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2017-03-21Fix for `find --explicit` #3374 (#3492)George Hartzell1-1/+1
This fixes the problem described in #3374, which describes `spack find` ignore explicit/implicit. I believe that this was broken in #2626. This restores the behavior of implicit/explicit for me. I believe that it does not screw anything else up, but ....
2017-03-21Convert isl to AutotoolsPackage (#3507)Adam J. Stewart1-10/+10
2017-03-21Add recommended patches to mpfr package (#3506)Adam J. Stewart3-1/+179
2017-03-21Replacing failing git clone by valid url (#3505)Kim Serradell1-6/+5
* Replacing failing git clone by valid url * Moving to previous version package (0.163) * Removing automake and autoconf dependencies and adding url_list to pick up newer versions * Corrected typo * Reorder versions and removed libtool
2017-03-21Add package openfst. (#3324)健美猫1-0/+54
2017-03-20llvm: Don’t copy “prefix/bin” into “prefix” during install (#3460)Erik Schnetter1-2/+1
2017-03-20Fix: setuptools is a runtime dependency for pudb (#3502)Adam J. Stewart1-4/+7
2017-03-20Add latest version of binutils (#3500)Adam J. Stewart1-8/+8
2017-03-20Update leveldb to 1.20 (#3441)Michael Kuhn1-4/+21
2017-03-20gasnet: Update to 1.28.2 (#3496)Erik Schnetter1-0/+1
2017-03-20cereal: Update to 1.2.2 (#3499)Erik Schnetter4-16/+32
2017-03-20jemalloc: Update to 4.5.0 (#3497)Erik Schnetter1-0/+1
2017-03-20py-yt: Update to 3.3.5 (#3498)Erik Schnetter1-0/+2
2017-03-20Improve output for compiler commands (#3480)scheibelp2-1/+14
* Order listed compiler sections "spack compiler list" output compiler sections in an arbitrary order. With this commit compiler sections are ordered primarily by compiler name and then by operating system and target. * Compiler search lists config files with compilers If a compiler entry is already defined in a configuration file that the user does not know about, they may be confused when that compiler is not added by "spack compiler find". This commit adds a message at the end of "spack compiler find" to inform the user of the locations of all config files where compilers are defined.
2017-03-20Fix issue with config.guess patching when the overwritten config.guess did ↵Matthew LeGendre1-9/+5
not have write permissions. (#3494)
2017-03-20fftw: Update to 3.3.6-pl1 (#3495)Erik Schnetter1-0/+1
2017-03-19Add ffmpeg package. (#3470)健美猫1-0/+47
2017-03-19Substitue ftp:// with http:// (#3491)健美猫1-1/+1
2017-03-19Add new version for intel package: 16.0.4 17.0.2 . (#3490)健美猫1-7/+12
2017-03-18Use byte-encoded UTF-8 for sourced environment in Python 2 (#3489)Todd Gamblin3-9/+52
- Fixes recurring errors on develop with unicode commit characters. - still Python3-proof: python3 will use str instead of bytestrings.
2017-03-18hdf5: Clean up building self-tests (#3483)Erik Schnetter1-9/+5
* hdf5: Clean up building self-tests * hdf5: Clean up running self-tests
2017-03-18Add missing dependencies to gawk (#3481)Adam J. Stewart4-6/+55
* Add missing dependencies to gawk * Fix make check * Add mawk packages and awk virtual dependency * Use mawk instead of gawk to build ncurses * Rearrange order of patches and dependencies
2017-03-18Fix deptype of various dependencies on Python packages (#3486)Adam J. Stewart20-32/+34
2017-03-18Adding new packages: py-argparse and py-importlib (#3488)Javier2-0/+72
2017-03-17setuptools is a runtime dependency of virtualenv (#3485)Adam J. Stewart1-5/+10
2017-03-17julia: Create cacert directory manually to ensure correct permissions (#3482)Erik Schnetter1-1/+3
2017-03-17Adding new package: py-future (#3401)Javier1-0/+39
* Adding new package: py-future * Commenting out deps needed when installing python@2.6
2017-03-17Don't use @system in packages.yaml (#3472)Adam J. Stewart3-73/+19
2017-03-17Add package for ESMF (#2831)Adam J. Stewart1-0/+253
* Add package for ESMF * Apparently mvapich2 is supported?
2017-03-17Add version constraints to VTK patch (#3357)Adam J. Stewart1-44/+41
2017-03-17hpx5: Convert to AutotoolsPackage, several updates (#3456)Erik Schnetter1-22/+78
* hpx5: Convert to AutotoolsPackage, several updates - convert to AutotoolsPackage - add several variants - add several dependencies - add new version 4.0.0 - don’t set compiler flags explicitly * hpx5: Don’t import os * hpx5: Clean up configure arguments * hpx5: Correct libffi configure declaration Also add new variant “+instrumentation”. * hpx5: Correct CUDA, MPI, OpenCL configuration * hpx5: Use built-in libffi Spack’s libffi installs its headers in a strange place, and hpx5 can’t pick them up.
2017-03-17libpciaccess: Convert to AutotoolsPackage, remove Darwin work-around (#3459)Erik Schnetter5-16/+8
* libpciaccess: Convert to AutotoolsPackage, remove Darwin work-around Other packages that depend on libpciaccess can do so via a conditional dependency (via a variant); we don’t need a dummy package for Darwin any more. * Disable libpciaccess dependency on non-Darwin platforms * hwloc: Remove direct dependency on libpciaccess
2017-03-16Add packages libbson and libmongoc (#3440)Michael Kuhn2-0/+86
2017-03-16simulationio: New package (#3422)Erik Schnetter1-0/+62
* simulationio: New package * simulationio: Rename development version to “develop” * simulationio: Try to make flake8 happy * simulationio: Correct flake8 error * simulationio: Extend Python * simulationio: Remove unused imports
2017-03-16Add latest version of NCO (#3469)Adam J. Stewart1-1/+2
2017-03-16Py keras extension (#3468)Brian Van Essen3-0/+51
* Added support for building Theano with GPU support. Added a package for the libgpuarry libary needed for Theano. * Added dependency on py-pexpect package which ipython requires.
2017-03-16Detect when OS updates affect compiler selection (#3410)scheibelp3-21/+77
Fixes #1476 Concretization uses compilers defined in config files and if those are not available defaults to searching typical paths where the detected operating system would have a compiler. If there is an OS update, the detected OS can change; in this case all compilers defined in the config files would no longer match (because they would be associated with the previous OS version). The error message in this case was too vague. This commit adds logic for detecting when it is likely that the OS has been updated (in particular when that affects compiler concretization) and improves the information provided to the user in the error message.
2017-03-16Dont propagate flags between different compilers (#3379)scheibelp2-41/+28
* Dont propagate flags between different compilers Fixes #2786 Previously when a spec had no parents with an equivalent compiler, Spack would default to adding the compiler flags associated with the root of the DAG. This eliminates that default. * added test for compiler flag propagation * simplify compiler flag propagation logic
2017-03-16Fix Qt4 build on Yosemite (10.11) (#3444)Todd Gamblin1-6/+17
2017-03-16gasnet: Convert to AutotoolsPackage, update (#3455)Erik Schnetter1-13/+16
* gasnet: Convert to AutotoolsPackage, update - convert to AutotoolsPackage - add new version 1.28.0 - create variants for IB and MPI support * gasnet: Don’t specify prefix explicitly * gasnet: Add missing variant descriptions * gasnet: Correct syntax error
2017-03-16Dont auto-init compiler conf for 'compiler find' (#3439)scheibelp2-8/+9
Fixes #3428 Users can run 'spack compiler find' to automatically initialize their compilers.yaml configuration file. It also turns out that Spack will implicitly initialize the compilers configuration file as part of detecting compilers if none are found (so if a user were to attempt to concretize a spec without running 'spack compiler find' it would not fail). However, in this case Spack was overlooking its own implicit initialization of the config files and would report that no new compilers were found. This commit removes implicit initialization when the user calls 'spack compiler find'. This did not surface until #2999 because the 'spack compiler' command defaulted to using a scope 'user/platform' that was not accounted for in get_compiler_config (where the implicit initialization logic predates the addition of this new scope); #2999 removed the scope specification when checking through config files, leading to the implicit initialization.
2017-03-16Add latest version of lmod (#3467)Adam J. Stewart1-1/+2
2017-03-16Add latest version of git, convert to AutotoolsPackage (#3466)Adam J. Stewart1-53/+59
2017-03-16julia: New variant +simd (#3458)Erik Schnetter1-0/+5
2017-03-16hwloc: Add missing dependencies (#3457)Erik Schnetter1-5/+22
* hwloc: Add missing dependencies - add several missing dependencies - add variants for various features - add new version 1.11.6 * hwloc: Add descriptions to variants
2017-03-16qthreads: New version 1.12 (#3464)Erik Schnetter1-0/+1
2017-03-16pocl: Introduce virtual package “opencl” (#3461)Erik Schnetter1-0/+4
OpenCL is a standard like MPI, with several versions and several implementations.
2017-03-16py-numpy: Correct typos in comment (#3462)Erik Schnetter1-2/+2
2017-03-16py-scipy: New version 0.19.0 (#3463)Erik Schnetter1-0/+2
2017-03-16Adding new package: py-jpype (#3402)Javier1-0/+44
* Adding new package: py-jpype * Moving jdk dependency