Commit graph

10537 commits

Author SHA1 Message Date
healther
d414d302f6 Fix log4cxx dependencies (#7570)
* Add ignore_conflicts to package activation

includes:
* with_dependency flag for do_activate
* ignore_conflicts flag for do_activate
* start of cleanup of activate cmd

* ensure that apr is picked up

* Update package.py

* add apr explicitly as dependency

* remove unnecessary newlines

* Update package.py

fixing dependencies
2018-03-30 14:58:08 -05:00
healther
9b5492ca19 add version 3.6.5 to python (#7643) 2018-03-30 12:20:16 +02:00
Matthias Diener
d71386cb53 ltrace: create new package (#7641)
* ltrace: create new package

* Update package.py

* Update package.py
2018-03-29 17:48:34 -05:00
Matthias Diener
9fa169baa6 strace: create new package (#7640) 2018-03-29 17:03:33 -05:00
Adam J. Stewart
499ed2385c
Fix Python3 bug in tut (#7627)
* Fix Python3 bug in tut

* Revert URL change
2018-03-29 14:43:12 -05:00
Yifan Zhu
90c0c12f2a gurobi: new package (#7639)
* gurobi: new pacakge

* fixed flake8 errors
2018-03-29 14:42:36 -05:00
scheibelp
5e758b979e
update tests: concretize mpileaks with gcc (#7635)
Fixes #7593

By default MacOS concretizes using the clang compiler. The unit tests
include a call to "spack spec mpileaks", which has elfutils as a
dependency; #7096 added a conflict in elfutils to avoid building
with clang, which lead to the MacOS unit tests to start failing.
This updates the concretization to force using gcc when concretizing
mpileaks.
2018-03-29 12:24:35 -07:00
Will Furnass
e4b5097375 Add Julia 0.6.2 + checksum (#7577) 2018-03-29 11:44:25 +02:00
Matthias Diener
1dc7b3d346 cmake: update package (#7633) 2018-03-29 11:36:55 +02:00
Howard Pritchard
cdd3f76bd1 libhio: add libhio package to spack (#7468)
spack brought out some configury/make issues with
libhio, so some patches come along for the ride.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-03-28 20:20:46 -05:00
Axel Huebl
4c6199923e mirrors.yaml: does not expand ~ (#7631)
Use `$HOME` for cli commands in `mirrors.yaml` and add
"username" example strings in the file itself.
2018-03-28 14:30:18 -05:00
Michael F. Herbst
fa7e92fa0a Update libcint versions (#7623) 2018-03-28 10:46:07 -05:00
Levi Baber
a6aa172072 gmap-gsnap: new version with numerous bug fixes (#7625) 2018-03-28 10:45:47 -05:00
Levi Baber
16f93464e7 R-snowfall: new package (#7464)
* r-snowfall: dep for phantompeakqualtools

* r-snowfall: fix version number

* r-snowfall: fix hash
2018-03-28 10:30:38 -05:00
Adam J. Stewart
4230c95093
Fix download URL for SCons and add latest version (#7614) 2018-03-28 10:29:44 -05:00
Michael F. Herbst
843e9f13a1 Add recent bohrium version (#7624) 2018-03-28 10:21:36 -05:00
Eric Müller
70a8219f92 Adds liblockfile (and patch to avoid need for root) (#7621)
* --enable-shared *additionally* builds shared libraries
  (and it builds fast, so no variant here)
2018-03-28 07:54:40 -05:00
Massimiliano Culpo
8e998247a3
openmpi: updated package (#7574)
Modifications:
* Added zlib dependency, starting from version 3.0.0
* Added memchecker support  for debugging
* Remove mpirun and similar links if slurm is selected as a scheduler
2018-03-28 10:13:56 +02:00
Denis Davydov
388bb2ab3e petsc: add 3.8.4 (#7616) 2018-03-27 17:41:17 -05:00
David Orman
b5c02a2145 added htslib 1.7 and checksum (#7617) 2018-03-27 17:40:57 -05:00
Nils Deppe
bac47ece70 Add Catch v2.2.1 and v1.12.1 (#7615)
Catch v1 and v2 are maintained independently since v2 requires C++11
support. Updating both to the latest.
2018-03-27 17:40:26 -05:00
Veselin Dobrev
b1628f0af1 [MUMPS] When building '+shared' put the 'inject_libs' after the object
files to get proper linking - this was needed on Ubuntu 14.04.
2018-03-27 14:31:00 -07:00
Patrick Gartung
52d55ea317 Fix buildcache relocate: only skip if rpaths are relative (#7605)
This fixes a check that decides when to skip buildcache relocation.
Originally the check was flawed in two ways: it would skip if the
source prefix matched the destination prefix, which no longer
matters since the source prefix is replaced with a placeholder
(so it always needs to be updated); it also would skip relocation
if the rpaths were not relative, when in fact it should be the
opposite (binaries without relative rpaths *should* be relocated,
and those without don't need it).
2018-03-27 10:54:26 -07:00
Leonhard Reichenbach
0d07be278a spades: fix build (#7608)
Version 3.11 works with gcc7
see: https://github.com/ablab/spades/issues/26
2018-03-27 07:22:34 -05:00
Yifan Zhu
d88f0b8e6d New package r-tidyverse and r-tidyselect (#6507)
* r-rlang: added version 0.1.4

* r-lubridate: added version 1.7.1 and dependency

* r-tidyselect: new package

* r-dplyr: added version 0.7.4

* r-rstudioapi: added version 0.7

* r-tidyr: added version 0.7.2 and other dependencies

* r-tidyverse: new package

* r-tidyr: updated dependencies

* r-tidyverse: added dependency r-rlang

* r-tidyverse: edited docstring

* r-tidyverse: fixed typo

* fix typo again
2018-03-26 14:27:12 -05:00
Eric Müller
28e49fa184 Add missing X-libs dependencies to vim+x (#7599) 2018-03-26 10:24:50 -05:00
Michael Kuhn
2a36c61d0f adios2: add support for Fortran bindings (#7600) 2018-03-26 16:16:38 +02:00
健美猫
658896a7a5 Remove pmi from the fabric list. (#7226) 2018-03-26 13:14:51 +02:00
Michael Kuhn
aeb73f958f zeromq: fix build (#7596)
pkg-config is also required for release versions.
2018-03-26 12:22:07 +02:00
Michael Kuhn
1aed76002a openssl: Add variant to use system certificates (#6396) 2018-03-26 12:20:55 +02:00
Massimiliano Culpo
a119a2d2d8
mpich: added version 3.2.1 (#7598) 2018-03-26 12:19:37 +02:00
Sinan
9f7dbd7f2d new package: Seqan (bioinformatics) (#7588)
* new package: Seqan (bioinformatics)

* add compiler requirements as conflicts

* fix typo

* add dependency types

* correct checksum
2018-03-25 08:50:17 -05:00
healther
9f07300982 fix outdated comments in config.yaml (#7594)
* `spack purge` now is `spack clean`
2018-03-25 08:49:55 -05:00
Adam J. Stewart
4332e75986
Various updates to Spack's Bash completion (#7590)
* Various updates to Spack's Bash completion

* Equals sign messes up tab completion
2018-03-25 08:03:29 -05:00
Massimiliano Culpo
dffd8f384c
python: added a variant to enable PGO + using --with-icc if compiled with Intel (#7496)
Added a variant to enable default optimizations for production builds.
Uses --with-icc if built with Intel compilers.
2018-03-25 09:10:40 +02:00
健美猫
8890dbe3d9 Add a new packag: sofa-c. (#7470) 2018-03-24 20:51:02 +01:00
Todd Gamblin
54f97d1dec
Update copyright on LLNL files for 2018. (#7592) 2018-03-24 12:13:52 -07:00
健美猫
756cb4e6d7 Add a new package: graph500. (#7499)
* Add a new package: graph500.

* Remove leading comments.

* graph500 is a MakefilePackage.

* Update.

* Update.
2018-03-24 11:48:31 -05:00
Todd Gamblin
af0f94a1af
Avoid stat-ing all packages at startup. (#7587)
- FastPackageChecker was being called at startup every time Spack runs,
  which takes a long time on networked filesystems.  Startup was taking
  5-7 seconds due to this call.

- The checker was intended to avaoid importing all packages (which is
  really expensive) when all it needs is to stat them.  So it's only
  "fast" for parts of the code that *need* it.

- This commit makes repositories instantiate the checker lazily, so it's
  only constructed when needed.
2018-03-24 07:39:10 -07:00
Todd Gamblin
998b5a6482
Remove case consistency check at startup. (#7585)
- This was needed when we transitioned to all lowercase packages because
  git didn't handle case changes well on case-insensitive filesystems.

- Now it just adds extra stat calls to startup, and we check for
  all-lowercase package names in tests, so we'll remove it.

- people using really old versions of Spack can re-clone.
2018-03-23 22:38:31 -07:00
Mario Melara
385622953d Cray clean environment (#7582)
* Create unload_module method

Extract code from load_module into unload_module.

* Unload modules to create a clean env on Cray

removes cray-libsci, cray-mpich and darshan to prevent any silent
linking with those packages.
2018-03-23 14:53:52 -07:00
Adam J. Stewart
666e8e3a9b Increment Spack version (#7565) 2018-03-23 14:43:22 -07:00
becker33
1c169ead8b
Grab crayos version from PrgEnv module versions (#7583) 2018-03-23 14:41:43 -07:00
Adam J. Stewart
5b810579fa
Only add python flag for newer versions of glib (#7579) 2018-03-23 15:35:09 -05:00
Jon Rood
04358f827f Adding bc and ed packages. (#7578)
* Adding bc package.

* Adding ed package which is actually a dependency of bc.
2018-03-23 15:24:35 -05:00
xfzhao
9799e6062d beast1: new package (#7544)
* beast1: new package

* beast1: taking suggestion
2018-03-23 15:19:26 -05:00
Mario Melara
2970a50ef6 Add the ability to separate architecture in path scheme (#4329)
* Add format to separate target and os for path

spec format can now handle separations of target and os for setting
up the path.

* Added ${PLATFORM} et al to spec.format()

${PLATFORM}, ${OS}, ${TARGET}

* Update tests

Updated tests and got rid of unnecessary code.

* Also update documentation to reflect this new ability.

* Add default path scheme to config.yaml

Added default path scheme to config.yaml. Users can overwrite this
section if they want.
2018-03-23 12:05:07 -07:00
healther
1391f0db44 add matplotlib version 2.2.2 (#7572) 2018-03-23 14:40:18 +01:00
Denis Davydov
adf972e7ff intel performance libraries: add 2018.2 (#7569) 2018-03-23 13:49:59 +01:00
Federico Ficarelli
213a3de539 Fix tclsh command for transitive dependencies (#7566) 2018-03-23 10:05:54 +01:00