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2016-11-03spack install: forward sys.stdin to child processes (#2158)Massimiliano Culpo3-36/+62
* spack install: forward sys.stdin to child processes fixes #2140 - [ ] redirection process is spawned in __enter__ instead of __init__ - [ ] sys.stdin is forwarded to child processes * log: wrapped __init__ definition
2016-11-03spack find: accepts anonymous specs as arguments fixes #2170 (#2188)Massimiliano Culpo5-58/+33
2016-11-02Set TAU_MAKEFILE env variable (#2210)Pramod Kumbhar1-1/+6
* In order to use TAU module, we have to set TAU_MAKEFILE env variable. * updated with suggestions from @citibeth
2016-11-02Fix style checker bug. (#2214)Todd Gamblin1-12/+42
* Fix style checker bug. * spack flake8: print cwd-relative paths by default, with root-relative option.
2016-11-02Add support for gfortran to be used with clang (#2192)Barry Smith2-4/+28
1) list gfortran as a fc and f77 compiler that can work with clang 2) allow compatible gfortran to ./spack compiler find with clang by matching version numbers This is based on the discussions in https://github.com/LLNL/spack/issues/237 https://github.com/dealii/dealii/wiki/deal.II-in-Spack#mixing-gcc-and-clang-on-osx This is not a long term solution but something to get us through the next months until the compiler infrastructure is reworked to allow mixing and matching for C/C++ and Fortran compilers Funded-by: IDEAS Project: IDEAS/xSDK Time: 1.5 hours
2016-11-02Added first version of the NCL package. (#2195)Sergey Kosukhin2-0/+263
Without GRIB2 and HDF-EOS support yet.
2016-11-01Nmap package added (#2206)Peter Doak1-0/+37
* works to build newest version of nmap with gcc@5.3.0 * formatting * clean up
2016-11-01Update references in debug command (#2204)scheibelp1-3/+3
2016-10-31Improved package.py error handling. (#2187)Todd Gamblin4-163/+219
- Detailed debug information is now handed back to the parent process from builds, for *any* type of exception. - previously this only worked for Spack ProcessErrors, but now it works for any type of error raised in a child. - Spack will print an error message and source code context for build errors by default. - It will print a stack trace when using `spack -d`, even when the error occurred in the child process.
2016-10-31Add `spack flake8` command. (#2186)Todd Gamblin3-78/+163
- Ported old run-flake8-tests qa script to `spack flake8` command. - New command does not modify files in the source tree - Copies files to a temp stage modifies them there, and runs tests. - Updated docs and `run-flake8-tests` script to call `spack flake8`.
2016-10-30Allow common args to be written the same way regular args are.Todd Gamblin2-49/+25
2016-10-30Bugfix: '::' only worked on top-level key in config.Todd Gamblin12-152/+257
- generalized and fixed to work with any key in YAML file - simplified schema writing, as well - add more unit tests for the config system - Rename test/yaml.py to test/spack_yaml.py - Add test/yaml.pyc to ignored pyc files.
2016-10-30Documentation for configurationTodd Gamblin15-388/+678
2016-10-30Add `spack arch --platform` optionTodd Gamblin1-2/+12
2016-10-30travis.yml: Only build master and develop on pushTodd Gamblin1-0/+6
2016-10-30Make provider_index use spack yaml for cleaner output.Todd Gamblin1-4/+4
2016-10-30source_cache, misc_cache, verify_ssl, checksum, & dirty in config.yamlTodd Gamblin17-77/+164
- Added new preferences to config.yaml: - source_cache - misc_cache - verify_ssl - checksum - dirty
2016-10-30Add module_roots to config.yamlTodd Gamblin5-41/+69
2016-10-30Move temp directory configuration to config.yamlTodd Gamblin9-176/+330
- Moved temp finding logic to spack.stage - Updated stage tests - Added tests for new path substaitution of $user, $spack, $tempdir
2016-10-30Rename install.yaml -> config.yaml, install_area -> "store"Todd Gamblin23-164/+266
- Added a schema for config.yaml - Moved install tree configuration to config.yaml - Moved etc/spack/install.yaml to etc/spack/defaults/config.yaml - renamed install_area to "store", to use a term in common with guix/nix. - in `config.yaml` file, it's called the `install_tree` to be more intuitive to users. - `install_tree` might've worked in the code, but `install_tree` is already a global function in the spack namespace, from llnl.util.filesystem.
2016-10-30add documentation for new option to set install areaBenedikt Hegner1-0/+11
2016-10-30refactor settings for install area and make them config optionsBenedikt Hegner22-161/+254
2016-10-30Removes cyclic dependency on spack.config. (#2121)Matt Belhorn3-51/+2
Merge #2030 added a cyclic dependency between the Cray platform needing to read a `targets.yaml` config file and `config.py` needing to get the platform names. This commit removes the cyclic dependency in favor of the more general config scheme. It also removes the now functionless `targets.yaml` config file. This breaks 'frontend' targets on the Cray platform but all architecture targets, including the frontend, that are provided by CrayPE are added to the Platform anyway so users can be explicit about the architecture targeted by the Cray compiler wrappers: ``` spack spec libelf arch=cray-CNL-frontend ``` becomes ``` spack spec libelf arch=cray-CNL-mc8 # on an XK7 or spack spec libelf arch=cray-CNL-sandybridge # on an older XC30, etc.. ``` The only way the 'frontend' target can be defined after this commit is through target environment variables.
2016-10-30python: PYTHONHOME may not be the same as the prefix of the python ↵Barry Smith1-2/+21
executable (#2173) On MacOS, brew installs /usr/local/bin/python but the Python prefix is not /usr/local/bin Use the python command sys.exec to get the correct directory, instead of the ad hoc self.prefix previously used This was a bear to debug; been driving me nuts since I started using spack. Since spack passes PYTHONHOME down to package builds in the environment it was passing PYTHONHOME of /usr/local/bin to the PETSc build that uses Python so the PETSc Python ./configure errored immediately with ImportError: No module named site since python could find no python modules. Todd Gamblin pointed out that my first try to fix this was wrong since it assumed the spack python was the same python used to run spack. Elizabeth Fischer suggested how to get it to work also with python3 Funded-by: IDEAS Project: IDEAS/xSDK Time: 7 hours Thanks-to: Todd Gamblin, Elizabeth Fischer
2016-10-30module file support: major rework of docs (#2169)Massimiliano Culpo3-566/+660
* module file support: major rework of docs * module file support: fixed issues found by @adamjstewart - list or enumeration should not be indented - use console instead of bash or csh in things that are not scripts - other typos * module file support: fixed other issues found by @adamjstewart - tables should not be indented - substitute lines with pyobject to import an entire function - get help output running commands - typos * module file support: fixes according to review comments - @citibeth moved `spack module loads` after `spack load` - @glennpj tried to clarify installation table + changes to language - @tgamblin Removed top level section and moved the whole thing into the reference manual * module file support: moved directive before spack module loads
2016-10-30configuration file for modules : fixed enable keyword (#2176)Massimiliano Culpo4-74/+10
- enable keyword works again - test/modules.py : proper clean-up after tests
2016-10-30updated gtk and gobject dependences (#2126)Gregory Lee2-0/+3
2016-10-29Do not check directory layout for external packages (#2172)Barry Smith1-1/+1
External packages do not have an spec.yaml file so don't check for it. Without this change any time a package depends on an external package when the new package is installed you will get the error Install prefix exists but contains no spec.yaml This problem has also haunted me since I started using Spack since PETSc depends on Python and I used an external python but fortunately it was relatively easy to debug once I could reproduce it at will. Funded-by: IDEAS Project: IDEAS/xSDK Time: 1 hour
2016-10-29Import dso_suffix from spack.build_environment in abi.py (#2174)Matthew Scott Krafczyk1-0/+1
Fixes #1845
2016-10-29Update license directory for intel-paralel-studio (#2163)Adam J. Stewart1-6/+15
2016-10-29Use Spec.format for token substitution in modules (#1848)scheibelp3-65/+87
This replaces a custom token-based substitution format with calls to Spec.format in modules.py This also resolves a couple issues: - LmodModules set configuration globally instead of in its initializer which meant test-specific configuration was not applied - Added support for setting hash_length=0 for LmodModules. This only affects the module filename and not the directory names for the hierarchy tokens in the path. This includes an additional unit test.
2016-10-28Update and Clean Up the Visit and VTK Packages (#2167)Joseph Ciurej2-62/+69
* Made some refactoring improvements to the 'visit' and 'vtk' packages. * Added a small fix for the 'vtk' package when building with 'qt+webkit'.
2016-10-27Fix rpath linking for NAG, add documentation on setup (#2142)Adam J. Stewart3-27/+57
2016-10-27Add latest version of Intel Parallel Studio XE (#2151)Adam J. Stewart1-15/+47
2016-10-26Remove support for deprecated package. See also #2085 and #2086 (#2090)Elizabeth Fischer1-1/+0
2016-10-26Get Trilinos 12.6.2 to build with Intel compilers and spack (#2102)Barry Smith1-8/+17
Funded-by: IDEAS Project: IDEAS/xSDK Time: 2 hours
2016-10-26Fix typo: _choiches -> _choices (#2127)George Hartzell1-1/+1
The breaks `spack create`.
2016-10-26typo: vlaues -> values (#2147)George Hartzell1-1/+1
2016-10-26Removed documentation on false paths as per #2083 (#2146)Elizabeth Fischer2-40/+1
Removed documentation on false paths as per #2083
2016-10-26document recommended usage of system blas/lapack (#2081)Denis Davydov1-0/+35
* document recommended usage of system blas/lapack * update doc * minor * reword
2016-10-26ProcessError : now the exception is correctly pickled and passed across ↵Massimiliano Culpo2-11/+32
processes. (#2143)
2016-10-26libSplash: Add 1.5.0 Release (#2137)Axel Huebl1-0/+1
Add the latest release of libSplash, version 1.5.0.
2016-10-26spack install : added --log-format option (incorporates test-install ↵Massimiliano Culpo5-281/+268
command) (#2112) * spack install : added --log-format option (incorporates test-install command) fixes #1907 * qa : removed extra whitespace
2016-10-26require fortran for MPI providers to avoid delayed compiler errors (#1937)Denis Davydov3-18/+21
* openmpi: require fortran for now * mpich: requre fortran for now * mvapich2: require fortran for now * openmpi: flake8 fixes
2016-10-26Develop: Resolve issue 2070 with new depends_on clause in the openspeedshop ↵Jim Galarowicz1-1/+1
package file. (#2136) * Update the krell institute products to use the latest features of spack for building on cluster platforms. * Address travis error messages and resubmit the pull request. * Update the contents of openspeedshop package.py so it passes the flake8 tests. * Fix flake8 error-whitespack issue in mrnet package.py file. * Add updates based on spack reviewer feedback. * More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH. * More review related changes. Update MPIOption.append lines and take out xercesc references. * Create a base options function for common openspeedshop base cmake options to reduce redundencies. * Add libxml2+python depends on to get around issues with the libxml2 package file.
2016-10-26add a unit test for conretization with develop version (#2064)Denis Davydov2-0/+44
2016-10-26veclibfort: add new package (#2080)Denis Davydov1-0/+70
* veclibfort: add new package * veclibfort: add a small test
2016-10-25Add package for ant (#2133)George Hartzell1-0/+44
Add a package for ant, a java build tool.
2016-10-25Add package for maven (#2132)George Hartzell1-0/+41
Add a package that installed the pre-built maven distribution. I've given up, for now, on building maven from source. That processed stumbled on two points before I gave up: 1. It downloaded several hundred .{pop,jar} files and I despaired of figuring out some way of mirroring and checksumming them; and 2. It exploded complaining about too many unacceptable license files, which seems odd in its own source tree. Perhaps someone with more Java fu that I admit to can figure it out. In the meantime, this is useful.
2016-10-25filter system paths (#2083)Denis Davydov3-3/+62
* add filter_system_paths() * filter system paths in set_build_environment_variables() * two function: lib/inc + bin * reverse order in bin * fix order * minor * improvements of the code * more cleanup * alternative solution for filter_bins * fiddle base alalazo's approach * minor * minor
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