` and ``LIBRARY_PATH``
modified by your dotkit modules. Then :
.. code-block:: yaml
modules:
dotkit:
all:
filter:
environment_blacklist: ['CPATH', 'LIBRARY_PATH'] # Exclude changes to any of these variables
will generate dotkit module files that will not contain modifications to either
``CPATH`` or ``LIBRARY_PATH`` and environment module files that instead will
contain those modifications.
Autoload dependencies
"""""""""""""""""""""
The following lines in ``modules.yaml``:
.. code-block:: yaml
modules:
tcl:
all:
autoload: 'direct'
will produce environment module files that will automatically load their direct
dependencies.
.. note::
Allowed values for ``autoload`` statements
Allowed values for ``autoload`` statements are either ``none``, ``direct``
or ``all``. In ``tcl`` configuration it is possible to use the option
``prerequisites`` that accepts the same values and will add ``prereq``
statements instead of automatically loading other modules.
Blacklist or whitelist the generation of specific module files
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Sometimes it is desirable not to generate module files, a common use case being
not providing the users with software built using the system compiler.
A configuration file like:
.. code-block:: yaml
modules:
tcl:
whitelist: ['gcc', 'llvm'] # Whitelist will have precedence over blacklist
blacklist: ['%gcc@4.4.7'] # Assuming gcc@4.4.7 is the system compiler
will skip module file generation for anything that satisfies ``%gcc@4.4.7``,
with the exception of specs that satisfy ``gcc`` or ``llvm``.
Customize the naming scheme and insert conflicts
""""""""""""""""""""""""""""""""""""""""""""""""
A configuration file like:
.. code-block:: yaml
modules:
tcl:
naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
all:
conflict: ['{name}', 'intel/14.0.1']
will create module files that will conflict with ``intel/14.0.1`` and with the
base directory of the same module, effectively preventing the possibility to
load two or more versions of the same software at the same time.
.. note::
Tokens available for the naming scheme
currently only the tokens shown in the example are available to construct
the naming scheme
.. note::
The ``conflict`` option is ``tcl`` specific
Regenerating module files
^^^^^^^^^^^^^^^^^^^^^^^^^
Sometimes you may need to regenerate the modules files. For example,
if newer, fancier module support is added to Spack at some later date,
you may want to regenerate all the modules to take advantage of these
new features.
.. _spack-module:
``spack module refresh``
""""""""""""""""""""""""
Running ``spack module refresh`` will remove the
``share/spack/modules`` and ``share/spack/dotkit`` directories, then
regenerate all module and dotkit files from scratch:
.. code-block:: sh
$ spack module refresh
==> Regenerating tcl module files.
==> Regenerating dotkit module files.
.. _extensions:
Extensions & Python support
------------------------------------
Spack's installation model assumes that each package will live in its
own install prefix. However, certain packages are typically installed
*within* the directory hierarchy of other packages. For example,
modules in interpreted languages like `Python
<https://www.python.org>`_ are typically installed in the
``$prefix/lib/python-2.7/site-packages`` directory.
Spack has support for this type of installation as well. In Spack,
a package that can live inside the prefix of another package is called
an *extension*. Suppose you have Python installed like so:
.. code-block:: sh
$ spack find python
==> 1 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
python@2.7.8
.. _spack-extensions:
``spack extensions``
~~~~~~~~~~~~~~~~~~~~~~~
You can find extensions for your Python installation like this:
.. code-block:: sh
$ spack extensions python
==> python@2.7.8%gcc@4.4.7=chaos_5_x86_64_ib-703c7a96
==> 36 extensions:
geos py-ipython py-pexpect py-pyside py-sip
py-basemap py-libxml2 py-pil py-pytz py-six
py-biopython py-mako py-pmw py-rpy2 py-sympy
py-cython py-matplotlib py-pychecker py-scientificpython py-virtualenv
py-dateutil py-mpi4py py-pygments py-scikit-learn
py-epydoc py-mx py-pylint py-scipy
py-gnuplot py-nose py-pyparsing py-setuptools
py-h5py py-numpy py-pyqt py-shiboken
==> 12 installed:
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2
py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10
py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1
py-matplotlib@1.4.2 py-pyparsing@2.0.3 py-six@1.9.0
==> None activated.
The extensions are a subset of what's returned by ``spack list``, and
they are packages like any other. They are installed into their own
prefixes, and you can see this with ``spack find -p``:
.. code-block:: sh
$ spack find -p py-numpy
==> 1 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
py-numpy@1.9.1 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/py-numpy@1.9.1-66733244
However, even though this package is installed, you cannot use it
directly when you run ``python``:
.. code-block:: sh
$ spack load python
$ python
Python 2.7.8 (default, Feb 17 2015, 01:35:25)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-11)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named numpy
>>>
Extensions & Environment Modules
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
There are two ways to get ``numpy`` working in Python. The first is
to use :ref:`shell-support`. You can simply ``use`` or ``load`` the
module for the extension, and it will be added to the ``PYTHONPATH``
in your current shell.
For tcl modules:
.. code-block:: sh
$ spack load python
$ spack load py-numpy
or, for dotkit:
.. code-block:: sh
$ spack use python
$ spack use py-numpy
Now ``import numpy`` will succeed for as long as you keep your current
session open.
Activating Extensions
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
It is often desirable to have certain packages *always* available as
part of a Python installation. Spack offers a more permanent solution
for this case. Instead of requiring users to load particular
environment modules, you can *activate* the package within the Python
installation:
.. _spack-activate:
``spack activate``
^^^^^^^^^^^^^^^^^^^^^^^
.. code-block:: sh
$ spack activate py-numpy
==> Activated extension py-setuptools@11.3.1%gcc@4.4.7=chaos_5_x86_64_ib-3c74eb69 for python@2.7.8%gcc@4.4.7.
==> Activated extension py-nose@1.3.4%gcc@4.4.7=chaos_5_x86_64_ib-5f70f816 for python@2.7.8%gcc@4.4.7.
==> Activated extension py-numpy@1.9.1%gcc@4.4.7=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7.
Several things have happened here. The user requested that
``py-numpy`` be activated in the ``python`` installation it was built
with. Spack knows that ``py-numpy`` depends on ``py-nose`` and
``py-setuptools``, so it activated those packages first. Finally,
once all dependencies were activated in the ``python`` installation,
``py-numpy`` was activated as well.
If we run ``spack extensions`` again, we now see the three new
packages listed as activated:
.. code-block:: sh
$ spack extensions python
==> python@2.7.8%gcc@4.4.7=chaos_5_x86_64_ib-703c7a96
==> 36 extensions:
geos py-ipython py-pexpect py-pyside py-sip
py-basemap py-libxml2 py-pil py-pytz py-six
py-biopython py-mako py-pmw py-rpy2 py-sympy
py-cython py-matplotlib py-pychecker py-scientificpython py-virtualenv
py-dateutil py-mpi4py py-pygments py-scikit-learn
py-epydoc py-mx py-pylint py-scipy
py-gnuplot py-nose py-pyparsing py-setuptools
py-h5py py-numpy py-pyqt py-shiboken
==> 12 installed:
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2
py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10
py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1
py-matplotlib@1.4.2 py-pyparsing@2.0.3 py-six@1.9.0
==> 3 currently activated:
-- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
py-nose@1.3.4 py-numpy@1.9.1 py-setuptools@11.3.1
Now, when a user runs python, ``numpy`` will be available for import
*without* the user having to explicitly loaded. ``python@2.7.8`` now
acts like a system Python installation with ``numpy`` installed inside
of it.
Spack accomplishes this by symbolically linking the *entire* prefix of
the ``py-numpy`` into the prefix of the ``python`` package. To the
python interpreter, it looks like ``numpy`` is installed in the
``site-packages`` directory.
The only limitation of activation is that you can only have a *single*
version of an extension activated at a time. This is because multiple
versions of the same extension would conflict if symbolically linked
into the same prefix. Users who want a different version of a package
can still get it by using environment modules, but they will have to
explicitly load their preferred version.
``spack activate -f``
^^^^^^^^^^^^^^^^^^^^^^^^^
If, for some reason, you want to activate a package *without* its
dependencies, you can use ``spack activate -f``:
.. code-block:: sh
$ spack activate -f py-numpy
==> Activated extension py-numpy@1.9.1%gcc@4.4.7=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7.
.. _spack-deactivate:
``spack deactivate``
^^^^^^^^^^^^^^^^^^^^^^^^^
We've seen how activating an extension can be used to set up a default
version of a Python module. Obviously, you may want to change that at
some point. ``spack deactivate`` is the command for this. There are
several variants:
* ``spack deactivate <extension>`` will deactivate a single
extension. If another activated extension depends on this one,
Spack will warn you and exit with an error.
* ``spack deactivate -f <extension>`` deactivates an extension
regardless of packages that depend on it.
* ``spack deactivate -a <extension>`` deactivates an extension and
all of its dependencies. Use ``-f`` to disregard dependents.
* ``spack deactivate -a <extendee>`` deactivates *all* activated
extensions of a package. For example, to deactivate *all* python
extensions, use::
spack deactivate -a python
Filesystem requirements
--------------------------
Spack currently needs to be run from a filesystem that supports
``flock`` locking semantics. Nearly all local filesystems and recent
versions of NFS support this, but parallel filesystems may be mounted
without ``flock`` support enabled. You can determine how your
filesystems are mounted with ``mount -p``. The output for a Lustre
filesystem might look like this:
.. code-block:: sh
$ mount -l | grep lscratch
pilsner-mds1-lnet0@o2ib100:/lsd on /p/lscratchd type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)
porter-mds1-lnet0@o2ib100:/lse on /p/lscratche type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)
Note the ``flock`` option on both Lustre mounts. If you do not see
this or a similar option for your filesystem, you may need ot ask your
system administrator to enable ``flock``.
This issue typically manifests with the error below:
.. code-block:: sh
$ ./spack find
Traceback (most recent call last):
File "./spack", line 176, in <module>
main()
File "./spack", line 154, in main
return_val = command(parser, args)
File "./spack/lib/spack/spack/cmd/find.py", line 170, in find
specs = set(spack.installed_db.query(**q_args))
File "./spack/lib/spack/spack/database.py", line 551, in query
with self.read_transaction():
File "./spack/lib/spack/spack/database.py", line 598, in __enter__
if self._enter() and self._acquire_fn:
File "./spack/lib/spack/spack/database.py", line 608, in _enter
return self._db.lock.acquire_read(self._timeout)
File "./spack/lib/spack/llnl/util/lock.py", line 103, in acquire_read
self._lock(fcntl.LOCK_SH, timeout) # can raise LockError.
File "./spack/lib/spack/llnl/util/lock.py", line 64, in _lock
fcntl.lockf(self._fd, op | fcntl.LOCK_NB)
IOError: [Errno 38] Function not implemented
A nicer error message is TBD in future versions of Spack.
Getting Help
-----------------------
.. _spack-help:
``spack help``
~~~~~~~~~~~~~~~~~~~~~~
If you don't find what you need here, the ``help`` subcommand will
print out out a list of *all* of ``spack``'s options and subcommands:
.. command-output:: spack help
Adding an argument, e.g. ``spack help <subcommand>``, will print out
usage information for a particular subcommand:
.. command-output:: spack help install
Alternately, you can use ``spack -h`` in place of ``spack help``, or
``spack <subcommand> -h`` to get help on a particular subcommand.
|