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2020-09-25refactor install_tree to use projections format (#18341)Greg Becker1-5/+4
* refactor install_tree to use projections format * Add update method for config.yaml * add test for config update config
2020-09-03Pillow-SIMD: use as default PIL provider (#18097)Adam J. Stewart1-1/+1
* Pillow-SIMD: use as default PIL provider * Fix concretization of pil * Fix build of older versions of pillow
2020-08-10Update packages.yaml format and support configuration updatesMassimiliano Culpo1-5/+8
The YAML config for paths and modules of external packages has changed: the new format allows a single spec to load multiple modules. Spack will automatically convert from the old format when reading the configs (the updates do not add new essential properties, so this change in Spack is backwards-compatible). With this update, Spack cannot modify existing configs/environments without updating them (e.g. “spack config add” will fail if the configuration is in a format that predates this PR). The user is prompted to do this explicitly and commands are provided. All config scopes can be updated at once. Each environment must be updated one at a time.
2020-07-23Revert "Add libglvnd packages/Add EGL support (#14572)" (#17682)Chuck Atkins1-6/+2
This reverts commit 573489db710c6fd315170a45d6c609db2e30e5e4.
2020-07-13Add libglvnd packages/Add EGL support (#14572)Omar Padron1-2/+6
* add new package: "libglvnd-frontend" * add +glvnd variant to opengl package * add +glvnd variant to mesa package * add +egl variant to paraview package * add libglvnd-frontend entries to default packages config * fix style * add default providers for glvnd virtuals add default providers for glvnd-gl, glvnd-glx, and glvnd-egl * WIP: rough start to external OpenGL documentation * rename libglvnd-frontend package and backend virtual dependencies * update documentation * fix ligvnd-be-* typos * fix libglvnd-fe package class name * fix doc parse error
2020-07-08add public spack mirror (#17077)Peter Scheibel1-0/+2
2020-06-25Separate Apple Clang from LLVM Clang (#17110)Massimiliano Culpo1-1/+5
* Separate Apple Clang from LLVM Clang Apple Clang is a compiler of its own. All places referring to "-apple" suffix have been updated. * Hack to use a dash in 'apple-clang' To be able to use autodoc from Sphinx we need a valid Python name for the module that contains Apple's Clang code. * Updated packages to account for the existence of apple-clang Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Added unit test for XCode related functions Co-authored-by: Gregory Becker <becker33@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-25hdf: new version, variants and refactoring (#16469)Sergey Kosukhin1-0/+1
* hdf: new version, variants and refactoring. * libc provides rpc * Fix szip-related configure argument. * Update dependent packages.
2020-05-25Fix typo for allow_sgid (#16806)Michael Kuhn1-1/+1
fixes #14425 The config: prefix should be included in the actual option name and makes it impossible to change this option.
2020-05-07Config option to disable setting S_ISGID bit when creating installation ↵iarspider1-0/+4
directory (#14479) * Add config option to disable setting S_ISGID bit when creating installation directory. Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-04-16darwin: cut DYLD_LIBRARY_PATH from default modulesGeoffrey Malcolm Oxberry1-2/+0
This commit removes the DYLD_LIBRARY_PATH variable from the default modules.yaml for darwin. The rationale behind deleting this environment variable is that paths in this environment variable take precedence over the default locations of libraries (usually the install path of the library), which can lead to linking errors in some circumstances. For example, executables intended to link with Apple's system BLAS and LAPACK will instead link to a spack-installed implementation (e.g., OpenBLAS), causing runtime errors. These errors are resolved by instead relying on paths set in DYLD_FALLBACK_LIBRARY_PATH, which is lower in precedence than default locations of libraries.
2020-03-28Hack to select iconv implementation - libiconv vs. libc iconv (#15437)iarspider1-0/+1
(re-do of #15213 due to changes in gnupg recipe)
2020-03-20multiprocessing: allow Spack to run uninterrupted in background (#14682)Greg Becker1-0/+1
Spack currently cannot run as a background process uninterrupted because some of the logging functions used in the install method (especially to create the dynamic verbosity toggle with the v key) cause the OS to issue a SIGTTOU to Spack when it's backgrounded. This PR puts the necessary gatekeeping in place so that Spack doesn't do anything that will cause a signal to stop the process when operating as a background process.
2020-03-17Module files won't use CPATH by default, but language specific vars (#14749)Massimiliano Culpo1-1/+5
fixes #11555 Every path in CPATH is equivalent to a -I path to the compiler, while every path in *_INCLUDE_PATH is equivalent to -isystem. The latter avoids the noise due to warnings coming from 3rd party libraries that a project depends on. Added INCLUDE env variable (Intel Fortran, .mod files)
2020-02-27config: Add a new option connect_timeoutMichael Kuhn1-0/+6
connect_timeout can be used to increase the time Spack waits for the server to answer. This can be used to work around slow connections or servers. Fixes #14700
2020-02-19Distributed builds (#13100)Tamara Dahlgren1-1/+1
Fixes #9394 Closes #13217. ## Background Spack provides the ability to enable/disable parallel builds through two options: package `parallel` and configuration `build_jobs`. This PR changes the algorithm to allow multiple, simultaneous processes to coordinate the installation of the same spec (and specs with overlapping dependencies.). The `parallel` (boolean) property sets the default for its package though the value can be overridden in the `install` method. Spack's current parallel builds are limited to build tools supporting `jobs` arguments (e.g., `Makefiles`). The number of jobs actually used is calculated as`min(config:build_jobs, # cores, 16)`, which can be overridden in the package or on the command line (i.e., `spack install -j <# jobs>`). This PR adds support for distributed (single- and multi-node) parallel builds. The goals of this work include improving the efficiency of installing packages with many dependencies and reducing the repetition associated with concurrent installations of (dependency) packages. ## Approach ### File System Locks Coordination between concurrent installs of overlapping packages to a Spack instance is accomplished through bottom-up dependency DAG processing and file system locks. The runs can be a combination of interactive and batch processes affecting the same file system. Exclusive prefix locks are required to install a package while shared prefix locks are required to check if the package is installed. Failures are communicated through a separate exclusive prefix failure lock, for concurrent processes, combined with a persistent store, for separate, related build processes. The resulting file contains the failing spec to facilitate manual debugging. ### Priority Queue Management of dependency builds changed from reliance on recursion to use of a priority queue where the priority of a spec is based on the number of its remaining uninstalled dependencies. Using a queue required a change to dependency build exception handling with the most visible issue being that the `install` method *must* install something in the prefix. Consequently, packages can no longer get away with an install method consisting of `pass`, for example. ## Caveats - This still only parallelizes a single-rooted build. Multi-rooted installs (e.g., for environments) are TBD in a future PR. Tasks: - [x] Adjust package lock timeout to correspond to value used in the demo - [x] Adjust database lock timeout to reduce contention on startup of concurrent `spack install <spec>` calls - [x] Replace (test) package's `install: pass` methods with file creation since post-install `sanity_check_prefix` will otherwise error out with `Install failed .. Nothing was installed!` - [x] Resolve remaining existing test failures - [x] Respond to alalazo's initial feedback - [x] Remove `bin/demo-locks.py` - [x] Add new tests to address new coverage issues - [x] Replace built-in package's `def install(..): pass` to "install" something (i.e., only `apple-libunwind`) - [x] Increase code coverage
2020-02-13hipsycl: new package and new 'sycl' virtual package (#14051)Federico Ficarelli1-0/+1
2019-11-14Config option to allow gpg warning suppression (#13743)Greg Becker1-0/+8
Add a configuration option to suppress gpg warnings during binary package verification. This only suppresses warnings: a gpg failure will still fail the install. This allows users who have already explicitly trusted the gpg key they are using to avoid seeing repeated warnings that it is self-signed.
2019-10-23Users can configure use of RPATH or RUNPATH (#9168)Massimiliano Culpo1-0/+5
Add a new entry in `config.yaml`: config: shared_linking: 'rpath' If this variable is set to `rpath` (the default) Spack will set RPATH in ELF binaries. If set to `runpath` it will set RUNPATH. Details: * Spack cc wrapper explicitly adds `--disable-new-dtags` when linking * cc wrapper also strips `--enable-new-dtags` from the compile line when disabling (and vice versa) * We specifically do *not* add any dtags flags on macOS, which uses Mach-O binaries, not ELF, so there's no RUNPATH)
2019-10-05Consistently support pkg-config files in share subdirectory (#12838)Michael Kuhn1-0/+2
While the build environment already takes share/pkgconfig into account, the generated module files etc. only consider lib/pkgconfig and lib64/pkgconfig.
2019-10-02Remove support for generating dotkit files (#11986)Massimiliano Culpo2-2/+0
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
2019-09-13Remove CombinatorialSpecSet in favor of environments + stacksScott Wittenburg1-16/+0
2019-09-03Use spack/user-specific stage root by default; stage cleaning (#12516)Tamara Dahlgren1-7/+12
* When cleaning the stage root, only remove directories that appear to be used for staging Spack packages. Previously Spack was clearing all directories in the stage root, which could remove content not related to Spack if the user chose a staging root which contains files/directories not managed by Spack. * The documentation is updated with warnings about choosing a stage directory that is only managed by Spack (although generally the check added in this PR for "spack clean" should avoid removing content that was not created by Spack) * The default stage directory (in config.yaml) is now $tempdir/$user/spack-stage and the logic is updated to omit the $user portion of this path if $tempdir already contains a $user directory. * When creating stage root assign user read/write permissions to all directories in the path under $user. Previously Spack was assigning the permissions of the first existing parent directory
2019-08-19features: Remove stage symlinks (#12072)Tamara Dahlgren1-8/+18
Fixes #11163 The goal of this work is to simplify stage directory structures by eliminating use of symbolic links. This means, among other things, that` $spack/var/spack/stage` will no longer be the core staging directory. Instead, the first accessible `config:build_stage` path will be used. Spack will no longer automatically append `spack-stage` (or the like) to configured build stage directories so the onus of distinguishing the directory from other work -- so the other work is not automatically removed with a `spack clean` operation -- falls on the user.
2019-07-25Make OpenJDK the default (#12106)Elizabeth Fischer1-1/+1
2019-07-01openfoam: rename openfoam-com to openfoam (#11876)Mark Olesen1-1/+0
The original packaging, with openfoam as a virtual and with openfoam-com, openfoam-org and openfoam-extend as providers, adds an obfuscation layer without any benefit. - Rename `openfoam-com` to `openfoam`, and remove the `openfoam` virtual package.
2019-06-10ninja{-fortran}: make pkgs nonvirtual (fix #11628) (#11629)Geoffrey Oxberry1-2/+0
2019-05-28Cap the maximum number of build jobs (#11373)Massimiliano Culpo1-4/+6
* config:build_jobs now controls the number of parallel jobs to spawn during builds, but cannot ever exceed the number of cores on the machine. * The default is set to 16 or the number of available cores, whatever is lowest. * Updated docs to reflect the changes done to limit parallel builds
2019-05-21Add Fujitsu compiler to Spack. (#11287)t-karatsu1-1/+1
* Add Fujitsu compiler to Spack. * Fixes for flake8 * Chenges location of FCC to subdirectory called case-insensitive * Add compiler tests for Fujitsu compiler * Modify the logic of taking compiler version for new version of Fujitsu compiler
2019-05-07ninja: drop python as a run dep (#11347)Chuck Atkins1-0/+2
* ninja: Make python a build-only dependency * ninja, ninja-fortran: allow the packages to provide eachother
2019-05-01mesa: re-written to new meson build system (#10482)Chuck Atkins1-1/+2
* mesa: re-writen to new meson build system * xorg-server: Remove unneeded mesa dependency * glx: provide the virtual GLX package * Convert most "mesa" dependencies to use virtual gl and glx dependencies * mesa: Switch to always building from the git repo instead of a tarball * Use gl and glx version ranges instead of exact versions * glx: provide a default package * add auto to swr variant * Revert "add auto to swr variant" This reverts commit 2e7cd8a8aca07767c00657d0d09985ddd6306883. * update mesa package to version 19.0 * set +glx by default only when running on linux * fix style issues in geant4 package * remove virtual package "egl"
2019-03-26mysql: Support client-only, cxxstd and more versions (#10911)Chris Green1-1/+1
* add cxxstd variant * add CMake constraints based on platform/version * add older versions * update boost dependency version constraints (which are closely tied to mysql version) and update boost cxxstd choice to be the same as the cxxstd chosen for mysql * add client-only support (including a patch for 5.5.x) * record the mysql package as a provider of the mysql-client virtual
2019-03-15New package: mariadb-c-client (#7729)Chris Green1-0/+2
* mariadb-c-client is a new package using the distinct, LGPL, MySQL-compatible client library from mariadb.com. It provides the virtual package mariadb-client * mariadb is recorded as a provider of the mariadb-client virtual * The mysql-client virtual package is also added, and mariadb-c-client is recorded as a provider for it
2019-03-12New package: ibm-java (#10777)Mark W. Krentel1-1/+1
* Add binary package of the IBM Java SDK for big and little-endian powerpc (power7, 8 and 9). The jdk and openjdk packages only install on x86_64. * Add ibm-java as a java provider * The jdk and openjdk packages only install on x86_64. Add conflicts for ppc64 and ppc64le to jdk and openjdk.
2019-03-07Create option to build compilers as needed (#10761)Greg Becker1-0/+6
* Create option to build missing compilers and add them to config before installing packages that use them * Clean up kwarg passing for do_install, put compiler bootstrapping in separate method
2019-02-21release workflow: Add spack command for generating the .gitlab-ci.ymlScott Wittenburg1-0/+16
This spack command adds a new schema for a file which describes the builder containers available, along with the compilers availabe on each builder. The release-jobs command then generates the .gitlab-ci.yml file by first expanding the release spec set, concretizing each spec (in an appropriate docker container if --this-machine-only argument is not provided on command line), and then combining and staging all the concrete specs as jobs to be run by gitlab.
2018-12-21Remove /nfs/tmp2 from default build_stage locations (#10170)Elsa Gonsiorowski, PhD1-1/+0
* Remove /nfs/tmp2 from default configuration * /nfs/tmp2 is going away from LC... and doesn’t exist for the rest of the world. * update documentation to remove /nfs/tmp2 as well
2018-11-11Minor changes to Basic Settings docs for SC18 (#9809)Adam J. Stewart1-4/+6
Grammar/spelling issues
2018-11-09Introduce fftw-api virtual package for Intel-MKL and FFTW (#9618)Nichols A. Romero1-0/+1
* Introduce FFTW2 and FFT3 providers for Intel-MKL and FFTW Spack packages. * make fftw default package for fftw-api virtual package * virtual package test assertion now provides location of default virtual packages. * Change name of virtual package to fftw-api and used versioned interface.
2018-10-18Allow setting language of compiler messages (#9486)Michael Kuhn1-0/+8
* Add a build_language config.yaml option which controls the language of compiler messages * build_language defaults to "C", in which case the compiler messages will be in English. This allows Spack log parsing to detect and highlight error messages (since the regular expressions to find error messages are in English) * The user can use the default language in their environment by setting the build_language config variable to null or ''
2018-10-11permissions: add permission configuration to packages.yaml (#8773)Greg Becker1-1/+3
Spack can now be configured to assign permissions to the files installed by a package. In the `packages.yaml` file under `permissions`, the attributes `read`, `write`, and `group` control the package permissions. These attributes can be set per-package, or for all packages under `all`. If permissions are set under `all` and for a specific package, the package-specific settings take precedence. The `read` and `write` attributes take one of `user`, `group`, and `world`. packages: all: permissions: write: group group: spack my_app: permissions: read: group group: my_team
2018-10-10Correct name for install_path_scheme in defaults config.yaml (#9482)Greg Becker1-1/+1
Default config.yaml mis-named `install_path_scheme` as `directory_layout`. This commit corrects the error.
2018-09-25Increase and customize lock timeouts (#9219)Peter Scheibel1-0/+13
Fixes #9166 This is intended to reduce errors related to lock timeouts by making the following changes: * Improves error reporting when acquiring a lock fails (addressing #9166) - there is no longer an attempt to release the lock if an acquire fails * By default locks taken on individual packages no longer have a timeout. This allows multiple spack instances to install overlapping dependency DAGs. For debugging purposes, a timeout can be added by setting 'package_lock_timeout' in config.yaml * Reduces the polling frequency when trying to acquire a lock, to reduce impact in the case where NFS is overtaxed. A simple adaptive strategy is implemented, which starts with a polling interval of .1 seconds and quickly increases to .5 seconds (originally it would poll up to 10^5 times per second). A test is added to check the polling interval generation logic. * The timeout for Spack's whole-database lock (e.g. for managing information about installed packages) is increased from 60s to 120s * Users can configure the whole-database lock timeout using the 'db_lock_timout' setting in config.yaml Generally, Spack locks (those created using spack.llnl.util.lock.Lock) now have no timeout by default This does not address implementations of NFS that do not support file locking, or detect cases where services that may be required (nfslock/statd) aren't running. Users may want to be able to more-aggressively release locks when they know they are the only one using their Spack instance, and they encounter lock errors after a crash (e.g. a remote terminal disconnect mentioned in #8915).
2018-08-23Set DYLD_LIBRARY_PATH on macOS (#9073)Adam J. Stewart3-2/+44
2018-08-06spack general packages.yaml defaults: add unwindGeoffrey Malcolm Oxberry1-0/+2
This commit adds 'libunwind' as the default 'unwind' provider in spack. This preference should be overridden by the darwin/packages.yaml file on macOS. Continues the changes discussed in
2018-08-06darwin packages.yaml defaults: add unwind providerGeoffrey Malcolm Oxberry1-0/+7
This commit adds default unwind providers to the default packages.yaml for darwin. Compiler versions are supplied with the apple-unwind package so that apple-unwind is only used with Apple's clang fork, and not with LLVM's clang.
2018-07-09Add ccache support (#3761)Christoph Junghans1-0/+4
If the user sets "ccache: true" in spack's config.yaml, Spack will use an available ccache executable when compiling c/c++ code. This feature is disabled by default (i.e. "ccache: false") and the documentation is updated with how to enable ccache support
2018-06-24refactor: move templates from root to share/spackTodd Gamblin1-1/+1
- This complies with the unix directory hierarchy standard (which Spack attempts to follow) - Also unclutters the repo root directory.
2018-05-18locks: add configuration and command-line options to enable/disable locks ↵Todd Gamblin1-0/+12
(#7692) - spack.util.lock behaves the same as llnl.util.lock, but Lock._lock and Lock._unlock do nothing. - can be disabled with a control variable. - configuration options can enable/disable locking: - `locks` option in spack configuration controls whether Spack will use filesystem locks or not. - `-l` and `-L` command-line options can force-disable or force-enable locking. - Spack will check for group- and world-writability before disabling locks, and it will not allow a group- or world-writable instance to have locks disabled. - update documentation
2018-05-05Change default elf provider on macOS (#7939)Adam J. Stewart1-0/+2