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2017-10-16portage: fixes + added v1.1.* (#5706)Christoph Junghans1-1/+7
2017-10-16armadillo: use libs to provide arpack and superlu libraries (#5777)Michael F. Herbst1-8/+4
2017-10-16petsc: a temporary workaround for concretizer bug in all packages which ↵Denis Davydov1-1/+3
depend on SLEPc (#5755)
2017-10-15Update llvm to version 5.0.0 (#5773)Johann Klähn1-0/+15
2017-10-15Add krims and lazyten (#5771)Michael F. Herbst2-0/+204
* Add krims to spack * Add lazyten to spack * Add description for lazyten * Changes suggested by @davydden and @junghans
2017-10-14boost: remove preferred 1.63 (#5770)Denis Davydov1-5/+1
1.64 had issues serialization (make_array and others) when built with +mpi+python. It appears that those issues are fixed in 1.65.1 so we can remove preferred tag from 1.63.
2017-10-14intel-tbb: add 2018.1 (#5769)Denis Davydov1-0/+2
2017-10-14gsl: add 2.4 (#5768)Denis Davydov1-0/+1
2017-10-14oce: add 0.18.2 (#5767)Denis Davydov1-0/+1
2017-10-14boost: call_once_variadic.patch is already part of 1.56.0 (#5341)Christoph Junghans1-1/+1
2017-10-14Revert "Use cflags instead of the args variable (#5756)" (#5765)Christoph Junghans1-5/+3
This reverts commit 6c3184820aa1052016d92f7ff0419b8085d8ad14.
2017-10-14Ensure that FileList makes it into the documentation (#5739)Adam J. Stewart1-0/+1
2017-10-13superlu_dist: update to latest version 5.2.1 (#5762)Satish Balay1-1/+4
The interface to +int64 changed from -D_LONGINT to XSDK_INDEX_SIZE=64. This change uses the appropriate interface for for the given version
2017-10-13Update Sundials package (#5696)David Gardner1-99/+375
* initial update of sundials package * fix bugs in initial sundials update * add xsdk cmake setup, fix generic math option, add cuda/raja Makefiles to install fixes * Fix lapack install bug, add new conflicts, clean up formatting * Address pull requeset comments and make fomatting style consistent Remove blas variant as blas is only needed when used by an external linear solver. Set related CMake blas variables as needed depending enabled external linear solvers. Add minimum required CMake version. Additional conflicts and dependencies for external libraries based on mpi, indextype, and precision. Fix SuperLU_MT logic to check which threading type SuperLU_MT was configured with. Add maintaiers. Change Sundials solver options to use an array of values. Consistently use % for formatting. * change triple-single quotes to single quotes * Change indextype option to a single int64 option
2017-10-13Clean up logic in Sepc.satisfies_dependencies()Todd Gamblin1-5/+9
- This puts in a fast path when there are no dependencies to satisfy. - Reduces time spent to concretize r-rminer by 2x, down to 5s from 10s
2017-10-13Remove single-root assertion from Spec.rootTodd Gamblin2-11/+6
- Assertion would search for root through all possible paths. - It's also really slow. - This isn't needed anymore. We're pretty good at ensuring single-rooted DAGs, and this assertion has never been thrown. - This shaves another 6 seconds off r-rminer concretization
2017-10-13Use list instead of OrderedDict to find virtual/external candidatesTodd Gamblin1-6/+3
- This reduces concretization time for r-rminer from over 1 minute to only 16 seconds. - OrderedDict ends up taking a *lot* of time to compare larger specs. - An OrderedDict isn't actually needed here. It's actually not possible to find duplicates, and we end up sorting the contents of the OrderedDict anyway.
2017-10-13avoid creating lots of dictionaries in traverse_edges()Todd Gamblin1-15/+14
- This is an optimization to the way traverse_edges iterates over successors. - Previous version called dependencies_dict(), which involved a lot of redundant work (creating dicts and calling caonical_deptype)
2017-10-13Don't redundantly check for providers of non-virtuals.Todd Gamblin1-0/+3
2017-10-13Cache compilers parsed from config filesTodd Gamblin1-29/+39
- Spack ends up constructing compilers frequently from YAML data. - This caches the result of parsing the compiler config - The logic in compilers/__init__.py could use a bigger cleanup, but this makes concretization much faster for now. - on macOS, this also ensures that xcrun is called only twice, as opposed to every time a new compiler object is constructed.
2017-10-13This fixes a bug in creating rpaths relative to $ORIGIN on linux. (#5726)Patrick Gartung3-29/+34
* This fixes a bug in creating rpaths relative to on linux. * fix for macOS as well * found in testing * flake8 * fix testing on macOS * flake8
2017-10-13r-preprocesscore: added versioned dependency on r (#5671)Yifan Zhu1-0/+1
2017-10-13r-rmpi: added list_url and updated md5 (#5698)Yifan Zhu1-2/+2
2017-10-13r-edger: added versioned dependency on r (#5669)Yifan Zhu1-0/+1
2017-10-13r-s4vectors: added versioned dependency on r (#5672)Yifan Zhu1-0/+2
2017-10-13likwid: update versions (#5757)Denis Davydov1-0/+3
2017-10-13r-xvector: added versioned dependency on r (#5731)Yifan Zhu1-0/+1
2017-10-13flake8: fix warnings (#5759)Satish Balay3-4/+4
2017-10-13Use cflags instead of the args variable (#5756)Ondřej Čertík1-3/+5
That way the user can still append things to CFLAGS.
2017-10-13py-espresso: initial commit (#5724)Christoph Junghans1-0/+52
2017-10-13espressopp -> py-espressopp (#5732)Christoph Junghans1-2/+6
* espressopp -> py-espressopp * Update package.py
2017-10-13Docker Workflow (#5582)Axel Huebl1-0/+143
This adds a workflow section on how to use spack on Docker. It provides an example on the best-practices I collected over the last months and circumvents the common pitfalls I tapped in. Works with MPI, CUDA, Modules, execution as root, etc. Background: Developed initially for PIConGPU.
2017-10-13Fix m4 to compile with Intel (#5728)Ondřej Čertík1-0/+3
Fixes #5705.
2017-10-13r-biostrings: added versioned dependency on r (#5667)Yifan Zhu1-0/+1
2017-10-13r-zlibbioc: added versioned dependency on r (#5674)Yifan Zhu1-0/+1
2017-10-13trilinos / oce : add missing if before calling macOS_version (#5743)Denis Davydov2-2/+3
* trilinos: add missing if before calling macOS_version * oce: add missing if before calling macOS_version
2017-10-13r-readr: created new package (#5741)Yifan Zhu1-0/+43
2017-10-13r-dorng: created new package (#5740)Yifan Zhu1-0/+46
2017-10-13r-stringr: added list_url and version 1.2.0 (#5738)Yifan Zhu1-0/+2
2017-10-13r-stringi: added list_url and version 1.1.5 and 1.1.3 (#5737)Yifan Zhu1-0/+3
2017-10-13r-summarizedexperiment: created new package (#5734)Yifan Zhu1-0/+47
2017-10-13r-yaqcaffy: added list_url and versioned dependency on r (#5730)Yifan Zhu1-0/+2
2017-10-13slepc: refine version constraints for petsc 3.8 (#5752)Denis Davydov1-4/+8
2017-10-13openblas: remove extra develop version (#5750)Denis Davydov1-2/+0
2017-10-13gettext: fix prefix (#5749)Denis Davydov1-1/+1
2017-10-12Lbann flags (#5747)Brian Van Essen2-3/+2
* Fixed the datatype flag in the LBANN package. Also added develop version to OpenBLAS. * Fixed where the datatype flag should be set.
2017-10-12r-gcrma: added versioned dependency on r (#5670)Yifan Zhu1-0/+1
2017-10-12r-simpleaffy: added versioned dependency on r (#5673)Yifan Zhu1-0/+1
2017-10-12petsc: add in maintainers (#5729)Satish Balay1-0/+2
2017-10-12Add the option for a versioned layout to boost (#5709)David Hows1-0/+6