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2020-06-05cajita: got merged in cabana (#16971)Christoph Junghans2-30/+0
2020-06-05cmake: add linker option for VerifyFortranC when using Fujitsu compiler. ↵Tomoki, Karatsu2-0/+14
(#16963)
2020-06-05cmake: modify FindMPI.cmake to treat Fujitsu MPI correctly (#16864)Tomoki, Karatsu2-9/+6
2020-06-05suite-sparse: change the condition to add C11 flag. (#16859)Tomoki, Karatsu1-1/+1
2020-06-05spack dev-build: Do not mark -u builds in database (#16333)Greg Becker4-21/+61
Builds can be stopped before the final install phase due to user requests. Those builds should not be registered as installed in the database. We had code intended to handle this but: 1. It caught the wrong type of exception 2. We were catching these exceptions to suppress them at a lower level in the stack This PR allows the StopIteration to propagate through a ChildError, and catches it properly. Also added to an existing test to prevent regression.
2020-06-05commands: use a single ThreadPool for `spack versions` (#16749)Massimiliano Culpo5-252/+229
This fixes a fork bomb in `spack versions`. Recursive generation of pools to scrape URLs in `_spider` was creating large numbers of processes. Instead of recursively creating process pools, we now use a single `ThreadPool` with a concurrency limit. More on the issue: having ~10 users running at the same time spack versions on front-end nodes caused kernel lockup due to the high number of sockets opened (sys-admin reports ~210k distributed over 3 nodes). Users were internal, so they had ulimit -n set to ~70k. The forking behavior could be observed by just running: $ spack versions boost and checking the number of processes spawned. Number of processes per se was not the issue, but each one of them opens a socket which can stress `iptables`. In the original issue the kernel watchdog was reporting: Message from syslogd@login03 at May 19 12:01:30 ... kernel:Watchdog CPU:110 Hard LOCKUP Message from syslogd@login03 at May 19 12:01:31 ... kernel:watchdog: BUG: soft lockup - CPU#110 stuck for 23s! [python3:2756] Message from syslogd@login03 at May 19 12:01:31 ... kernel:watchdog: BUG: soft lockup - CPU#94 stuck for 22s! [iptables:5603]
2020-06-04add erlang version 23.0 (#16961)eugeneswalker1-0/+1
2020-06-04Rust v1.44.0 (#16957)Andrew Gaspar1-10/+17
* libgit2 v1.0.1 * Rust 1.44.0 * Fix flake8
2020-06-04libgit2 v1.0.1 (#16952)Andrew Gaspar1-0/+1
2020-06-04sz: patch in ctag optionality from robertu94/sz 3637a87f986c (#16953)eugeneswalker2-0/+44
2020-06-04pass hwloc to configure via useropt; use lib/ or lib64/ as appropriate for ↵eugeneswalker2-0/+37
libunwind (#16941)
2020-06-04Fix obsolete references to wx package (#16944)Adam J. Stewart2-2/+2
2020-06-04NumPy: add 1.18.5 (#16943)Adam J. Stewart1-1/+2
2020-06-03Add matplotlib 3.1.0 (#16921)iarspider1-0/+1
2020-06-03Add py-jupyter-core@4.6.1 (#16922)iarspider1-0/+1
2020-06-03Trilinos: add Stratimikos package (#16925)Seth R. Johnson1-0/+9
Stratimikos is an optional dependency for our project. It depends on Thyra, and thyra has subpackages that should be enabled based on tpetra/epetra/epetraext.
2020-06-03+ Add opppy-0_1_3 (#16926)Mathew Cleveland1-2/+4
+ Update maintainers for OPPPY package + remove "run" requirement for setuptools and sphynx Co-authored-by: Cleveland <cleveland@lanl.gov>
2020-06-03Add pytest@5.3.4 (#16927)iarspider1-1/+2
Dropping atomicwrites dependency: https://github.com/pytest-dev/pytest/issues/6147
2020-06-03mpfr: update hash for 4.0.2 patch (#16937)Seth R. Johnson1-1/+1
2020-06-03py-openpyxl: add 3.0.3 (#16940)Adam J. Stewart1-2/+6
2020-06-03IPython: fix setuptools dependency (#16915)Adam J. Stewart1-2/+4
* IPython: fix setuptools dependency * Remove extra colon
2020-06-03Fix parsing of EvtGen URL (#16883)Adam J. Stewart2-9/+11
* Fix parsing of EvtGen URL * Flake8 fix
2020-06-03Ignore __pycache__ directory (#16836)Adam J. Stewart1-1/+2
2020-06-03Gnuplot fix 16928 (#16929)Tom Payerle1-1/+1
* gnuplot: Fix for #16928 Dependency for --with-wx flag mistyped (should be wxwidgets) * Revert "gnuplot: Fix for #16928" This reverts commit 2b85814e5ccf5c9b2c70c7959994e89c18fdc3d8. * gnuplot: Fix for #16928 Dependency spec for --with-wx flag mistyped (should be wxwidgets, not wx)
2020-06-03update darshan-runtime & darshan-util versions (#16934)shanedsnyder2-0/+4
* update darshan-runtime & darshan-util versions includes up through the current release, 3.2.1 * remove pre-releases, not needed in spack
2020-06-03Mirrors: add option to exclude packages from "mirror create" (#14154)Peter Scheibel4-24/+99
* add an --exclude-file option to 'spack mirror create' which allows a user to specify a file of specs to exclude when creating a mirror. this is anticipated to be useful especially when using the '--all' option * allow specifying number of versions when mirroring all packages * when mirroring all specs within an environment, include dependencies of root specs * add '--exclude-specs' option to allow user to specify that specs should be excluded on the command line * add test for excluding specs
2020-06-03patch lambda capture issue for @1.1906.1, fixed in upstream faodel@master ↵eugeneswalker2-0/+27
(#16935)
2020-06-03Feature: add option to create view by copying/relocating files (#16480)Greg Becker6-17/+108
* add subcommand `spack view copy/relocate` * update bash completions * add copy/relocate commands to view tests * allow copied views to be removed
2020-06-03Implicit rpaths for NAG/GCC mixed toolchain (#14782)Sergey Kosukhin6-38/+139
* Implicit rpaths for NAG. * set up environment when checking for implicit rpaths
2020-06-03spack uninstall: improve help message (#16886)Massimiliano Culpo1-7/+15
fixes #12527 Mention that specs can be uninstalled by hash also in the help message. Reference `spack gc` in case people are looking for ways to clean the store from build time dependencies. Use "spec" instead of "package" to avoid ambiguity in the error message.
2020-06-03amber: updated dependency constraint on cuda (#16919)dmorone1-1/+1
Fix message 'amber requires cuda version :10.1.243, but spec asked for 10.2.89'
2020-06-03openssh: added v8.3p1 and v8.1p1 (#16917)Amjad Kotobi1-0/+2
2020-06-03git: added v2.27.0 (#16918)Amjad Kotobi1-1/+5
2020-06-02mummer4: new package at 4.0.0-beta2 (#16907)Justin S1-0/+21
2020-06-02Add new package: sbml (#16898)Robert Blake1-0/+122
* Adding a module for sbml. * Adding support for all the languages. * Update var/spack/repos/builtin/packages/sbml/package.py Co-authored-by: Greg Becker <becker33@llnl.gov> * Update var/spack/repos/builtin/packages/sbml/package.py Co-authored-by: Greg Becker <becker33@llnl.gov> Co-authored-by: Robert Blake <rob.c.blake.3@gmail.com> Co-authored-by: Greg Becker <becker33@llnl.gov>
2020-06-02Ruby: add warning about Avira antivirus (#16882)Adam J. Stewart1-0/+4
2020-06-02Unify tests for compiler command in the same file (#16891)Massimiliano Culpo3-113/+105
* Unify tests for compiler command in the same file Tests for the "spack compiler" command were previously scattered among different files. * Tests should use mutable_config, since they modify the compiler list
2020-06-02alsa-lib: Add new version and python dependency. (#16905)Toyohisa Kameyama2-1/+44
Add version 1.2.2. Add conditional python dependency. Add patch for 1.1.4.1 and python.
2020-06-02gmap-gsnap: add 2020-06-01 (#16906)Justin S1-0/+1
2020-06-02Bump ADIOS to 2.6.0 (#16908)Chuck Atkins1-1/+2
2020-06-02Add ipython 7.5.0 (#16801)iarspider1-3/+8
* Add ipython 7.5.0 * Update dependencies * Update package.py
2020-06-02ruby: fixed build with Fujitsu compilers (#16889)takanori-ihara1-0/+2
2020-06-02environment-modules: added v4.5.1 (#16896)Xavier Delaruelle1-1/+2
2020-06-02Fix satisfaction checks for excluding variants from matrices (#16893)Greg Becker8-50/+80
Because of the way abstract variants are implemented, the following spec matrix does not work as intended: ``` matrix: - [foo] - [bar=a, bar=b] exclude: - bar=a ``` because abstract variants always satisfy any variant of the same name, regardless of values. This PR converts abstract variants to whatever their appropriate type is before running satisfaction checks for the excludes clause in a matrix. fixes #16841
2020-06-02py-grpcio: fixed build with Fujitsu compilers (#16900)takanori-ihara1-0/+4
2020-06-02ccache: added v3.7.9 (#16902)Axel Huebl1-1/+2
Add the latest CCache release. Fixes issues with `-x cu` that are not present in the last checksummed release. This fixes workflows with CMake.
2020-06-02qt: add conflict for old gcc (#16904)Sinan1-0/+4
Co-authored-by: Sinan81 <Sinan81@github>
2020-06-02go: added v1.14.4 and v1.13.12 (#16903)Michael Kuhn1-0/+2
2020-06-01openmpi: add opa-psm2 dependency (#16873)Jonathon Anderson2-1/+124
Also document with_or_without and enable_or_disable, (which are used to configure the opa-psm2 dependency).
2020-06-01r-exactextractr: package type fixed (#16881)Amjad Kotobi1-3/+3
* r-exactextractr: should inherit from RPackage * r-exactextractr: fixed URL
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