forked from easybuilders/easybuild-easyconfigs
-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathRELEASE_NOTES
847 lines (765 loc) · 53.4 KB
/
RELEASE_NOTES
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
This file contains a description of the major changes to the easybuild-easyconfigs EasyBuild package.
For more detailed information, please see the git log.
These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
The latest version of easybuild-easyconfig provides 5,093 easyconfig files, for 799 different software packages,
34 different (compiler) toolchains, 12 software bundles and 1 meta-package.
v2.6.0 (January 26th 2016)
--------------------------
feature + bugfix release
- add easyconfigs for foss/2016a and intel/2016 common toolchains (#2310, #2311, #2339, #2363)
incl. easyconfigs for Boost, CMake, Python, Perl using these toolchains
- added example easyconfig files for 21 new software packages:
BLASR (#922), BioKanga (#2247), BoltzTraP (#2365), basemap (#2221), CppUnit (#2271), EggLib (#2335),
FLASH (#2281), GLM (#2288), hub (#2249), MACS2 (#1983), MotEvo (#843), numba (#2243), PGI (#1833, #2367),
PLY (#2305), PaStiX (#2319, #2326), patchelf (#2327), pip (#2284), RSEM (#2316), RcppArmadillo (#2289),
SCDE (#2289), slepc4py (#2318)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including BamTools 2.4.0, Boost 1.60.0, Clang 3.7.1, DOLFIN/FFC/FIAT/Instant/UFL 1.6.0, GATE 7.0, GCC 5.3.0,
LLVM 3.7.1, pandas 0.17.1, PETSc 3.6.3, SAMtools 1.3, scipy 0.16.1, SLEPc 3.6.2, Trilinos 12.4.2,
Trinity 2.1.1, VTK 6.3.0
- various other enhancements, including:
- added new Cray* toolchain versions with pinned dependency versions (#2222)
- don't hardcode .so, use SHLIB_EXT constant instead (#2245)
- add custom sanity check in GEOS easyconfigs (#2285)
- various bug fixes, including:
- add Autotools (M4) as a build dependency in GMP v6.x easyconfigs (#2096)
- remove argparse from list of extensions in Python 3.2+ easyconfigs, since it became part of stdlib (#2323)
- various style fixes, including:
- get rid of tabs (#2302)
- remove trailing whitespace (#2341)
v2.5.0 (December 17th 2015)
---------------------------
feature + bugfix release
- add GCCcore easyconfig that can be used as base for all compilers (without getting in the way) (#2214)
- + easyconfig for GCC/4.9.3-2.25: bundle of GCCcore 4.9.3 and binutils 2.25
- intended to replace the GNU toolchain
- added example easyconfig files for 39 new software packages:
DIRAC (#2212), GeoIP (#2172, #2185), GeoIP-C (#2172, #2185), graph-tool (#1591), gtkglext (#2217),
Intel Advisor (#2210), InterProScan (#2225, #2227, #2234), intltool (#2136), kallisto (#2173), LibUUID (#1930),
LuaJIT (#2153), libXcursor (#2136), libXrandr (#2136), libXtst (#2143), libdap (#1930), libtasn1 (#2208),
libxkbcommon (#2136), MRtrix (#2217, #2218), MultiNest (#2166, #2168), Nipype (#2150), PPfold (#2183, #2187),
p11-kit (#2208), pangox-compat (#2217), Qt5 (#2136), randrproto (#2136), rhdf5 (#2175), Stampy (#2180, #2182),
scikit-umfpack (#2061), scp (Python pkg) (#2196), sleuth (#2175), traits (#2150), vincent (#2169, #2185),
XKeyboardConfig (#2136), xcb-util (#2136), xcb-util-image (#2136), xcb-util-keysyms (#2136),
xcb-util-renderutil (#2136), xcb-util-wm (#2136), zlibbioc (#2175)
- added new easyconfigs for existing toolchains:
intel/2015.08 (#2194), intel/2016.00 (#2209), intel/2016.01 (#2219), iomkl/2015.03 (#2155)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including CMake 3.4.1, HDF5 1.8.16, netCDF 4.3.3.1, netCDF-Fortran 4.4.2, numpy 1.10.1, Octave 4.0.0,
OpenFOAM 3.0.0, OpenFOAM-Extend 3.2, Python 2.7.11
- various other enhancements, including:
- add tidyr to R 3.2.1 easyconfigs (#2174)
- enable C++ support in MIGRATE-N (#2178)
- also installed shared libraries for AMD and UMFPACK in SuiteSparse (#2061)
- fix software name for ParaView (was: Paraview) (#2132)
- enable building of shared libraries for binutils (#2133)
- harden binutils built with dummy toolchain by linking to system libraries via RPATH (#2228)
- enhance easyconfig unit tests to check that each easyconfig file is in the right subdirectory (#2232)
- various bug fixes, including:
- fix ALADIN patch file to not use relative paths, and adjust list of ALADIN sources accordingly (#2207, #2213)
- rename patch files for OpenFOAM to be in line with other patches (#2226)
- fix typo in bzip2 source URLs (#2204)
- force linking of ncurses in libreadline (#2206)
- enable -fPIC in all zlib 1.2.8 easyconfigs (#2220)
- move Net-LibIDN/SRA-Toolkit/bbftpPRO/o2scl easyconfigs to right location (#2232)
- restrict parallel build in OpenFOAM-Extend easyconfigs via 'maxparallel', not 'parallel' (#2233)
v2.4.0 (November 10th 2015)
---------------------------
feature + bugfix release
- added example easyconfig files for 45 new software packages:
animation (#2007), ANSYS CFD (#1969), ANTLR (#1191, #1980), APR (#1970), APR-util (#1970), Aspera Connect (#2005),
ChIP-Seq (#2119), deap (#2082), DISCOVARdenovo (#1932), FastQC (#1984), fontsproto (#1618, #2038),
GraphicsMagick (#2007), HBase (#1990), ISIS (#1972), libedit (#293), libfontenc (#1618, #2038), libGLU (#1627),
libXdamage (#1618, #2038), libXfont (#1618, #2038), LLVM (#1620, #1989, #2031), MIGRATE-N (#1944), MIRA (#1938),
mympingpong (#2049), MySQLdb (#2011), NCO (#1191, #1980), NIPY (#2064), Nilearn (#2064), NiBabel (#2064),
PBZIP2 (#1038), PIL (#2062), PhyloCSF (#2018), pycairo (#2085), pydicom (#2063), Salmon (#2051), Samcef (#1941),
scikit-image (#1974, #2006), Serf (#1970), SSAHA2 (#1039), Subversion (#1970), SWASH (#2059, #2128), time (#1954),
Trim_Galore (#1984), Trimmomatic (#1987), WEKA (#1986), x264 (#2017)
- added new easyconfigs for existing toolchains: gimkl/2.11.5 (#2093)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Clang + LLVM 3.7.0, CMake 3.3.2, CUDA 7.5.18, hanythingondemand v3.0.1, Mesa 11.0.2, mpi4py v2.0.0,
ncurses 6.0, OpenFOAM 2.4.0, Paraview 4.4.0, Python 3.5.0, QuantumESPRESSO v5.2.1
- various other enhancements, including:
- enable 'pic' toolchain option in libxml2 easyconfigs (#1993)
- extend list of R libraries included in R v3.2.1 easyconfigs (#2042, #2046, #2067, #2072)
- add Rsubread in Bioconductor easyconfigs (#1971)
- various bug fixes, including:
- fix software name for BEEF (was 'libbeef') (#1679)
- add patch to install qhull.pc (pkgconfig) file with Qhull (#1975)
- don't enable experimental nouveau API in libdrm easyconfigs (#1994)
- fix dev version to follow PEP-440, as required by recent setuptools versions (#1997)
- required to avoid that setuptools transforms the version itself
- see also https://www.python.org/dev/peps/pep-0440/#developmental-releases
- correct homepage in Cufflinks easyconfigs (#2060)
- fix imports for set_tmpdir in easyblock unit tests after function was moved in EasyBuild framework (#2097)
- add patch for Tk 8.6.4 to fix problem with tk.tcl not being found (#2102)
- don't use %(version)s template in toolchain version, causes problems with HierarchicalMNS (#2104)
- fix sanity check paths in several easyconfig (#2109, #2120, #2121, #2125)
- required because of bug fix in sanity_check_step implementation
- CVXOPT, h5py, LIBSVM, libunistring, MDP, monty, PhyloCSF, Pyke, pandas, pycosat, pyhull, pymatgen,
python-dateutils, Seaborn, Theano, XML-LibXML, XML-Simple
v2.3.0 (September 2nd 2015)
---------------------------
feature + bugfix release
- added example easyconfig files for 19 new software packages:
ATK (#1780), Atkmm (#1780), cairomm (#1780), GLibmm (#1780), GlobalArrays (#1868), gdk-pixbuf (#1780),
gtk+ (#1780), Gtkmm (#1780), libbeef (#1827), libsigc++ (#1780), libsodium (#1876), MACS (#1869), MCR (#1677),
Molpro (#1880), NFFT (#1921), p7zip (#1931), Pangomm (#1780), pygraphviz (#1861), pycosat (#1859)
- added new easyconfigs for existing toolchains: GNU/4.9.3-2.25 (#1836), foss/2015b (#1695), intel/2015b (#1696)
add easyconfigs using this toolchain for BLAST+ 2.2.31, Boost 1.58.0, CP2K 2.6.1, OpenFOAM 2.3.1,
Perl 5.20.2 + 5.22.0 (bare), Python 2.7.10, R 3.2.1
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Boost 1.59.0, CP2K 2.6.1, GCC 5.2.0
- various other enhancements, including:
- enhance texinfo easyconfig w.r.t. texmf, only use it as a build dependency (#1840)
- enable building of ld.gold in binutils 2.25 (#1885)
- various bug fixes, including:
- fix enabling MPI support for h5py 2.5.0 (#1825)
- fix versions of Bioconductor packages + add a couple extra (#1828, #1852, #1895, #1917)
- put dummy values in place for builddir/installdir templates in easyconfigs unit tests (#1835)
- fix easyconfigs unit tests w.r.t. changes made in framework (#1853, #1870, #1874, #1875)
- add GMP as missing dep in Python 2.7.10 easyconfigs, required for pycrypto extension (#1858)
- specify installation prefix for SIP (#1888, #1892)
- add custom sanity check paths in various easyconfigs (#1889, #1894, #1897 - #1909)
- required because of fix in EasyBuild framework, causing default sanity check paths to be considered
for extensions that are installed as a module
- affected easyconfigs include: AnalyzeFMRI, Biggus, bibtexparser, DB_File, DBD-Pg, DBD-SQLite, DBD-mysql,
evmix, fmri, FPM, GraphViz, gsl, GSSAPI, MDP, mpi4py, ncdf, ncdf4, netifaces, NetLibIDN, networkx,
ordereddict, Parallel-ForkManager, paycheck, PyQuante, Pyke, PyQt, r2py, rjags, runjags, scikit-learn,
SOBAcl, vsc-processcontrol, vsc-mympirun-scoop, XML, XML-Dumper, XML-Parser, XML-Twig, YAML-Syck
- don't enable 'static' toolchain option in SuiteSparse 4.4.3 easyconfig (#1911)
- add --exclude unpack options for OpenFOAM 2.3.1 to avoid cyclic symlink causing problems when unpacking (#1925)
v2.2.0 (July 15th 2015)
-----------------------
feature + bugfix release
- added example easyconfig files for 62 new software packages:
ADF (#899), AutoDock_Vina (#808), bibtexparser (#1726), Biggus (#1770), Bismark (#990), blasr (#1662), BSMAP (#1171),
Check (#811), Circuitscape (#1222), CONTRAfold (#689), cramtools (#1741), DBD-Pg (#1066), DendroPy (#995),
EMAN2 (#1737), ETSF_IO (#727), eudev (#1578), fastqc (#1636), FDS (#814, #1617, #1625), FPM (#1440),
frealign (#1619), g2log (#1035), GC3Pie (#1692, #1756, #1768), GenotypeHarmonizer (#1672), gensim (#1762),
GraphViz (#1658), hisat (#1674), IDBA-UD (#1045), IMa2 (#828), IMPUTE2 (#824), JUBE (#1396), LAMARC (#760),
libXScrnSaver (#1653), MATIO (#1004), MuTect (#1483), ncdf (#617), NEMO (#1640), ngspice (#1116),
ordereddict (#1774), OSU Micro-Benchmarks (#1777), Parallel-ForkManager (#847), pBWA (#1009), PeakSeq (#1412),
Pillow (#1702), Pindel (#1126), PLUMED (#1596, #1665), PostgreSQL (#1066), PROJ (#1006), PyAMG (#1222), Pyke (#1776),
rpy2 (#1775), Sailfish (#1035), SCANMS (#1386), Seaborn (#1763), snpEff (#1680), SOBAcl (#1658),
SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot360ex (#1100), Vampir (#512),
VampirServer (#512), verifyBamID (#1675)
- added easyconfigs for 4 new software bundles:
R-bundle-Bioconductor (#1573, #1795), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759),
R-bundle-pbd (#1659)
- added easyconfigs for new GNU toolchain (#1346, #1669)
- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06
- added example easyconfig for generating buildenv module (#1503)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1,
Python 2.7.10, R 3.2.0 + 3.2.1, WRF 3.6.1
- various other enhancements, including:
- update all ncurses easyconfigs to enable ncursesw and use ConfigureMake easyblock (#1337)
- update PDT easyconfigs to use PDT easyblock (#1687)
- add custom sanity_check_paths in libxml2 easyconfigs (#1690)
- enhance unit tests to also cover EasyConfig.dump() method on all easyconfigs (#1761)
- include snappy as dependency in Hadoop easyconfigs (#1758, #1773)
- enable SSL support in CMake v3.2.3 easyconfigs (#1784)
- add additional extensions in R easyconfigs (#1637)
- various bug fixes, including:
- add patch file required for correct CUDA-aware OpenMPI v1.7.3 build (#631)
- fix issue with OpenMPI dependency in ECore easyconfigs (#777)
- don't run the Bloom tests for Jellyfish, they can randomly fail (#1016)
- fix source URLs in BioPerl easyconfigs (#1075)
- patch out svnversion command in Python 2.5.6 to fix build on recent systems (#1576)
- consistently use https for PyPI URLs in homepage/source_urls (#1616, #1722)
- include Tcl and Tk as dependencies in R easyconfig (#1623)
- add patch for installing paycheck as Py3 extension (#1629)
- add Perl dependency in git 2.x easyconfigs (#1631)
- fix easyconfig for GMP 6.0.0, don't use 6.0.0a sources (#1635)
- fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs (#1652)
- include Tk as dependency in Python 2.7.9 easyconfigs (#1654)
- include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works (#1655)
- drop gpfs versionsuffix and stop using no longer existing --enable-gpfs configopt for recent HDF5 versions (#1657)
- include missing libxml2 dep in GLib easyconfigs (#1666)
- fix source URLs in Qt easyconfigs (#1673)
- fix source URLs for argparse Python extension (#1697)
- fix source URLs for deap Python extension (#1699)
- fix easyconfigs unit tests after making ModulesTool a non-singleton class (#1708)
- fix names for Xmipp easyconfigs and patches (#1719)
- add patch for Qt 4.8.6 to fix build issue on RHEL6 with intel/2015a (#1734)
- add M4 as build dep for GCC 5.1.0 (#1735)
- fix Bioconductor extension versions in R 3.1.3 easyconfigs (#1748)
- remove custom exts_filter definition from Python 3.4.3 easyconfig (#1765)
- fix source_urls in netCDF easyconfigs (#1766)
- fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs (#1767)
v2.1.1 (May 18th 2015)
----------------------
bugfix release
- added example easyconfig files for 3 new software packages:
networkx (#1592), Platanus (#1597), SaguaroGW (#1600)
- added new easyconfigs for existing toolchains: ictce/7.3.5, CrayCCE/5.2.40, CrayGNU/5.2.40, CrayIntel/5.2.40
- added easyconfigs using CrayGNU/5.2.25 and CrayGNU/5.2.40 toolchains (#1610, #1611)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3
- various bug fixes, including:
- enable usempi in GROMACS easyconfig using CrayGNU toolchain (as required by GROMACS easyblock) (#1590)
- use system-provided tcsh when building WRF on Cray systems, to avoid hanging build (#1595)
- only use 'dynamic' toolchain option, not 'shared', in easyconfigs using Cray toolchain (#1609)
v2.1.0 (April 30th 2015)
------------------------
feature + bugfix release
- added example easyconfig files for 27 new software packages:
AFNI (#1322, #1521), BCFtools (#1492), getdp (#1518), gmsh (#1518), gtest (#1244), hanythingondemand (#1530),
mawk (#1369), Minimac (#815), Minimac3 (#1502), monty (#1548), Octave (#1563), pbs_python (#1530), pigz (#1036),
Pygments (#1536), pyhull (#1539), pymatgen (#1549), PyQt (#1322, #1521), Ray (#1494), requests (#1536),
seqtk (#1524), SIP (#1322, #1521), S-Lang (#1369), Spark (#1554), spglib (#1549), TINKER (#1465), tmux (#1369),
Xmipp (#1489)
- added easyconfigs for new (Cray-specific) toolchains (#1538): CrayGNU, CrayIntel, CrayCCE
- initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558)
- see also https://github.com/hpcugent/easybuild/wiki/EasyBuild-on-Cray
- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1
- various other enhancements, including:
- include 'pbr' dependency for 'lockfile' Python extension in Python v2.7.9 easyconfigs + mock/pytz/pandas (#1462, #1540)
- include SQLite as dependency in Python v2.7.9 easyconfigs (#1468)
- set $LD_PRELOAD for Hoard and jemalloc (#1470)
- fix homepage in SCOTCH easyconfigs (#1485)
- adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (#1504, #1505, #1506, #1507, #1508, #1509, #1510)
- enable pic toolchain option in expat easyconfigs (#1562)
- extend list of source URLs for Bioconductor packages in R easyconfigs to include 'release' source URLs (#1568)
- various bug fixes, including:
- adding missing zlib dependency in all Tcl easyconfig files (#1344)
- fix homepage in FLUENT easyconfigs (#1472)
- use --with-verbs rather than deprecated --with-openib in OpenMPI configure options (#1511)
- stop relying on OS_NAME constant to specify OS dependencies in OpenMPI easyconfigs (#1512)
- replace use of $root with %(installdir)s to ensure compatibility with module files in Lua syntax (#1532)
- stop relying on $MKLROOT in ROOT easyconfigs (#1537)
- use proper Bundle easyblock for biodeps/PRACE (#1566)
- make source_urls in Cube and Scalasca easyconfigs compatible with --try-software-version (#1574)
- add patch for Cube to fix configure script w.r.t. Qt dependency, add --without-java-reader configure option (#1574)
v2.0.0 (March 6th 2015)
-----------------------
feature + bugfix release
- added example easyconfig files for 29 new software packages:
bsoft (#1353), Coot (#1400), Cuby (#1258), DSRC (#1242), Exonerate (#568), fastqz (#1242), FSA (#568),
fqzcomp (#1242), GAMESS-US (#1153, #1406), Grep (#1308), Hadoop (#1418), Hoard (#1415), IMB (#1284), ISL (#1389),
jemalloc (#1416), libdwarf (#1283), libelf (#1283), MPC (#1310), multitail (#1327), Pmw (#1403), Quip (#1242),
rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370),
ZPAQ (#1242)
- added easyconfigs for new (common) toolchains
foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238),
intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401)
- added new software bundle: Autotools (#1385)
- various other enhancements, including:
- don't define $LDSHARED in zlib easyconfigs (#1350)
- this fixes the long-standing "no version information available" issue with zlib
- see also https://github.com/hpcugent/easybuild-framework/issues/108
- add unit test to check that all extra_options keys are defined in EasyConfig instance (#1378)
- add source MD5 checksums in all GCC easyconfigs (#1391)
- speeding up the unit tests by avoiding rereading of same easyconfig file (#1432)
- fix conflict detection in unit tests by considering build deps separately from runtime deps (#1447)
- fix toolchain for Bison build dep in MVAPICH2-1.9-iccifort-2011.13.367.eb easyconfig (#1448)
- use Bundle generic easyblock for HPCBIOS bundles and fix moduleclass (#1451)
- various bug fixes, including:
- revert version of Libint dependency to 1.1.4 in CP2K v2.5.1 easyconfig (#1144)
- added Java dependencies to EMBOSS easyconfigs (#1167)
- don't list 'lto' as a language in GCC easyconfigs (#1286)
- related to the fixes in the GCC easyblock, see hpcugent/easybuild-easyblocks#535
- rename libint2 easyconfigs as Libint v2 easyconfigs (#1287)
- fix mpi4py source_urls in Python easyconfigs (#1306)
- consistently use CLooG 0.18.0 for GCC 4.8 series (#1392)
- rename GenomeAnalysisTk easyconfigs to GATK (#1399)
- include openssl-devel SLES11 OS dependency in cURL/MySQL/Python easyconfigs (#1422)
- add missing Perl dependency in parallel easyconfigs (#1430)
- correct name in BLAST+ easyconfigs (#1443)
- fix name for sparsehash easyconfigs (#1452)
v1.16.2.0 (March 6th 2015)
--------------------------
(no changes compared to v1.16.1.0, simple version bump to stay in sync with easybuild-easyblocks)
v1.16.1.0 (December 19th 2014)
------------------------------
- set default easyblock to ConfigureMake in TEMPLATE.eb (#1277)
v1.16.0.0 (December 18th 2014)
------------------------------
feature + bugfix release
- added example easyconfig files for 39 new software packages:
ANTs (#1232), BEOPS (#1264), Chhimera (#1255), ctffind (#1249), DBD-SQLite (#1064), DBD-mysql (#1063),
DIALIGN-TX (#668), ffmpeg (#1088), GObject-Introspection (#1079), GTS (#1079), Graphviz (#1079), GraphViz2 (#1079),
grace (#1131), HarfBuzz (#1079), HTSlib (#1161), GSSAPI (#1048), Kerberos_V5 (#1048), libevent (#1063),
libXdmcp (#1129), libXft (#1017), libXinerama (#1017), libXrender (#1017), Maven (#1094), MySQL (#1063),
Net-LibIDN (#1060), OpenCV (#1088), OpenMD (#1105), Qhull (#1105), Pango (#1079), psmpi (#1245, #1246),
RELION (#1017), renderproto (#1017), rjags (#1125), runjags (#1125), SPRNG (#1138, #1141), xineramaproto (#1017),
XML-Dumper (#1061), XML-Parser (#1061), XML-Twig (#1061)
- added easyconfigs for new toolchains
intel/2014.10 & intel/2014.11 (#1219), intel-para/2014.12 (#1246), gpsolf/2014.12 (#1245), iompi/6.6.4 (#1215)
- include easyblock = 'ConfigureMake' in relevant easyconfigs to deal with deprecation of automagic fallback to ConfigureMake (#1248)
- see also easybuild-framework#1113 and Automagic fallback to ConfigureMake
- clean up use of deprecated functionality in existing easyconfigs (#1252, #1259)
- stop using deprecated makeopts, premakeopts and shared_lib_ext
- check for use of deprecated functionality in easyconfigs unit tests
- see also http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#easyconfig-parameters
- various other enhancements, including:
- also build fftw3_threads libraries, and enhance sanity checks (#1013)
- add unit test to verify specified sanity_check_paths (#1119)
- update and clean up README, refer to http://easybuild.readthedocs.org documentation (#1184, #1224)
- various bug fixes, including:
- fix unit tests w.r.t. changes in framework (#1146)
- remove unnecessary build dependencies for OpenMPI (#1168)
- remove duplicate line in OpenMPI easyconfigs (#1207)
- fix affiliation/mail address for Fotis in headers (#1237)
- fix permissions of easyconfig files for consistency (#1210)
- disable symbol lookup feature in cairo to fix build on SL6 (#1241)
- fix easyconfig gmpolf toolchain w.r.t. MPICH software name (#1217)
- see also easybuild-framework#1112
- fix source_urls for WRF and WPS (#1225)
- fix and clean up GATE easyconfigs (#1228)
- fix broken CLHEP builds by including -gcc in $CXXFLAGS (#1254)
- add patch to fix broken test in Go (#1257)
- fix name of GMAP easyconfigs, should be GMAP-GSNAP (#1268)
- fix easyconfig filenames, enhance unit test to check easyconfig filenames (#1271)
v1.15.2.0 (October 7th 2014)
----------------------------
bugfix release
- disable parallel build for slalib (#968)
- fix compatibility of goolfc with HierarchicalMNS by using GCC toolchain for installing CUDA (#1106, #1115)
- fix zlib OS dependency spec for Debian in Boost easyconfigs (#1109)
- fix compatibility of gimkl with HierarchicalMNS by using gimpi subtoolchain (#1110)
- make both GCC and Clang first-class members in Clang-based toolchains to fix compatibility with HierarchicalMNS (#1113)
v1.15.1.0 (September 23rd 2014)
-------------------------------
bugfix release
- minor bug fixes, including:
- use SHLIB_EXT in GMP/MPFR easyconfigs (#1090)
- fix TopHat homepage and source_urls since page moved (#1092)
- make iomkl toolchain compatible with HierarchicalMNS (#1099)
v1.15.0.0 (September 12th 2014)
-------------------------------
feature + bugfix release
- added example easyconfig files for 13 new software packages:
Circos (#780), DB_File (#913), Emacs (#970), evmix (#1077), GD (#780), gsl (#1077), IOR (#949), JAGS (#1076),
libgd (#780), MethPipe (#1070), Modeller (#825), NAMD (#835), netCDF-C++4 (#1015)
- added easyconfigs for new toolchains (#986, #1051):
gimkl/1.5.9, ictce/7.1.2
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Python 2.7.8/3.4.1, Perl 5.20.0, R 3.1.1, NWChem 6.3, OpenFOAM-Extend 3.1, GCC 4.9.1, Clang 3.4.2, ...
- various enhancements, including:
- make existing ictce/intel toolchains compatible with HierarchicalMNS (#1069)
- this involves installing impi with an iccifort toolchain, and imkl with an iimpi toolchain
- various bug fixes, including:
- download link for Perl modules changed to use cpan.metapan.org
- fix missing MPI-based OpenFOAM libraries (Pstream, (pt)scotchDecomp), make sure provided SCOTCH is used (#957)
v1.14.0.0 (July 9th 2014)
-------------------------
feature + bugfix release
- added example easyconfig files for 17 new software packages:
ANSYS (#836), Beast (#912), ELPH (#910, #911), FastTree (#900, #947), GEM-library (#858), HPCG (#853),
mdtest (#925), ncview (#648), PRANK (#917), RDP-Classifier (#903), SDPA (#955), SIBELia (#886),
SOAPaligner (#857), SPAdes (#884), stemming (#891), WHAM (#872), YAXT (#656)
- added easyconfigs for new toolchains (#935, #944, #948):
foss/2014b, ictce/6.3.5, intel/2014b
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- various enhancements, including:
- replace use of deprecated (pre)makeopts with (pre)buildopts in all easyblocks (#954)
- disable running embossupdate on installation of EMBOSS (#963)
- various bug fixes, including:
- really enable OpenMP support in FastTree easyconfigs (#947)
- fix easyconfigs unit tests after changes in framework (#958)
v1.13.0.0 (May 29th 2014)
-------------------------
feature + bugfix release
- added example easyconfig files for 32 new software packages:
APBS (#742), BayesTraits (#770), bc (#888), BitSeq (#791), CEM (#789), CVS (#888), eXpress (#786), file (#888),
GEMSTAT (#861), GMAP (#594), Go (#887), iscp (#602), IsoInfer (#773), Jellyfish (#868), less (#888),
libcircle (#883), mcpp (#602), MMSEQ (#795), MUSTANG (#800), OpenFOAM-Extend (#437), popt (#759), pscom (#759),
psmpi2 (#759), QuadProg++ (#773), rSeq (#771), RSEQtools (#870), Ruby (#873), segemehl (#792), SOAPec (#879),
SOAPdenovo2 (#874), SRA-Toolkit (#793), texinfo (#888)
- added easyconfig for new toolchain goolfc/1.4.10
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- e.g. older versions of Boost (1.47.0), GCC (4.1-4.4), & recent versions of Clang, GCC, Lmod, etc.
- various enhancements, including:
- add OpenSSL dependency for cURL, to enable HTTPS support (#881)
- also install esl-X binaries for HMMER (#889)
- various bug fixes, including:
- properly pass down compiler flags for ParMGridGen (#437)
- specify proper make options for PLINK, fixing the build on SL6 (#594, #772)
- fix netloc version (0.5 rather than 0.5beta) (#707)
- remove Windows-style line ending in netCDF patch file (#796)
- bump version of OpenSSL dep for BOINC (#882)
v1.12.1.0 (April 25th 2014)
---------------------------
(no changes compared to v1.12.0, simple version bump to stay in sync with easybuild-framework)
v1.12.0.0 (April 4th 2014)
--------------------------
feature + bugfix release
- added example easyconfig files for 6 new software packages:
CLooG (#653), ELPA (#738), LIBSVM (#788), netaddr (#753), netifcas (#753), slalib-c (#750)
- added easyconfigs for new toolchains:
ClangGCC/1.3.0 (#653), goolf/1.4.10-no-OFED (#749), goolf/1.5.14(-no-OFED) (#764, #767), ictce/6.2.5 (#726), iomkl (#747)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- various enhancements, including:
- tweak BOINC easyconfig to make use of glob support available for files_to_copy (#781)
- enable -fPIC for libreadline, so it can be linked into shared libs (e.g. libpython2.x.so) (#798)
- various bug fixes, including:
- fix Qt source_urls (#756)
- enable -fPIC in ncurses 5.9 ictce/5.2.0 easyconfig, just like in the others (#801)
- fix unit tests after changes to framework (#763, #766, #769)
v1.11.1.0 (February 28th 2014)
------------------------------
(no changes compared to v1.11.0, simple version bump to stay in sync with easybuild-framework)
v1.11.0.0 (February 16th 2014)
------------------------------
feature + bugfix release
- added example easyconfig files for 30 new software packages:
argtable (#669), Clustal-Omega (#669), Coreutils (#582), GMT (#560), gperftools (#596), grep (#582), h4toh5 (#597),
libunwind (#596), Lmod (#600, #692), Lua (#600, #692), MAFFT (#654), Molekel (#597), NEdit (#597),
netcdf4-python (#660), nodejs (#678), OCaml (#704), patch (#582), PhyML (#664),
PRACE Common Production Environment (#599), protobuf (#680), python-dateutil (#438), sed (#582), sickle (#651),
Tesla-Deployment-Kit (#489), TREE-PUZZLE (#662), VCFtools (#626), Vim (#665), vsc-mympirun-scoop (#661),
vsc-processcontrol (#661), XZ (#582)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- OpenSSL with ictce toolchain (#703)
- various enhancements, including:
- using more constants and templates (#613, #615)
- specify OS dependency for SSL support, with OpenSSL dependency as fallback (#703)
- various bug fixes, including:
- fix unit tests after (internal) framework API changes (#667, #672)
- fix homepage in vsc-mympirun easyconfig file (#681)
- align OpenMPI easyconfigs (#650)
- add additional source URL in Qt easyconfigs (#676)
- specify correct $PATH specification and define $CHPL_HOME for Chapel (#683)
v1.10.0.0 (December 24th 2013)
------------------------------
feature + bugfix release
- added example easyconfig files for 18 new software packages:
BEDTools (#579, #632, #635), CAP3 (#548), CHARMM (#584), cutadapt (#620), ErlangOTP (#556, #630),
Ghostscript (#547, #632), HTSeq (#554, #632), Jansson (#545), libjpeg-turbo (#574), Molden (#566),
netloc (#545), o2scl (#633), packmol (#566), PP (#405), qtop (#500), TAMkin (#566), vsc-base (#621),
vsc-mympirun (#621)
- added easyconfigs for new toolchains (#545, #609, #629):
gcccuda/2.6.10, gompic/2.6.10, goolfc/2.6.10, ictce/6.0.5, ictce/6.1.5
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- new versions of icc, ifort, imkl, impi (#609, #629)
- large collection of ictce/5.3.0 easyconfigs (#627)
- various enhancements, including:
- extended list of Python packages as extensions to Python (#625)
- add MPI-enabled version of GROMACS + easyconfigs using ictce (#606, #636)
- clean up templating of source_urls (#637)
- various bug fixes, including:
- provide alternative download URL for Mesa (#532)
- add Python versionsuffix in OpenBabel filenames (#566)
- apply no-gets patch in all M4 v1.4.16 easyconfigs (#623)
- fix patching of Python w.r.t. libffi/_ctypes issues (#625, #642)
- bug fixes in GROMACS easyconfigs (#606)
- change versionsuffix for non-MPI GROMACS easyconfigs to '-mt'
- stop using 'CMakeMake' easyblock for GROMACS now that there's a dedicated GROMACS easyblock,
which correctly specifies building against external BLAS/LAPACK libraries
- fix Qt dependency for CGAL (#642)
- fix libctl, libmatheval, Meep, PSI build issues caused by full paths in guile-config/python-config shebang (#642)
- make sure HDF easyconfigs specify dedicated 'include/hdf' include dir (#642)
- this is required to avoid build issues with NCL, because HDF ships it's own netcdf.h
- this also triggered removal of patch files for NCL that rewrote 'include/hdf' to 'include'
- fix WPS v3.5.1 patch file after upstream source tarball was changed, supply checksum for verification (#642)
v1.9.0.0 (November 17th 2013)
-----------------------------
feature + bugfix release
- added example easyconfig files for 58 new software packages:
- Allinea (#468), ARB + dependencies (#396, #493, #495), arpack-ng (#451, #481), CDO (#484, #521), Cube (#505),
ed (#503), FLTK (#503), GenomeAnalysisTK (#467), GIMPS (#527), GTI (#511), IPython (#485, #519), LWM2 (#510),
MPICH2 (#460), MUST (#511), ncdf (#496, #522), OPARI2 (#505), OpenBabel (#504, #524), OTF (#505), OTF2 (#505),
PandaSEQ (#475), ParaView (#498, #514), ParFlow (#483, #520), PCC (#486, #528), PDT (#505), picard (#467),
PnMPI (#511), PyQuante (#499, #523), pysqlite (#519), Scalasca (#505), Score-P (#505), SDCC (#486, #528),
Silo (#483, #520), Stride (#503), SURF (#503), TCC (#486, #528)
- ARB dependencies (23): fixesproto, imake, inputproto, kbproto, libICE, libSM, libX11, libXau, libXaw,
libXext, libXfixes, libXi, libXmu, libXp, libXpm, libXt, lynx, motif, printproto,
Sablotron, xbitmaps, xextproto, xtrans
- added easyconfigs for new gmpich2/1.4.8, gmpolf/1.4.8 and goolf/1.6.10 toolchains (#460, #525, #530)
- added additional easyconfigs for various software packages (list too long to include here)
- version updates, different toolchains, ...
- various bug fixes, including:
- enable building of shared libraries for MPICH (#482)
- fix HDF configure option for Szip, should be --with-szlib (#533)
- for HDF5, this issue is fixed in the HDF5 easyblock
- other
- add build status badges for master/develop branches to README (#490)
v1.8.2.0 (October 18th 2013)
----------------------------
bugfix release
- port thread pool patch to PSI 4.0b4 and include it to avoid hanging tests (#471)
v1.8.1.0 (October 14th 2013)
----------------------------
bugfix release
- added additional easyconfigs for various software packages (#457):
- Boost, bzip2, libreadline, ncurses, PSI, Python, zlib
- various bug fixes, including:
- fix faulty easyconfig file names for HPCBIOS_Math, MUSCLE, XML-LibXML and YAML-Syck (#459, #462)
- stop (re)specifying default maximum ratio for failed tests in NWChem easyconfig (#457)
v1.8.0.0 (October 4th 2013)
---------------------------
feature + bugfix release
- added example easyconfig files for 9 new software packages:
- BOINC (#436), DB (#343, #449), fastahack (#374), FDTD Solutions (#387), FoldX (#440, #442), Mathematica (#394),
Mesquite (#447), MUMPS (#447), ParMGridGen (#447)
- added additional easyconfigs for goalf, gompi, ClangGCC, cgmvapich2, cgmvolf toolchains (#350, #441)
- added additional easyconfigs for various software packages:
- ATLAS, Bison, bzip2, Clang, CMake, cURL, EasyBuild, expat, FFTW, GDB, gettext, git, HPL, LAPACK, libreadline,
M4, METIS, MVAPICH2, Mercurial, ncurses, OpenBLAS, OpenMPI, ParMETIS, Python, ScaLAPACK, SCOTCH, Valgrind, zlib
- various 'bug' fixes, including:
- fix source URL for lockfile in Python easyconfigs (#428)
- correct dependency specifications w.r.t. versionsuffix and toolchain (#431)
- this is required to support building the affected easyconfigs with a custom module naming scheme
- correct PSI patch file to avoid errors w.r.t. memcpy not being in scope (#446)
- fix gettext build with adding --without-emacs configure options, add gettext as dependency for a2ps (#448)
- exclude EMACS support in a2ps because of build failures (#452)
v1.7.0.0 (September 2nd 2013)
-----------------------------
feature + bugfix release
- added example easyconfig files for 15 new software packages:
- Glib (#294, #400), GLPK (#400), horton (#413), libint2 (#413), molmod (#413), Rosetta (#336), SCons (#336), Stacks (#367, #377), sympy (#413),
Qt (#294), XML-LibXML (#397), XML-Simple (#397), yaff (#413), YAML-Syck (#380), zsh (#376)
- added additional easyconfigs for various software packages:
- BLAST, BamTools, BioPerl, Bison, Boost, bzip2, CMake, Cython, CUDA, FFTW, FIAT, GCC, GMP, gettext, git, h5py,
HDF5, libffi, libreadline, libxc, matplotlib, METIS, ncurses, Oases, Python, RAxML, ScientificPython, Szip,
tcsh, imkl, MVAPICH2, TotalView, VTune, WRF, zlib
- added toolchain easyconfig files for HPCBIOS policies (#402, #407)
- HPCBIOS_BioInfo, HPCBIOS_Debuggers, HPCBIOS_LifeSciences, HPCBIOS_Math, HPCBIOS_Profilers
- various enhancements, including:
- added more XML Perl modules to non-bare Perl easyconfigs (#375)
- various 'bug' fixes, including:
- fix website/description in scipy easyconfigs (#399)
- specify OpenMPI libibverbs-dev(el) OS dependency in an OS-dependent way (#403)
- add patch file for M4 to fix building on systems with recent glibc (>=2.16) (#406)
- align moduleclass in R easyconfigs (#411)
- fixed filename of Biopython/CD-HIT easyconfig files (#407)
- disable parallel building of otcl (#419)
v1.6.0.0 (July 11th 2013)
-------------------------
feature + bugfix release
- added example easyconfig files for 26 new software packages:
- ALLPATHS-LG (#359), AutoMake (#347), BamTools (#319, #338), BLAT (#340), Biopython (#356), cairo (#361),
CCfits (#327), CD-HIT (#344), CFITSIO (#327), Diffutils (#347), FASTA (#358, #361), findutils (#347),
fontconfig (#361), gawk (#347), gettext (#361), GLIMMER (#357, #361), libidn (#361), LibTIFF (#347),
libungif (#347), make (#355), MUSCLE (#339), Oases (#354), pixman (#361), PLINK (#352), RCS (#347), SQLite (#347)
- added additional easyconfigs for various software packages:
- ant, Bash, Bison, bzip2, cURL, expat, GCC, EasyBuild, freetype, FFTW, GDB, git, HMMER, JUnit, libreadline, libpng,
libtool, libxml2, libxslt, M4, makedepend, Mothur, MVAPICH2, Mercurial, ncurses, OpenBLAS, Python, ScaLAPACK, Tcl,
tcsh, TopHat, Trinity, Valgrind, Velvet, VTune, zlib
(see #169, #297, #298, #301, #309, #323, #331, #332, #341, #347, #349, #351, #355, #361)
- various enhancements, including:
- added easyconfigs for ictce/5.4.0, ictce/5.5.0 and gmvolf/1.7.12 toolchain modules (#297, #332, #349)
- added a template sanity_check_paths as 'MUST' in TEMPLATE.eb (#329)
- introduced biodeps 'toolchain' to ease keeping common dependencies for bio* software in sync (#309)
- added collection of easyconfigs for ictce/5.3.0 (#309, #323)
- bam2fastq, bbFTP, BLAST, Boost, DL_POLY Classic, EMBOSS, FFTW, libharu, libxml2, libxslt, libyaml, lxml,
Mercurial, Mothur, mpi4py, ncurses, ns, orthomcl, otcl, PAML, Perl, PyYAML, pandas, problog, scikit-learn,
TiCCutils, TiMBL, TinySVM, TopHat, tclcl, YamCha
- added missing dependencies for various software packages (#323, #328, #348, #361)
- style fixes in various easyconfigs (#309, #323, #345, #349, #355, #361)
- various 'bug' fixes, including:
- added 'pic' toolchain option for Perl goolf easyconfig (#299)
- fixed source URLs for R (use correct template 'version_major') (#302)
- synced libreadline easyconfigs w.r.t. ncurses dependency (#303)
- make sure EasyBuild configuration is initialized when running unit tests (#334)
- specify 'lowopt' (-O1) optimization level for OpenIFS, to avoid floating-point related issues (#328)
- fix naming of 'beagle-lib' (used to be 'BEAGLE'), to avoid name clashes with other software package(s) (#346)
v1.5.0.0 (June 1st 2013)
------------------------
feature + bugfix release
- added example easyconfig files for 23 new software packages:
- bam2fastq (#287), CBLAS (#263), EMBOSS (#265, #290), FCM (#272), FRC_align (#273), freeglut (#271),
FreeSurfer (#271), FSL (#271), GATK (#287), libharu (#290), libxslt (#235), MariaDB (#292), Mothur (#265)
mpi4py (#276), OpenIFS (#272), orthomcl (#265), PAML (#287), pandas (#262), phonopy (#235), problog (#277),
PSI (#258), PyYAML (#235), RAxML (#277)
- added additional example easyconfig files for:
- ABINIT (#235), ACML (#267), BLAST (#275), Boost (#273), BWA (#270), bzip2 (#263), Chapel (#240), CMake (#290),
FFTW2 (#247, #267), flex (#267), freetype (#235), grib_api (#272), gzip (#265), Java (#279), libpng (#240, #279),
libreadline (#267), libxml2 (#235), libxml (#235), matplotlib (#235), MCL (#265), MUMmer (#265), ncurses (#267),
numpy (#267), OpenFOAM (#267), Perl (#265), Python (#276, #263), R (#240, #279), SCOTCH (#267), ScaLAPACK (#267),
TopHat (#289), Valgrind (#255), zlib (#267)
- various enhancements, including:
- enhance unit test suite, include testing for module conflicts (#256) and presence of patch files (#264)
- use provided constants and templates in easyconfig files where appropriate (#248, #266, #281)
- various 'bug' fixes, including:
- get rid of hardcoded license_file paths for VTune, Inspector (#253)
- assign proper moduleclass where they were missing (#278)
- fix naming for LZO (#280)
- make unit tests clean up after themselves more thoroughly (#283, #284, #285, #286)
- fix TopHat dependencies (#289)
- fix source URLs for XML (#279)
- fix versions for all listed R extensions (#279)
- fix CUDA easyconfig file for use on Debian Squeeze (#291)
- correct easyconfig filename and module name mismatches (bbcp, DL_POLY Classic, ...) (#295)
v1.4.0.0 (May 2nd 2013)
-----------------------
feature + bugfix release
- added a unit test suite for easyconfigs (#228, #230)
- added example easyconfig files for 20 new software packages:
- ABAQUS (#231), BioPerl (#242), Bowtie (#227), Clang (#177), CRF++ (#131), DL_POLY Classic (#132), ESMF, GROMACS (#165),
HH-suite (#219), Inspector (#232), likwid (#131), Perl (#242), scikit (#133), TiCCutils (#131), TiMBL (#131), TinySVM (#131),
UDUNITS (#167), VTune (#232), YamCha (#131)
- add example easyconfigs for new compiler toolchains (use `eb --list-toolchains` for a full list of supported toolchains):
- the newly added toolchains only differ in compilers/MPI library, and all feature OpenBLAS, LAPACK, ScaLAPACK and FFTW
- goolfc: GCC, CUDA (co-compiler), OpenMPI (#191)
- a goolfc easyconfig for GROMACS is inluded as proof-of-concept (#165)
- cgmpolf: Clang (C/C++ compilers), GCC (Fortran compilers), MPICH (#213)
- cgmvolf: Clang, GCC, MVAPICH2 (#218)
- cgoolf: Clang, GCC, OpenMPI (#213)
- gmvolf: GCC, MVAPICH (#202, #222)
- ported already available easyconfigs to new compiler toolchains:
- ictce-5.3.0: 193 easyconfigs (#229)
- cgmpolf: 11 easyconfigs (#213)
- cgmvolf: 11 easyconfigs (#218)
- cgoolf: 12 easyconfigs (#213)
- gmvolf: 10 easyconfigs (#215)
- added additional example easyconfig files for:
- CMake (#163), git (#210), Java (#206), #221, Mercurial (#201, #215), ncurses (#225), TotalView (#160)
- various enhancements, including:
- added ESMF and UDUNITS dependencies to NCL easyconfigs (#211)
- changed value of source_urls in R easyconfigs, to be generic enough for version 3.0 and possibly beyond (#251)
- various 'bug' fixes, including:
- add --enable-mpirun-prefix-by-default configure option for all OpenMPI easyconfigs (#205)
v1.3.0.0 (April 1st 2013)
-------------------------
feature + bugfix release
- added example easyconfig files for 13 new software packages:
- Bash, CUDA, ccache, Ferret, gzip, libxc, ns, numactl, OpenBLAS, otcl, Tar, tclcl, tcsh
- several of these easyconfig files were contributed by attendees of the EasyBuild hackathon in Cyprus!
- added example easyconfigs for goolf toolchain (#158)
- added example easyconfigs for builds with goolf toolchain, i.e. for all goalf easyconfigs (#189)
- for several software packages, a patch file was needed to get them to build with GCC 4.7:
AMOS, BEAGLE, Cufflinks, DOLFIN, GATE, ns, Pasha, Trilinos, Trinity
- for PETSc, a patch file was required to make it build with a toolchain that doesn't include BLACS
- added additional example easyconfig files for:
gompi, hwloc, LAPACK, MVAPICH2, OpenMPI, ScaLAPACK
- various enhancements, including:
- define a proper module class in *all* easyconfigs, cfr. default module classes defined in framework (#150, #159, #161, #162, #179, #181)
- extend FFTW easyconfig to 'fat' builds that include single, double, long double and quad precision libraries in the same module
- quad precision is disabled for Intel compiler based builds (it requires GCC v4.6+)
- the imkl easyconfigs used for the ictce 3.2.2.u3 toolchain now also enable FFTW interfaces
- various 'bug' fixes, including:
- fix filename for Mercurial and ROOT easyconfig files
- fix homepage/description for Hypre
- fix enabling OpenMP support in OpenMPI: use '--enable-openmp', not 'with-openmp'
- use correct configure flag for enabling OpenMPI threading support in v1.6 (#186)
- '--enable-mpi-thread-multiple' instead of '--enable-mpi-threads'
- explicitely add '--without-openib --without-udapl' configure options in OpenMPI easyconfig using versionsuffix -no-OFED (#168)
- this avoids that OpenMPI auto-detects that it can enable Infiniband (OpenIB) support, which doesn't fit the -no-OFED versionsuffix
- Note: this makes goalf-1.1.0-no-OFED effectively not suitable to produce software builds that are IB-capable!
- remove explicit '--with-udapl' from OpenMPI easyconfigs, does more harm than good (#178)
- remove libibvers, libibmad, libibumad as explicit dependencies for OpenMPI/MVAPICH2 (#173, #182)
leave it up to the OS to provide these, since the required version is too much tied to the version of IB drivers
- use 'license_file' in Intel tools easyconfigs, as opposed to the new generic 'license' parameter with a different meaning (#180)
- modify patch for impi to avoid installation problems due to hardcoded path in /tmp (#185)
- now uses '$USER-$RANDOM' subdir to avoid clashes between different users on the same system
- the patch file for numpy was extended to also supporting ATLAS and other BLAS libraries spread across multiple directories
- the extension for ATLAS is required because we now no longer rely on the automatic numpy mechanism to find the ATLAS libs
- fixed dependencies:
- libibumad as dependency for libibmad
- ncurses as dependency for libreadline
- ncurses and zlib as dependency for SAMtools (+ enhanced patch)
- remove explicit FFTW dependency for Meep, ... since toolchain already provided FFTW
v1.2.0.0 (February 28th 2013)
---------------------------
feature + bugfix release
- added example easyconfig files for 41 new software packages:
- a2ps, AnalyzeFMRI, aria, bbcp, bbFTP, bbftpPRO, binutils, Bonnie++, ccache, cflow, cgdb, Corkscrew, EasyBuild,
Elinks, EPD, FLUENT, fmri, GDB, GDAL, gnuplot, gnutls, gperf, Iperf, lftp, libyaml, lzo, MATLAB, mc, nano, NASM,
nettle, numexpr, parallel, pyTables, QLogic MPI, Stow, TotalView, Valgrind, VTK, Yasm, zsync
- added example easyconfigs for iqacml and iiqmpi toolchains
- added additional example easyconfig files for:
- ABINIT, ABySS, ACML, BFAST, Bison, BLACS, Cython, cURL, Doxygen, FFTW, flex, g2clib, g2lib, GHC, h5py, HDF, HDF5,
HMMER, JasPer, icc, ictce, ifort, imkl, impi, libpng, libreadline, M4, matplotlib, MCL, MEME, mpiBLAST, NCL,
ncurses, netCDF, netCDF-Fortran, NWChem, R, ScaLAPACK, Tcl, Tk, WPS, WRF, zlib
- various enhancements, including:
- fix version of xtable R library in list of extensions for R, to avoid installation failures
- various 'bug' fixes, including:
- fix toolchain and file names for ABINIT easyconfigs
- fix sanity check paths for cURL
- don't disable 'optarch' for WRF, it's not needed (only disable heavy optimizations is required)
- fix homepage/description for ALADIN
v1.1.0.0 (January 27th 2013)
--------------------------
feature + bugfix release
- added example easyconfig files for 48 new software packages:
- ABINIT, ABySS, ACML, ALADIN, ant, BFAST, BLAST, Chapel, CLHEP, Cufflinks, ESPRresSo, GATE, GHC, Geant4,
Greenlet, google-sparsehash, grib_api, HMMER, Java, JUnit, libibmad, libibumad, libibverbs, MCL, MDP,
MEME, mpiBLAST, NCBI Toolkit, NEURON, NWChem, numpy, MDP, Oger, OpenPGM, paycheck, PyZMQ, QuantumESPRESSO,
R, ROOT, SCOOP, scipy, Tophat, Trinity, util-linux, VSC-tools, wiki2beamer, XML, ZeroMQ
- added example easyconfigs for gmacml, gmvapich2, iccifort, ictce, iomkl toolchains
- added additional example easyconfig files for:
- ATLAS, BLACS, Boost, Bowtie2, bzip2, CP2K, Doxygen, FFTW, GCC, HDF5, hwloc, icc, ifort, imkl, impi,
JasPer, Libint, libreadline, libsmm, libxml, ncurses, netCDF, M4, Meep, MVAPICH2, OpenMPI, Python,
ScaLAPACK, Szip, zlib
- various enhancements, including:
- major style cleanup of all example easyconfig file (PEP008 compliance)
- added setuptools to list of Python extensions
- get rid of 'parallel' versionsuffix for HDF5, as its meaningless (MPI-enabled build is always parallel)
- various 'bug' fixes, i.e. added missing dependencies or replaced os dependencies with proper dependencies
v1.0.0.2 (December 8th 2012)
----------------------------
bugfix release
- fixed source URL for ligtextutils (toolchain refactoring error)
v1.0.0.1 (November 24th 2012)
-----------------------------
bugfix release
- remove patch file for OpenMPI to resolve issue with pax hanging configure
- tar_config_opts should be enabled as needed
- disable parallel build for PAPI, seems to be causing problems
v1.0.0 (November 13th 2012)
---------------------------
- split up EasyBuild across three repositories: framework, easyblocks and easyconfigs
- packaged EasyBuild, different parts can now be installed easily using easy_install
- added example easyconfig files for 106 new software packages:
AMOS, Armadillo, ASE, Autoconf, BiSearch, Boost, Bowtie2, BWA, byacc, bzip2, CGAL, ClustalW2, CMake,
CPLEX, cURL, CVXOPT, Cython, Docutils, DOLFIN, ECore, Eigen, expat, FASTX-Toolkit, FFC, FIAT,
freetype, FSL, GEOS, git, glproto, GMP, gmvapich2, gompi, GPAW, GSL, guile, h5py, h5utils, Harminv,
hwloc, Hypre, Infernal, Instant, Jinja2, libctl, libdrm, libffi, libgtextutils, libmatheval,
libpciaccess, libpthread-stubs, libreadline, libtool, libunistring, libxcb, libxml2, makedepend,
matplotlib, Meep, Mercurial, Mesa, MetaVelvet, METIS, MPFR, MTL4, MUMmer, ncurses, OpenFOAM, OpenSSL,
ORCA, PAPI, ParMETIS, Pasha, PCRE, PETSc, petsc4py, pkg-config, Primer3, python-meep, RNAz, SAMtools,
ScientificPython, SCOTCH, setuptools, Shapely, SHRiMP, SLEPc, SOAPdenovo, Sphinx, SuiteSparse, SWIG,
Tcl, Theano, Tk, Tornado, Trilinos, UFC, UFL, Velvet, ViennaRNA, Viper, WIEN2k, xcb-proto, XCrySDen,
xorg-macros, xproto
- added additional example easyconfig files (versions, builds) for several software packages
Bison, BLACS, Doxygen, flex, GCC, HDF5, icc, ifort, libpng, M4, MVAPICH2, OpenMPI, Szip, tbb, zlib
- replaced GCC/OpenMPI based easyconfig files with equivalents using the gompi toolchain
ATLAS, BLACS, FFTW, LAPACK, ScaLAPACK
- enhanced Python example easyconfig files (more dependencies required for features, e.g. libreadline, bzip2, zlib, ...)
- corrected file name of easyconfig files to adher to standard as followed by EasyBuild robot dependency resolver
- style cleanup in existing easyconfig files
v0.8 (June 29th 2012)
---------------------
- added support for building/installing 17 additional software packages:
- BEAGLE, Doxygen, g2clib, g2lib, HDF, HDF5, JasPer, libpng, Maple,
MrBayes, NCL, netCDF, netCDF-Fortran, Szip, WPS, WRF, zlib
- the build procedure for WRF and WPS includes running the tests available for these packages
- various bug fixes and enhancements:
- made support for interactive installers (run_cmd_qa) more robust
- fixed Python git package check
- implemented toolkit functions for determine compiler family, MPI type, MPI run command, ...
v0.7 (June 18th 2012)
---------------------
- fixed BLACS build
- diagnostic tools to determine INTERFACE and TRANSCOMM values are now used
- added support for building Bison, CP2K, flex
- with regression test enabled for CP2K as part of build process
- note: BLACS built with EasyBuild prior to v0.7 needs to be rebuilt for CP2K to work correctly
- added --enable-mpi-threads to OpenMPI example easyconfigs
- required for correct CP2K psmp build
- adjusted libsmm example easyconfig for lower build time
- to make the full regression test finish in a reasonable amount of time
- added script to make porting of easyblocks from old to new EasyBuild codebase easier
- takes care of refactoring, checks for PyLint warnings/errors, ...
- fixed several small bugs
- prefixed EasyBuild messages with "=="
- full regression test passed (58 easyconfigs tested)
v0.6 (May 11th 2012)
---------------------
- added support for Intel compiler toolkit (ictce)
- which included the Intel compilers, Intel Math Kernel Library (imkl) and Intel MPI library (impi)
- added support for building Python with nose/numpy/scipy packages
- added simple regression test
- this version is able to build all supplied example easyconfigs
v0.5 (April 6th 2012)
----------------------
- first public release of EasyBuild
- after a thorough cleanup of the EasyBuild framework of the in-house version
- supports building HPL with goalf compiler toolkit
- the goalf toolkit consists of the GCC compilers, and the OpenMPI, ATLAS, LAPACK, FFTW and ScaLAPACK libraries
- also support build and installation of MVAPICH2