Commit graph

22787 commits

Author SHA1 Message Date
Alec Scott
ed3aa9633d
Add Picard v2.26.2 (#26125) 2021-09-22 04:04:44 -06:00
kjrstory
24ca007448
su2: add version 7.0.4-7.2.0 (#25956) 2021-09-22 01:07:44 -06:00
Alec Scott
86ddcd0e2d
Add Slepc v3.15.2 (#26123) 2021-09-21 23:13:51 -06:00
Edward Hartnett
5097a41675
gfsio: add NOAA software maintainers (#26106)
* added NOAA software maintainers to maintainer list

* added comment about NCEPLIBS
2021-09-21 19:20:47 -06:00
Harmen Stoppels
3b55c2e715 Bump version and update changelog 2021-09-21 16:58:41 -07:00
Harmen Stoppels
7caa844d49 Fix style tests 2021-09-21 16:58:41 -07:00
Harmen Stoppels
4cd6381ed5 Remove centos:6 image references
This was EOL November 30th, 2020. I believe the "builds" are failing on
develop because of it.
2021-09-21 16:58:41 -07:00
Massimiliano Culpo
aebc8f6ce5 docker: remove boto3 from CentOS 6 since it requires and updated pip (#24813) 2021-09-21 16:58:41 -07:00
Massimiliano Culpo
073c92d526 docker: Fix CentOS 6 build on Docker Hub (#24804)
This change make yum usable again on CentOS 6
2021-09-21 16:58:41 -07:00
Greg Becker
0e85d7011e Ensure all roots of an installed environment are marked explicit in db (#24277) 2021-09-21 16:58:41 -07:00
Todd Gamblin
77e633efa1 locks: only open lockfiles once instead of for every lock held (#24794)
This adds lockfile tracking to Spack's lock mechanism, so that we ensure that there
is only one open file descriptor per inode.

The `fcntl` locks that Spack uses are associated with an inode and a process.
This is convenient, because if a process exits, it releases its locks.
Unfortunately, this also means that if you close a file, *all* locks associated
with that file's inode are released, regardless of whether the process has any
other open file descriptors on it.

Because of this, we need to track open lock files so that we only close them when
a process no longer needs them.  We do this by tracking each lockfile by its
inode and process id.  This has several nice properties:

1. Tracking by pid ensures that, if we fork, we don't inadvertently track the parent
   process's lockfiles. `fcntl` locks are not inherited across forks, so we'll
   just track new lockfiles in the child.
2. Tracking by inode ensures that referencs are counted per inode, and that we don't
   inadvertently close a file whose inode still has open locks.
3. Tracking by both pid and inode ensures that we only open lockfiles the minimum
   number of times necessary for the locks we have.

Note: as mentioned elsewhere, these locks aren't thread safe -- they're designed to
work in Python and assume the GIL.

Tasks:
- [x] Introduce an `OpenFileTracker` class to track open file descriptors by inode.
- [x] Reference-count open file descriptors and only close them if they're no longer
      needed (this avoids inadvertently releasing locks that should not be released).
2021-09-21 16:58:41 -07:00
Todd Gamblin
2ae92ebdbb Use AWS CloudFront for source mirror (#23978)
Spack's source mirror was previously in a plain old S3 bucket. That will still
work, but we can do better. This switches to AWS's CloudFront CDN for hosting
the mirror.

CloudFront is 16x faster (or more) than the old bucket.

- [x] change mirror to https://mirror.spack.io
2021-09-21 16:58:41 -07:00
Harmen Stoppels
7f29dd238f Cray: fix extracting paths from module files (#23472)
Co-authored-by: Tiziano Müller <tm@dev-zero.ch>
2021-09-21 16:58:41 -07:00
Adam J. Stewart
0f486080b3 Fix use of quotes in Python build system (#22279) 2021-09-21 16:58:41 -07:00
Michael Kuhn
6b0c775448 clang/llvm: fix version detection (#19978)
This PR fixes two problems with clang/llvm's version detection. clang's
version output looks like this:

```
clang version 11.0.0
Target: x86_64-unknown-linux-gnu
```

This caused clang's version to be misdetected as:

```
clang@11.0.0
Target:
```

This resulted in errors when trying to actually use it as a compiler.

When using `spack external find`, we couldn't determine the compiler
version, resulting in errors like this:

```
==> Warning: "llvm@11.0.0+clang+lld+lldb" has been detected on the system but will not be added to packages.yaml [reason=c compiler not found for llvm@11.0.0+clang+lld+lldb]
```

Changing the regex to only match until the end of the line fixes these
problems.

Fixes: #19473
2021-09-21 16:58:41 -07:00
Adam J. Stewart
9120856c01 Fix fetching for Python 3.9.6 (#24686)
When using Python 3.9.6, Spack is no longer able to fetch anything. Commands like `spack fetch` and `spack install` all break.

Python 3.9.6 includes a [new change](https://github.com/python/cpython/pull/25853/files#diff-b3712475a413ec972134c0260c8f1eb1deefb66184f740ef00c37b4487ef873eR462) that means that `scheme` must be a string, it cannot be None. The solution is to use an empty string like the method default.

Fixes #24644. Also see https://github.com/Homebrew/homebrew-core/pull/80175 where this issue was discovered by CI. Thanks @branchvincent for reporting such a serious issue before any actual users encountered it!

Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2021-09-21 16:58:41 -07:00
Edward Hartnett
90d953d3f6
w3emc: add NOAA software maintainers (#26110) 2021-09-21 17:54:19 -06:00
Tiziano Müller
d34b2638c7
boost: fix for @1.77.0%intel (#25965)
Add patch for build script from boost repo.
2021-09-21 16:07:25 -07:00
bernhardkaindl
979c355c99
spack/build_environment.py: Clean MAKEFLAGS, DISPLAY and TERM (#26092)
clean_environment(): Unset three more environment variables:

MAKEFLAGS: Affects make, can eg indirectly inhibit enabling parallel build
DISPLAY: Tests of GUI widget libraries might try to connect to an X server
TERM: Could make testsuites attempt to color their output
2021-09-22 00:23:10 +02:00
Edward Hartnett
92f199d57b
added NOAA software maintainers to the maintainers list (#26102) 2021-09-21 16:16:49 -06:00
Edward Hartnett
fd716ce0c5
sfcio: add NOAA software maintainers (#26108)
* added NOAA software maintainers to maintainer list

* added comment about NCEPLIBS project
2021-09-21 15:28:37 -06:00
Edward Hartnett
d865caa7f7
ip2: add NOAA software maintainers and deprecation note (#26107)
* added NOAA software maintainers to maintainer list, added comment about library being deprecated

* deleted trailing whitespace
2021-09-21 14:49:13 -06:00
bernhardkaindl
981551b47f
libtool: fix running the unit-tests with spack install --test root (#25707)
Besides adding autoconf and automake as needed for tests of 2.4.6,
skip Fortran test cases when Fortran compilers are not provided.
2021-09-21 14:18:29 -06:00
Tamara Dahlgren
c3cb863b82
Feature: Add deprecated versions section to spack info output (#25972) 2021-09-21 11:49:36 -07:00
AMD Toolchain Support
8de77bb304
Fix for - Installation issue: amdlibflame #25878 (#25987)
* Fix for - Installation issue: amdlibflame #25878

* Updated with python+pythoncmd - Symlink 'python3' executable to 'python'
2021-09-21 11:15:23 -07:00
Edward Hartnett
a8977f828e
w3nco: add NOAA software maintainers (#26111) 2021-09-21 12:08:43 -06:00
Jonas Thies
6c487f4c6d
packages/phist new version 1.9.5 (#26114) 2021-09-21 11:57:22 -06:00
Edward Hartnett
24500d4115
added noaa software maintainers to maintainer list (#26103) 2021-09-21 09:58:53 -07:00
iarspider
2741037c69
Fix FORM recipe (#26104) 2021-09-21 09:57:40 -07:00
Edward Hartnett
d278837316
sigio: add NOAA software maintainers (#26109) 2021-09-21 10:39:05 -06:00
bernhardkaindl
22cfc19bcb
ddd,debuild,flux-sched: add missing dependencies (#26090) 2021-09-21 18:08:11 +02:00
Melven Roehrig-Zoellner
c24413a530
petsc: fix for enabling openmp (#25942)
* petsc: fix for enabling openmp

* petsc: shorten comment (style guidelines)

* petsc: move flag to make code more clear
2021-09-21 07:13:35 -06:00
natshineman
544b3f447d
mvapich2-gdr: add v2.3.6 (#26076)
Co-authored-by: Nick Contini <contini.26@buckeyemail.osu.edu>
2021-09-21 06:19:56 -06:00
Gregory Lee
05ca19d9d7
fgfs: fix missing autotools depends_on (#26005)
* added build deps for fgfs

* added build deps when building master branch
2021-09-21 07:40:59 -04:00
Harmen Stoppels
a326713826
py-abcpy: new package (#25713) 2021-09-21 13:10:16 +02:00
bernhardkaindl
1b95c97bb3
ccfits: add v2.6 (#26089)
ccfits@2.5 doesn't compile on Ubuntu 18.04: Update to version 2.6.
2021-09-21 04:43:48 -06:00
bernhardkaindl
c6a33c28de
Fix deps of diffmark,faiss,fgsl,fipcheck,nbdkit,ncbi-magicblast,xcb-util-cursor (#26091)
Fix missing type='build' deps for cpio, m4, pkg-config and python in
diffmark, faiss, fgsl, fipcheck, nbdkit, ncbi-magicblast and xcb-util-cursor
2021-09-21 04:16:43 -06:00
Harmen Stoppels
58663692a4
Rename 'variant_name' to 'variant' and document it in autotools build system (#26064) 2021-09-21 11:27:41 +02:00
Christoph Junghans
45ba4d94bd
votca-* packages: add version 2021.2 (#26058) 2021-09-20 16:14:19 -07:00
Adam J. Stewart
3e3b7b1394
New package: py-torchgeo (#26059) 2021-09-20 16:12:55 -07:00
Jordan Ogas
d0fd9e6d5f
charliecloud package: add version 0.25 (#26073) 2021-09-20 16:08:41 -07:00
adityakavalur
88880c5369
Include newer versions of UCX (#26072) 2021-09-20 23:41:26 +02:00
Danny McClanahan
aa7e354a3a
patch serf and scons to use #!/usr/bin/env python3 (#26062) 2021-09-20 22:12:30 +02:00
iarspider
f3d2f62468
Add variants to FORM recipe (#25963) 2021-09-20 13:53:54 -06:00
Edward Hartnett
65f285831e
added NOAA maintainers to ip package (#26055) 2021-09-20 11:36:03 -06:00
Olivier Cessenat
0197b364a2
mfem and petsc: alter hypre dependencies (#25902)
Hypre latest version 2.22.1 breaks MFEM and PETSc.
2021-09-20 09:51:29 -07:00
Edward Hartnett
96eefea9a3
added NOAA software team to maintainers list (#26056) 2021-09-20 09:01:53 -06:00
Olivier Cessenat
1ea58e0cb9
p7zip: resolve gcc 10 conflict (#25676)
Fix credit: Eric Brugger
2021-09-20 07:43:07 -04:00
Tamara Dahlgren
c6f9e9baf6
strumpack: Update stand-alone test to use stage directory (#25751) 2021-09-20 07:36:58 -04:00
kjrstory
430caaf5f6
paraview: patch for version 5.9.1 with gcc 11.1.0 (#25887)
* paraview: patch for version 5.9.1 with gcc 11.1.0

* Fix : blank line contains whitespace
2021-09-20 07:31:54 -04:00