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2019-10-03Generic x86_64 code compiled with GCC uses non deprecated mtune flags (#13022)Massimiliano Culpo2-6/+15
fixes #12928
2019-10-02Remove support for generating dotkit files (#11986)Massimiliano Culpo34-426/+121
Dotkit is being used only at a few sites and has been deprecated on new machines. This commit removes all the code that provide support for the generation of dotkit module files. A new validator named "deprecatedProperties" has been added to the jsonschema validators. It permits to prompt a warning message or exit with an error if a property that has been marked as deprecated is encountered. * Removed references to dotkit in the docs * Removed references to dotkit in setup-env-test.sh * Added a unit test for the 'deprecatedProperties' schema validator
2019-10-02added tasmanian version 7.0 to spack (#13003)Miroslav Stoyanov3-4/+52
2019-10-02New package: mapnik (#12708)Sinan1-0/+54
2019-10-02libint + cp2k: 2-stage build with 'tune' and 'fortran' variants (#12475)Tiziano Müller2-20/+128
* libint: switch to 2-stage build for 2.6.0+ * libint: add tune and fortran variants * cp2k: add support for libint >= 2.0 * cp2k: use pkg-config for linking libxc
2019-10-02cdhit: add zlib dependency. (#13015)Toyohisa Kameyama1-3/+7
* cdhit: add zlib dependency. * Add zlib variant.
2019-10-02denovogear: Add missing zlib depenbdency and fix open handling error. (#13017)Toyohisa Kameyama2-0/+15
2019-10-02cnpy: add zlib dependency. (#13016)Toyohisa Kameyama1-0/+2
2019-10-02Add cuda to paraview build. (#12996)Dan Lipsa1-1/+11
2019-10-02Singularity 3.4.1 still needs the makefile patch (#13008)George Hartzell1-1/+1
* Singularity 3.4.1 still needs the makefile patch * Constrain build patch to 3.4.0:3.4.1
2019-10-02new package: openldap (#12748)Sinan1-0/+92
* new package: openldap * fix mistake * remove template text * fix build error involving perl * flake8 * improvements * introduce multi valued variant for tls support * improve tls variant * overwrite build phase as opposed install * improve style
2019-10-02ants: missing zlib dependency and fix working directory in install. (#13010)Toyohisa Kameyama1-1/+6
2019-10-02breakdancer: missing ncurses dependency. (#13011)Toyohisa Kameyama1-0/+2
2019-10-02breseq: fix dependency and limit compiler version. (#13013)Toyohisa Kameyama1-1/+4
2019-10-02fujitsu compiler: Add 'required_libs'. (#13014)t-karatsu1-0/+2
2019-10-02update py-jupyter-notebook to use the real releases (#13020)Andreas Baumbach1-13/+9
* github releases are not released versions, but from-source releases * they lack the mimification of the JS/CSS components and as such require node-js and npm, this conflicts with python@3: * this commit * drops the from-source dependencies on node-js and npm and * updates the checksums to the correct sha256 hashes of the pypi releases. The pypi-tarballs are different
2019-10-02Replace expensive store.reindex() call with db.add() call. (#13021)Patrick Gartung1-1/+1
2019-10-01ZFP: CMake Package (#12999)Axel Huebl4-38/+65
* ZFP: CMake Package ZFP is primarily build via CMake, which will have all install logic and configuration files generated. The 0.5.0 release did not support this yet, so we toss it. * Patch ADIOS1: ZFP 0.5.1+ support * ZFP: Expose all CMake variants
2019-10-01'spack buildcache list' should show all buildaches available. (#13002)Patrick Gartung1-5/+1
* binary cache: show all packages for compatible differing targets * Don't restrict spack buildcache list to arch or os * Fix from merge conflict
2019-10-01direnv: add info for version 2.20.0 (#13007)George Hartzell1-0/+1
2019-10-01Add all compatible system types directory to module pathsMassimiliano Culpo4-3/+21
fixes #12915 closes #12916 Since Spack has support for specific targets it might happen that software is built for targets that are not exactly the host because it was either an explicit user request or the compiler being used is too old to support the host. Modules for different targets are written into different directories and by default Spack was adding to MODULEPATH only the directory corresponding to the current host. This PR modifies this behavior to add all the directories that are **compatible** with the current host.
2019-10-01new package: py-python-ldap (#12599)Sinan1-0/+24
* new package: py-python-ldap * fix dependency types * improvements * Update var/spack/repos/builtin/packages/py-python-ldap/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-python-ldap/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * add openldap dependency
2019-10-01New package: py-python-mapnik (#12786)Sinan1-0/+29
2019-10-01picard: add 2.20.8codeandkey1-0/+1
2019-10-01go-md2man: disable module-mode (#12985)Daryl W. Grunau1-0/+1
* go-md2man: disable module-mode * Update var/spack/repos/builtin/packages/go-md2man/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01add singularity 3.4.1 (#12995)Eduardo Arango1-1/+3
* add singularity 3.4.1 Signed-off-by: ArangoGutierrez <eduardo@sylabs.io> * revert some changes Signed-off-by: ArangoGutierrez <eduardo@sylabs.io> * add maintainers list to pkg singularity Add @alalazo and me to the Singularity maintainers list * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01binary cache: show all packages for compatible differing targets (#12943)Greg Becker1-3/+6
2019-10-01Dataspaces: Fix Fetch URL, Savanna Spec (#13001)Axel Huebl2-2/+2
2019-10-01GCC package: don't set CC etc. based on bin dir if it doesn't exist (#13000)Peter Scheibel1-0/+4
7bcb306 updated setup_environment in the GCC package to examine the bin/ directory to find alternatively-named instances of CC, but this failed to account for when GCC was being installed and failed when it attempted to list the not-yet-existing installation prefix. This commit updates the logic to skip this search if the bin/ directory doesn't exist.
2019-10-01libaio: fixed a condition that checks whether we are running on OS X (#12976)Massimiliano Culpo4-37/+52
* libaio: fixed a condition that checks whether we are running on OS X * libaio: simplified package by adding an explicit conflict for darwin * libaio: added information to the docstring * fio: added version 3.16, added conflict when using libaio, docstring * lvm2: conflict due to libaio dep, improved docstring, simpler install * mariadb: conflict due to libaio dep, improved docstring, version 10.4.7 * mariadb: the dependency on libaio is now conditional, removed conflict * mariadb: fixed a typo in previous commit Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * libaio: turned into a MakefilePackage
2019-10-01When removing a file from a view, don't fail if it doesn't exist (#12960)Jeffrey Salmond1-0/+3
Sometimes when remove_file is called on a link, that link is missing (perhaps ctrl-C happened halfway through a previous action). As removing a non-existent file is no problem, this patch changes the behavior so Spack continues rather than stopping with an error. Currently you would see ValueError: /path/to/dir is not a link tree! and now it continues with a warning.
2019-10-01Kaldi package: add version 7637de7 and egs (#12911)Jimmy Tang1-0/+8
2019-10-01add new mercurial versions (#12997)Jeffrey Salmond1-1/+3
2019-10-01Update chapel to current (1.19 -> 1.20) (#12991)Christopher Edsall1-1/+2
2019-10-01ADIOS2: 2.5.0 (#12987)Axel Huebl1-0/+1
Add the latest ADIOS2 release, v2.5.0 .
2019-10-01hypre: add version 2.18.0 (#12992)Satish Balay1-0/+1
2019-10-01add adios2 dependency and configuration for newest OpenFOAM (#12993)Mark Olesen1-4/+11
2019-10-01libcerf:add CFLAGS for fujitsu compiler (#12990)noguchi-k1-0/+3
* libcerf:add CFLAGS for fujitsu compiler * fix for flake8
2019-09-30Update nano (#12980)egreen771-3/+51
2019-09-30Revert "update neovim (#12965)" (#12978)Adam J. Stewart1-2/+1
This reverts commit 86a85b7eb22ccf69489a4bfbd947da7dfedcf233.
2019-09-30petsc, slepc: add new versions - 3.12.0 (#12979)Satish Balay2-2/+8
2019-09-30Fix GCC environment variables for external installations (#12454)Seth R. Johnson1-5/+25
Unlike the compiler binary name search logic, the `setup_environment` in GCC's package assumes the compiler names are *exactly* `gcc`, `g++`, etc. In many external installations (Homebrew, Macports) the installation includes only *suffixed* versions such as `gcc-9`. This patch uses the GCC compiler search suffixes to actually locate the correct filenames for the installed compilers, allowing the Spack-generated module file to have useful definitions of CC, CXX, etc. It also allows for the possibility that the user's external installation of GCC is compiled without Fortran support, in which case the `FC` environment variables are not defined.
2019-09-30otf2: add configure args to specify compiler commands. (#12711)t-karatsu1-0/+4
* otf2: add configure args to specify compiler commands. * Modify the reference of the compile commands.
2019-09-29make license check slightly more lenientTodd Gamblin1-1/+1
bin/spack now needs to have a "-*- python -*-" line after the shebang, so that emacs will interpret it as a python file instead of as a shell script. Add one line to the license check limit to accommodate this.
2019-09-29prefer Python 3 to Python 2 for running SpackTodd Gamblin1-1/+17
The Python landscape is going to be changing in 2020, and Python 2 will be end of life. Spack should *prefer* Python 3 to Python 2 by default, but we still need to run on systems that only have Python2 available. This is trickier than it sounds, as on some systems, the `python` command is `python2`; on others it's `python3`, and RHEL8 doesn't even have the `python` command. Instead, it makes you choose `python3` or `python2`. You can thus no longer make a simple shebang to handle all the cases. This commit makes the `spack` script bilingual. It is still valid Python, but its shebang is `#!/bin/sh`, and it has a tiny bit of shell code at the beginning to pick the right python and execute itself with what it finds. This has a lot of advantages. I think this will help ensure that Spack works well in Python3 -- there are cases where we've missed things because Python2 is still the default `python` on most systems. Also, with this change, you do not lose the ability to execute the `spack` script directly with a python interpreter. This is useful for forcing your own version of python, running coverage tools, and running profiling tools. i.e., these will not break with this change: ```console $ python2 $(which spack) <args> $ coverage run $(which spack) <args> $ pyinstrument $(which spack) <args> ``` These would not work if we split `spack` into a python file and a shell script (see #11783). So, this gives us the best of both worlds. We get to control our interpreter *and* remain a mostly pure python executable.
2019-09-29The perl-uri-escape package duplicates perl-uri (#12971)Glenn Johnson6-25/+6
* The perl-uri-escape package duplicates perl-uri The Perl URI::Escape module is in the Perl URI package so the Spack perl-uri-escape package is a duplicate of the perl-uri package. This PR does the following: - replace `depends_on('perl-uri-escape')` with `depends_on('perl-uri')` in packages that dependend on perl-uri-escape - add the version from perl-uri-escape to perl-uri - remove the unneeded dependency from perl-uri - remove the perl-uri-escape package * Reinstated perl-test-needs dependency Put the perl-test-needs dependency for perl-uri back in but set it to type='test'. * For tests to succeed the type must be ('build', 'test')
2019-09-28Add all the 'generic' architectures that are mentioned in recipes (#12958)Massimiliano Culpo1-0/+35
LLVM, mesa and other packages check for these generic microarchitectures. One solution is to let Spack know they exist.
2019-09-28raxml: simplified recipe by removing SIMD variants (#12952)Massimiliano Culpo1-46/+12
Now the support for SSE3 or AVX is tested on the selected target
2019-09-28bowtie: fix for aarch64, and bugfix about c++11-narrowing. (#12953)t-karatsu3-0/+86
2019-09-28vdt: simplified recipe by removing SIMD variants (#12954)Massimiliano Culpo1-55/+8
Now the support for SSE3 or AVX is tested on the selected target
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