Commit graph

9374 commits

Author SHA1 Message Date
Jon Rood
956faa50cc Confine the xlf_seacas.patch for trilinos to version 12.12.1 (#8725)
* The xlf_seacas.patch fails on the latest trilinos develop branch so confine it up to version 12.12.1.

* Fixing likely mistak in seacas patch version range.
2018-07-17 14:45:39 -05:00
Massimiliano Culpo
373b3d2444 Packages must be added to DB to be considered installed (#8038)
Fixes #8036

Before this PR Package.installed was returning True if the spec prefix
existed, without checking the DB. This is wrong for external packages,
whose prefix exists before being registered into the DB. Now the property
checks for both the prefix and a DB entry.
2018-07-17 11:43:30 -07:00
Adam J. Stewart
8ce62ba513 Add documentation on build systems (#5015)
Spack provides a number of classes based on commonly-used build systems
that users can extend when writing packages; the classes provide functionality
to perform the actions relevant to the build system (e.g. running "configure" for
an Autotools-based package). This adds documentation for classes supporting the
following build systems:

* Makefile
* Autotools
* CMake
* QMake
* SCons
* Waf

This includes build systems for managing extensions of the following packages:

* Perl
* Python
* R
* Octave

This also adds documentation on implementing packages that use a custom build
system (e.g. Perl/CMake).

Spack also provides extendable classes which aggregate functionality for related
sets of packages, e.g. those using CUDA. Documentation is added for
CudaPackage.
2018-07-17 11:28:38 -07:00
Christoph Junghans
25062d0bd4
lammps: added v20180629 (#8695) 2018-07-17 11:13:04 -06:00
Christoph Junghans
ab60e2258f fftw: version bump (#8723)
* fftw: version bump

* fftw: add gcc-8 conflict for v3.3.7
2018-07-17 11:11:19 -05:00
Lukasz
9f0f18dad6 fix link to blas libs (#8721) 2018-07-17 08:24:52 -05:00
James Dickson
0a80d94a46 Add fix for bug causing MACSio build failure when hdf5 or typhonio enabled (#8722)
* Add fix for bug causing build failure when hdf5 enabled

* Added correct hdf5 dependency to typhonio
2018-07-17 08:24:16 -05:00
Levi Baber
b12d5aecaa r: add memory profiling variant (#8717)
* r: add memory profiling variant

* r: change memory_profiling to underscores
2018-07-16 22:23:09 -05:00
Todd Gamblin
06418a3dcd
add spack --print-shell-vars to speed up setup-env.[c]sh (#8101)
- The setup-env.sh script currently makes two calls to spack, but it
  should only need to make one.

- Add a fast-path shell setup routine in `main.py` to allow the shell
  setup to happen in a single, fast call that doesn't load more than it
  needs to.

- This simplifies setup code, as it has to eval what Spack prints

- TODO: consider eventually making the whole setup script the output of a
  spack command
2018-07-16 15:43:44 -07:00
健美猞猁
d006139e3c aspera-cli: a new package. (#8715)
* aspera-cli: a new package.

* flak8.
2018-07-16 13:53:23 -05:00
Matthias Diener
dfc1f70aa4 Charm: set default backend to netlrts (#8714)
This allows building MPI applications on top of charm/AMPI without
to specify another backend.
2018-07-15 16:41:36 -05:00
Matthias Diener
badf913fc4 Charm: more info about build targets (#8713)
* Charm: more info about build targets

* fix whitespace
2018-07-15 16:41:25 -05:00
Matthias Diener
b25187bfa6 Scotch: update package (#8711) 2018-07-15 15:54:28 -05:00
Matthias Diener
067c8466bd yasm: add develop version (#8712) 2018-07-15 15:54:13 -05:00
Matthias Diener
4df673e401 charm: provide MPI (#8647)
* Charm: provide MPI
* add mpicc wrappers
* clarify MPI comment
2018-07-15 08:33:57 -07:00
Andreas Baumbach
79b407f59e clean up of spack clean (#8610)
* update help of `clean --all` to include `-p`
* remove old orphaned `.pyc` removal
* restrict removal or orphaned pyc files to `lib/spack` and `var/spack`
2018-07-14 17:20:49 -07:00
Jon Rood
5192a3d6d6 Fixing error in amrvis package. (#8710) 2018-07-14 18:19:26 -05:00
Matthias Diener
da5663a52a Py-opentuner: new package (#8707) 2018-07-14 13:51:58 -05:00
Jon Rood
e367d1fb3a Unset F90 and F90FLAGS in mvapich2 (#8698)
* Unset F90 in mvapich2 when using intel compilers.

* Fixing typo.

* Unset F90 and F90FLAGS for mvapich2 at all times.

* Adding comment.
2018-07-13 20:32:02 -05:00
Matthias Diener
4c5cbfeb29 py-fn: new package (#8705) 2018-07-13 20:31:39 -05:00
Levi Baber
44c999e2e1 mothur: mpi not used (#8706) 2018-07-13 20:31:25 -05:00
Matthias Diener
2cf9c7955c Scotch: fix compilation of 6.0.5a (#8704)
Prevent this error:

metis_graph_part.c:301:7: error: non-void function 'METIS_PartGraphVKway' should return a value
      [-Wreturn-type]
2018-07-13 15:51:04 -05:00
Sajid Ali
aec91d1cca update version for numexpr (#8702)
* 	modified:   package.py

* 	deleted:    var/spack/repos/builtin/packages/py-numexpr/numexpr-2.6.5.tar.gz
2018-07-13 15:50:21 -05:00
Sajid Ali
4c5e4cb960 Add py-backcall (#8701)
* 	new file:   var/spack/repos/builtin/packages/py-backcall/package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
2018-07-13 10:59:02 -05:00
Christoph Junghans
d569a9c124
flang: add support for llvm-6 (#8073)
* flang: add support for llvm-6

* flang: review changes

* pgmath: make flake8 happy
2018-07-12 18:37:50 -06:00
Todd Gamblin
650786c812 locks: improve errors and permission checking
- Clean up error messages for when a lock can't be created, or when an
  exclusive (write) lock can't be taken on a file.

- Add a number of subclasses of LockError to distinguish timeouts from
  permission issues.

- Add an explicit check to prevent the user from taking a write lock on a
  read-only file.
  - We had a check for this for when we try to *upgrade* a lock on an RO
    file, but not for an initial write lock attempt.

- Add more tests for different lock permission scenarios.
2018-07-12 19:59:53 +02:00
Todd Gamblin
ab794fa741 locks: llnl.util.lock now only writes host info when in debug mode
- write locks previously wrote information about the lock holder (host
  and pid), and read locks woudl read this in.

- This is really only for debugging, so only enable it then

- add some tests that target debug info, and improve multiproc lock test
  output
2018-07-12 19:59:53 +02:00
Todd Gamblin
b9af52a888 tests: Separate tests for llnl.util.lock and spack.util.lock
- llnl.util.lock tests are now independent of Spack
2018-07-12 19:59:53 +02:00
Todd Gamblin
7626ec4579 refactor: move spack.util.multiproc to llnl.util.multiproc
- multiproc doesn't depend on Spack
- llnl.util.lock test uses it, but shouldn't use parts of Spack.
2018-07-12 19:59:53 +02:00
Todd Gamblin
fe0fe1caa1 tests: add lib/spack/spack/test/.cache to gitignore for pytest
- this shoudl have been moved when we moved pytest.ini to lib/spack/spack/test
2018-07-12 19:59:53 +02:00
Tim Law
2a27a37597 Add Git development versions for Typhon and BookLeaf_Cpp. (#8694) 2018-07-12 07:37:42 -05:00
Nicolas Richart
d8921ac323 First try on pytorch (#8649)
* initial version of the package pyTorch (#171)

* adding version 0.4

* flake8 correction

* reordering version, removing run dependecies

* Changing depends_on type to default
2018-07-12 07:30:59 -05:00
Levi Baber
1846bc5ed6 mitofates: more deps and a patch to make it functional (#8686)
* mitofates: more deps and a patch to make it functional
2018-07-12 10:23:22 +02:00
Adam J. Stewart
ecff47538e Remove unnecessary version-specific URL overrides (#8693) 2018-07-12 07:28:11 +02:00
Levi Baber
2561d1d656 transdecoder: needs perl-uri-escape (#8690) 2018-07-11 17:38:58 -05:00
Levi Baber
f29c1d9096 beast1: new version (#8691) 2018-07-11 17:07:20 -05:00
Levi Baber
feb4701ae3 mothur: new version (#8692) 2018-07-11 17:07:02 -05:00
Massimiliano Culpo
10e628a5a0
py-ply: added version 3.11 (#8383) 2018-07-11 22:21:55 +02:00
Massimiliano Culpo
e3a556cd2a Don't propagate version-specific URL overrides to newer versions (#8565)
When a user specifies a URL for a specific version of a package, Spack originally
would use that URL for all newer versions of the package. This behavior has
proven to be generally more harmful than useful, so this PR removes the feature
such that a version-specific URL override affects only that version.
2018-07-11 13:12:19 -07:00
Levi Baber
aa9bb06b89 py-cutadapt: needs py-setuptools at runtime (#8689) 2018-07-11 14:53:35 -05:00
Howard Pritchard
be9dfc2d73 openmpi: add 3.1.1 (#8684)
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-07-11 12:42:00 -05:00
Jannek Squar
6a3f36c4e3 Adjusted sublime-text package (#8685) 2018-07-11 12:41:48 -05:00
Levi Baber
d27133b3cd perl-math-cephes: new package (#8671) 2018-07-11 12:40:39 -05:00
Jimmy Tang
5780eadf64 Update kaldi (#8682)
* Update kaldi

always use the --fst-version otherwise it does the wrong thing with
selecting the fst version.

also enable speex by default

* Give version a more meaningful name

* Update older version with a date string instead
2018-07-11 12:38:06 -05:00
健美猞猁
a985dc859c New packages: libbeato bwtool. (#8681) 2018-07-11 10:33:44 -05:00
Adam J. Stewart
f036f17f61
Retire the py-dev package (#8679) 2018-07-11 10:26:38 -05:00
Sergey Kosukhin
6479ec6def Patch for 'netlib-lapack'. (#8677) 2018-07-11 08:52:21 -05:00
健美猞猁
391d89a853 Bump gromacs versions. (#8676) 2018-07-11 08:05:39 -05:00
Jon Rood
a1bfa8eca0 Adding psm as a dependency of mvapich2. (#8674) 2018-07-10 19:32:50 -05:00
Kshitij Mehta
3c4ef576d9 Gtkorvo updates (#8663)
* gtkorvo-atl: Updated to version 2.2

* gtkorvo-dill: Updated to version 2.4

* gtkorvo-enet: Updated to version 1.3.14

* libevpath: Updated to version 4.4.0

* libffs: Updated to version 1.5

* gtkorvo-atl: Bugfix: Fixed cmake args

* gtkorvo-enet: Switched order of versions to have the latest version on the top

* gtkorvo-atl: Cleaned up cmake_args. Added conditional self.run_tests

* gtkorvo-dill: Cleaned up cmake_args. Added conditional self.run_tests

* libffs: Correction in dependency versions. Cleaned up cmake_args. Added conditional self.run_tests

* libevpath: Correction in dependency versions. Cleaned up cmake_args. Added conditional self.run_tests

* gtkorvo-atl: Removed unused option from cmake args
2018-07-10 12:50:10 -05:00