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2020-06-09Testing: create mock executable fixture (#16999)Massimiliano Culpo2-9/+19
2020-06-09SpecList: fix recursion for references (#16897)Greg Becker2-29/+59
* SpecList: fix and refactor variable expansion
2020-06-09[util-linux] disabling systemd (#17008)Jen Herting1-0/+1
If systemd support is enabled, install will attempt to modify files in system systemd directories.
2020-06-09Set the BOOST_ROOT environment variable when library is loaded (#16818)Nathan1-0/+3
* Adding BOOST_ROOT env variable * Update var/spack/repos/builtin/packages/boost/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-09suite-sparse: build libraries without running demos (#17007)Massimiliano Culpo1-1/+1
fixes #16638
2020-06-08Update miniconda3@4.8.2 (#17003)oracleLee1-0/+1
* Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py
2020-06-08Cray: fix Blue Waters support and user-built MPIs on Cray (#16593)Adam J. Stewart4-17/+31
* Cray: fix Blue Waters support * pkg-config env vars needed on Blue Waters * cray platform: fix support for user-build MPI on cray machines * reintroduce cray environment cleaning behind cnl version guard * cray platform: fix support for user-build MPI on cray machines Co-authored-by: Gregory <becker33@llnl.gov>
2020-06-08HELICS: add version 2.5.1 (#17014)Ryan Mast1-0/+1
2020-06-08rt-tests: fix build error (#16998)darmac1-2/+4
This is a makefile package and needs to invoke make.
2020-06-08Add new package: py-devlib (#16982)darmac1-0/+34
* Add new package: py-devlib * Update var/spack/repos/builtin/packages/py-devlib/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * add depends Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-08Add Package HSF-CMakeTools (#16951)vvolkl1-0/+26
* [hsf-cmaketools] add package * fix formatting * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * [hsf-cmaketools] remove cmake_prefix_path which is set already by spack Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-08R: url-version custom, release 4 (#16962)Amjad Kotobi1-1/+9
* R: url-version custom, release 4 * r: pcre condition
2020-06-08Add py-storm@0.23 and update URL (#16991)iarspider1-2/+6
* Add py-storm@0.23 and update URL * Update package.py
2020-06-08ltr-retriever: new package at v2.8.7 (#16832)Justin S1-0/+45
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-08view remove: directly check whether specs own files before removing from ↵Greg Becker3-5/+72
view (#16955) Bugfix for hardlinks and copies
2020-06-08hpcviewer, ibm-java: updates versions (#16987)Mark W. Krentel2-0/+8
hpcviewer: added v2020.05. ibm-java: added v8.0.6.10.
2020-06-08py-ipykernel: added v5.1.1 (#16988)iarspider1-0/+1
2020-06-07boost: Don't use pre-compiled headers for Fujitsu compiler (#16914)Toyohisa Kameyama1-1/+1
* boost: Dopn't use pre compile header. * move %fj.
2020-06-07rose: Add build dependencies for flex and bison (#16981)John Jolly1-0/+2
2020-06-07py-gast: add version 0.3.3 (#16945)Sinan1-0/+2
* py-gast: add version 0.3.3 * add python version constraints Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-06-06Add rpy2@3.0.4 (#16924)iarspider1-5/+12
* Add rpy2@3.0.4 * Style fixes * Update package.py * Proper Python version requirement
2020-06-06ffr: fix mpi programs to use mpi compiler wrapper. (#16948)Toyohisa Kameyama1-3/+12
2020-06-06[prmon] add package (#16949)vvolkl1-0/+27
2020-06-06mongo-c-driver: Add 1.16.2 (#16956)Michael Kuhn2-10/+116
This also updates libbson to the corresponding version and adds a few missing older versions.
2020-06-06added CTRE package (#16964)Matthieu Dorier1-0/+25
2020-06-06gcc: Fix error 'size of array is negative' (#16969)John Jolly4-3/+183
gcc 9.3.0 and glibc 2.31 (found in the base install of Ubuntu 20.04) cause the gcc package to error during build with the error: "size of array 'assertion_failed__####' is negative" Previous to this fix, the error was resolved for v8.1.0 <= gcc <= v9.2.0 via two patches. This fix backports those patches for v5.3.0 <= gcc <= v7.4.0 Potentially these patches need to be backported to versions of gcc before v5.3.0, but other compile issues need to be resolved for earlier versions of gcc first. Fixes #16968
2020-06-06intel-tbb: Fix for #16938 add custom libs method (#16972)Tom Payerle1-6/+12
* intel-tbb: Fix for #16938 add custom libs method Override the libs method to look for libraries of form libtbb* (instead of inherited which looks for libintel-tbb*) * Fixing pre-existing flake8 issues
2020-06-06Add new package: py-louie (#16983)darmac1-0/+21
2020-06-06Add new package: lxc (#16984)darmac1-0/+33
2020-06-06py-mysqlclient: relax dependency constraint, add new versions (#16985)Sinan1-4/+5
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-06-06ensure xla is turned off (#16974)Sinan1-0/+7
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-06-06py-astunparse: add version 1.6.3 (#16946)Sinan1-0/+1
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-06-06protobuf: support aarch64 @2.5.0 (#16862)darmac2-3/+149
* protobuf: support aarch64 @2.5.0 * refine cmake args * fix patch name
2020-06-06Update package for MVAPICH2 2.3.4 release (#16960)Nithin Senthil Kumar1-1/+2
Co-authored-by: senthilkumar.16 <senthilkumar.16@nowlab.cse.ohio-state.edu>
2020-06-06iegenlib: add build dependencies for automake and libtool (#16980)John Jolly1-2/+4
2020-06-05py-flake8: add version 2.8.2 (#16959)Andrew Gaspar3-6/+14
* py-flake8: add version 3.8.2 * This version depends on different versions of py-pycodestyle and py-pyflakes * When built for python@:3.7, this depends on the py-importlib-metadata backport library * py-pycodestyle: add version 2.6.0 * py-pyflakes: add version 2.2.0
2020-06-05xrootd: add version 4.12.1 (#16966)Amjad Kotobi1-0/+1
2020-06-05New package: py-asteval (#16976)Sinan1-0/+19
2020-06-05pkgconf: Add 1.7.3Michael Kuhn1-0/+1
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)
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