Commit graph

650 commits

Author SHA1 Message Date
wiz
a688924e6f ganglia-monitor-core: add buildlink3.mk
From Edgar Fuß in PR 55479.

Some pkglint cleanup while here.
2020-07-13 18:40:47 +00:00
nia
f55345b7ef parallel: Add lua-lanes
Lua Lanes is a Lua extension library providing the possibility to run multiple
Lua states in parallel. It is intended to be used for optimizing performance
on multicore CPUs and to study ways to make Lua programs naturally parallel
to begin with.
2020-07-11 16:15:08 +00:00
otis
b48e8031ed paexec: Pull in libmaa
Fix build on platforms without system-wide libmaa, like SmartOS.
2020-06-16 10:38:40 +00:00
adam
6bd0c30da6 Revbump for icu 2020-06-02 08:22:31 +00:00
cheusov
6c6859bf3b Update to version 1.1.4
Remove local function pr_open and use it from libmaa library.
  So, now paexec requires libmaa.

  "mkcmake help" shows configuring variables and descriptions for
  targets.

  Use mkc's feature "getdelim" instead of local implementation.
  So, we need at least mk-configure 0.33.0

  Optimization flags defaults to "-O2 -g"
2020-06-01 16:18:16 +00:00
wiz
188111f641 *: reset MAINTAINER for fhajny on his request 2020-05-27 19:37:36 +00:00
adam
d62c903eea revbump after updating security/nettle 2020-05-22 10:55:42 +00:00
nia
f583de88fa parallel: Update to 20200422
20200422

This release celebrates GNU Parallel's 10 years as a GNU tool:

> commit ed2dfb1043768154d4e7678e01e10287155fa834
> Author: Ole Tange <ole@tange.dk>
> Date:   Thu Apr 22 01:23:00 2010 +0200
>
>    Name change: Parallel is now GNU Parallel.
>    Basic structure for sshlogin and sshloginfile.

New in this release:

* parsort makes GNU sort run faster for files with more than 1M lines.

* Bug fixes and man page updates.

News about GNU Parallel:

* Several clusters have updated their documentation of GNU Parallel:
  https://www.grid5000.fr/w/GNU_Parallel
  https://research-it.berkeley.edu/virtual-training-running-jobs-parallel-savio
  http://www.hpc.lsu.edu/training/archive/tutorials.php

* add_pho uses GNU Parallel: https://github.com/SeedlingsBabylab/add_pho

* GNU parallel使用笔记https://zhuanlan.zhihu.com/p/37340011

* Virtual Workshop: Running Jobs in Parallel on Savio
  https://ais.berkeley.edu/events/virtual-workshop-running-jobs-parallel-savio/2020-04-20

* Free Concurrency with GNU Parallel
  https://phili.pe/posts/free-concurrency-with-gnu-parallel/


20200322

* Bug fixes and man page updates.

News about GNU Parallel:

* The GNU Parallel course in Copenhagen is cancelled
  https://www.prosa.dk/nc/arrangementer/arrangement/gnu-parallel-med-ole-tange/

* The GNU Parallel course in Århus is cancelled
  https://www.prosa.dk/nc/arrangementer/arrangement/gnu-parallel-og-parallelisering-i-unix-shellen/

* The 10 year anniversary may be cancelled, see
  https://www.gnu.org/software/parallel/10-years-anniversary.html

* Running shell commands in parallel, via GNU Parallel
  https://dev.to/saveriomiroddi/running-shell-commands-in-parallel-via-gnu-parallel-3a72

* Faster nmap scanning with the help of GNU parallel
  https://badshah.io/experiment/faster-nmap-scanning-with-the-help-of-gnu-parallel/


20200222

* Bug fixes and man page updates.


20200122

* --blocktimeout dur - Time out for reading block when using
  --pipe. If it takes longer than dur to read a full block, use the
  partial block read so far.

* Bug fixes and man page updates.

News about GNU Parallel:

* GNU Parallel course in Copenhagen
  https://www.prosa.dk/nc/arrangementer/arrangement/gnu-parallel-med-ole-tange/

* GNU Parallel course in Århus
  https://www.prosa.dk/nc/arrangementer/arrangement/gnu-parallel-og-parallelisering-i-unix-shellen/

* GNU Parallel pour accélérer vos process sous Linux
  https://www.yvonh.com/gnu-parallel-pour-accelerer-vos-process-sous-linux/

* How to copy a file to multiple directories in Linux
  https://net2.com/how-to-copy-a-file-to-multiple-directories-in-linux/

* Running linux commands in parallel https://dev.to/voyeg3r/runing-linux-commands-in-parallel-4ff8


20191222

* GNU Parallel course in Copenhagen
  https://www.prosa.dk/nc/arrangementer/arrangement/gnu-parallel-med-ole-tange/

* GNU Parallel course in Århus
  https://www.prosa.dk/nc/arrangementer/arrangement/gnu-parallel-og-parallelisering-i-unix-shellen/

* GNU Parallel is used in
  https://github.com/JeffersonLab/rfw_tsf_extractor

* Bug fixes and man page updates.


20191122

* GNU Parallel was presented at Driving IT. Slides:
  cloud.prosa.dk/s/drivingit

* Restarting supervisord processes in parallel
  https://blog.naderman.de/2019/11/14/restarting-supervisord-processes-in-parallel/

* Using GNU Parallel to Create Archives Faster
  https://www.reddit.com/r/DataHoarder/comments/dsgmhc/parallel_archiving_techniques/

* Bug fixes and man page updates.


20191022

* --tee will use --output-error=warn-nopipe if supported by tee.

* GNU Parallel will be presented at Driving IT 2019:
  https://ida.dk/arrangementer-og-kurser/konferencer/driving-it/tools

* UMN Duluth: Job parallelization with task arrays and GNU parallel
  https://www.msi.umn.edu/tutorials/umn-duluth-job-parallelization-task-arrays-and-gnu-parallel

* Genome updater uses GNU Parallel
  https://github.com/pirovc/genome_updater

* Using GNU-Parallel for bioinformatics
  https://www.danielecook.com/using-gnu-parallel-for-bioinformatics/

* Speeding up PostgreSQL ETL pipeline with the help of GODS
  https://cfengine.com/company/blog-detail/speeding-up-postgresql-etl-pipeline-with-the-help-of-gods/

* Runing linux commands in parallel
  https://dev.to/voyeg3r/runing-linux-commands-in-parallel-4ff8

* Research Computing University of Colorado Boulder contains an intro
  to GNU Parallel
  https://readthedocs.org/projects/curc/downloads/pdf/latest/

* 如何使用Parallel在Shell中并行执行命令
  https://www.myfreax.com/gnu-parallel/

* 如何测试 Amazon Elastic File System
  https://aws.amazon.com/cn/blogs/china/how-to-test-drive-amazon-elastic-file-system/

* Bug fixes and man page updates.


20190922

* --nice is now inherited by the nice level that GNU Parallel is
  started at. So 'nice -n10 parallel' will also cause remote jobs to
  be run at nice level 10.

* --delay is now accurate to within 10 ms

* GNU Parallel will be presented at Driving IT 2019:
  https://ida.dk/arrangementer-og-kurser/konferencer/driving-it/tools

* Greenland Ice Sheet solid ice discharge from 1986 through 2017
  https://www.earth-syst-sci-data.net/11/769/2019/essd-11-769-2019.pdf

* App Center Cloud Build Machines > Installed Software > Utilities
  https://docs.microsoft.com/en-us/appcenter/build/software

* Curryfinger - SNI & Host header spoofing utility
  https://dualuse.io/blog/curryfinger/

* Hyak parallel-sql
  https://wiki.cac.washington.edu/display/hyakusers/Hyak+parallel-sql

* A meditation on analysing data with Perl in parallel using GNU Parallel
  https://www.reddit.com/r/perl/comments/cyo2qc/a_meditation_on_analysing_data_with_perl_in/

* Accélérer ses tâches avec GNU Parallel et les lots de tâches (UL)
  https://www.eventbrite.ca/e/inscription-accelerer-ses-taches-avec-gnu-parallel-et-les-lots-de-taches-ul-71412840729

* RMACC Summit GNU Parallel
  https://curc.readthedocs.io/en/latest/software/GNUParallel.html

* Introducing Parallel into Shell
  https://petelawson.com/post/parallel-in-shell/

* Linux Productivity Tools
  https://www.usenix.org/conference/lisa19/presentation/maheshwari

* Gnu/parallel + Nfs 实现共享文件网络的并发计算等操作
  http://atomicer.cn/2018/01/18/gnu-parallel-nfs-%E5%AE%9E%E7%8E%B0%E5%85%B1%E4%BA%AB%E6%96%87%E4%BB%B6%E7%BD%91%E7%BB%9C%E7%9A%84%E5%B9%B6%E5%8F%91%E8%AE%A1%E7%AE%97%E7%AD%89%E6%93%8D%E4%BD%9C/#more

* Bug fixes and man page updates.
2020-05-19 14:35:25 +00:00
nia
4bb58570a7 Recursive revbump for json-c-0.14 2020-05-19 12:09:07 +00:00
adam
36fd36ec4c py-billiard: updated to 3.6.3.0
3.6.1:
- Logging max memory reached at INFO rather than WARNING
- Pass arguments when wrapping sys.exit
- Remove win32/py2k special
- Ensure READY messages sent out by exiting worker are consumed prior to it actually existing.
- Pass max_memory_per_child to child worker process
- Fix compatibility with Python 2.7 on Windows
2020-05-17 19:16:38 +00:00
cheusov
e91b3b25d1 Update to 1.1.3:
Fix use of uninitialized array.
  As a rsult paexec generates incorrect shell command to run
  on nodes. Seen with "clang-7.0.1" with -O2 and -D_FORTIFY_SOURCE=2

  Add one line description to projects.
  So, one can run "mkcmake help"
2020-05-15 13:32:19 +00:00
rillig
abb3a5782b parallel/ganglia-monitor-core: clean up SUBST_FILES
The package has switched to autoconf's .in files to get the paths into
the source code.
2020-05-10 14:18:54 +00:00
adam
7d4b705c63 revbump after boost update 2020-05-06 14:04:05 +00:00
adam
2141d9615b openmp: updated to 10.0.0
10.0.0:
Unknown changes
2020-04-18 08:05:11 +00:00
cheusov
dd5eaccf99 Update to paexec-1.1.2
paexec -x:
    * fix handling tasks with leading spaces
    * fix handling tasks with backslashes

  paargs:
    * on SunOS-5.10 use /usr/xpg4/bin/sh
      instead of horribly broken /bin/sh

  Fix build failure on SunOS-5.10 (getdelim(3) is absent)

  Introduce PAEXEC_SH environment variable
  for fixing /bin/sh on SunOS-5.10

  Introduce PAEXEC_FIND variable for regression tests (required on
  SunOS-5.10)
2020-03-30 19:22:57 +00:00
rillig
ae203d610c parallel/paexec: remove REPLACE_SH without effect
Both files don't exist. If corrected, the first file would end up in
share/examples, and mk/check/check-interpreter.mk allows /usr/bin/env is
those files.
2020-03-22 21:35:37 +00:00
nia
4b51d9715f *: Convert broken sourceforge HOMEPAGEs back to http 2020-03-20 11:57:53 +00:00
wiz
4e3b1b97c2 librsvg: update bl3.mk to remove libcroco in rust case
recursive bump for the dependency change
2020-03-10 22:08:37 +00:00
wiz
f669fda471 *: recursive bump for libffi 2020-03-08 16:47:24 +00:00
jperkin
d8b0bac91c openmpi: Support SunOS/x86_64 inline assembly. 2020-02-06 11:28:49 +00:00
bacon
378e388fe2 parallel/slurm-wlm: Upgrade to 19.05.5
CVE-2019-6438 resolved upstream
Numerous enhancements and bug fixes
Remove some old patches and hacks
2020-02-01 00:15:01 +00:00
rillig
9637f7852e all: migrate homepages from http to https
pkglint -r --network --only "migrate"

As a side-effect of migrating the homepages, pkglint also fixed a few
indentations in unrelated lines. These and the new homepages have been
checked manually.
2020-01-26 17:30:40 +00:00
rillig
b686dd9180 all: migrate several HOMEPAGEs to https
pkglint --only "https instead of http" -r -F

With manual adjustments afterwards since pkglint 19.4.4 fixed a few
indentations in unrelated lines.

This mainly affects projects hosted at SourceForce, as well as
freedesktop.org, CTAN and GNU.
2020-01-18 23:30:43 +00:00
jperkin
26c1bffc9f *: Recursive revision bump for openssl 1.1.1. 2020-01-18 21:48:19 +00:00
ryoon
eedd1e806f *: Recursive revbump from devel/boost-libs 2020-01-12 20:19:52 +00:00
adam
fa003e0fad llvm: updated to 9.0.1
9.0.1 is a bug-fix release.
2019-12-29 15:31:21 +00:00
rillig
4a81be3b70 parallel: align variable assignments
pkglint -Wall -F --only aligned --only indent -r

No manual corrections.
2019-11-04 19:18:09 +00:00
mef
d7666c0eba (parallel/parallel) Updated 20160822 to 20190922. See NEWS (in source tree) 2019-10-31 22:57:37 +00:00
tnn
c7776faa13 more packages with wrong LICENSE tag 2019-10-24 11:52:20 +00:00
adam
8f0828b10e lld: updated to 9.0.0
9.0.0:
Non-comprehensive list of changes in this release

ELF Improvements

ld.lld now has typo suggestions for flags: $ ld.lld --call-shared now prints unknown argument '--call-shared', did you mean '--call_shared'.

--allow-shlib-undefined and --no-allow-shlib-undefined options are added. --no-allow-shlib-undefined is the default for executables.

-nmagic and -omagic options are fully supported.

Segment layout has changed. PT_GNU_RELRO, which was previously placed in the middle of readable/writable PT_LOAD segments, is now placed at the beginning of them. This change permits lld-produced ELF files to be read correctly by GNU strip older than 2.31, which has a bug to discard a PT_GNU_RELRO in the former layout.

-z common-page-size is supported.

Diagnostics messages have improved. A new flag --vs-diagnostics alters the format of diagnostic output to enable source hyperlinks in Microsoft Visual Studio IDE.

Linker script compatibility with GNU BFD linker has generally improved.

The clang --dependent-library form of autolinking is supported.

This feature is added to implement the Windows-style autolinking for Unix. On Unix, in order to use a library, you usually have to include a header file provided by the library and then explicitly link the library with the linker -l option. On Windows, header files usually contain pragmas that list needed libraries. Compilers copy that information to object files, so that linkers can automatically link needed libraries. --dependent-library is added for implementing that Windows semantics on Unix.

AArch64 BTI and PAC are supported.

lld now supports replacing JAL with JALX instructions in case of MIPS-microMIPS cross-mode jumps.

lld now creates LA25 thunks for MIPS R6 code.

Put MIPS-specific .reginfo, .MIPS.options, and .MIPS.abiflags sections into corresponding PT_MIPS_REGINFO, PT_MIPS_OPTIONS, and PT_MIPS_ABIFLAGS segments.

The quality of RISC-V and PowerPC ports have greatly improved. Many applications can now be linked by lld. PowerPC64 is now almost production ready.

The Linux kernel for arm32_7, arm64, ppc64le and x86_64 can now be linked by lld.

x86-64 TLSDESC is supported.

DF_STATIC_TLS flag is set for i386 and x86-64 when needed.

The experimental partitioning feature is added to allow a program to be split into multiple pieces.

The feature allows you to semi-automatically split a single program into multiple ELF files called “partitions”. Since all partitions share the same memory address space and don’t use PLT/GOT, split programs run as fast as regular programs.

With the mechanism, you can start a program only with a “main” partition and load remaining partitions on-demand. For example, you can split a web browser into a main partition and a PDF reader sub-partition and load the PDF reader partition only when a user tries to open a PDF file.

See the documentation for more information.

If “-” is given as an output filename, lld writes the final result to the standard output. Previously, it created a file “-” in the current directory.

-z ifunc-noplt option is added to reduce IFunc function call overhead in a freestanding environment such as the OS kernel.

Functions resolved by the IFunc mechanism are usually dispatched via PLT and thus slower than regular functions because of the cost of indirection. With -z ifunc-noplt, you can eliminate it by doing text relocations at load-time. You need a special loader to utilize this feature. This feature is added for the FreeBSD kernel but can be used by any operating systems.

--undefined-glob option is added. The new option is an extension to --undefined to take a glob pattern instead of a single symbol name.

COFF Improvements

Like the ELF driver, lld-link now has typo suggestions for flags.
lld-link now correctly reports duplicate symbol errors for object files that were compiled with /Gy.
lld-link now correctly reports duplicate symbol errors when several resource (.res) input files define resources with the same type, name and language. This can be demoted to a warning using /force:multipleres.
lld-link now rejects more than one resource object input files, matching link.exe. Previously, lld-link would silently ignore all but one. If you hit this: Don’t pass resource object files to the linker, instead pass res files to the linker directly. Don’t put resource files in static libraries, pass them on the command line.
Having more than two /natvis: now works correctly; it used to not work for larger binaries before.
Undefined symbols are now printed only in demangled form. Pass /demangle:no to see raw symbol names instead.
Several speed and memory usage improvements.
lld-link now supports resource object files created by GNU windres and MS cvtres, not only llvm-cvtres.
The generated thunks for delayimports now share the majority of code among thunks, significantly reducing the overhead of using delayimport.
IMAGE_REL_ARM{,64}_REL32 relocations are supported.
Range extension thunks for AArch64 are now supported, so lld can create large executables for Windows/ARM64.
The following flags have been added: /functionpadmin

WebAssembly Improvements

Imports from custom module names are supported.
Symbols that are in llvm.used are now exported by default.
Initial support for PIC and dynamic linking has landed.
wasm-ld now add __start_/__stop_ symbols for data sections.
wasm-ld now doesn’t report an error on archives without a symbol index.
The following flags have been added: --emit-relocs

MinGW Improvements

lld now correctly links crtend.o as the last object file, handling terminators for the sections such as .eh_frame properly, fixing DWARF exception handling with libgcc and gcc’s crtend.o.
lld now also handles DWARF unwind info generated by GCC, when linking with libgcc.
PDB output can be requested without manually specifying the PDB file name, with the new option -pdb= with an empty value to the option. (The old existing syntax -pdb <filename> was more cumbersome to use with an empty parameter value.)
--no-insert-timestamp option is added as an alias to /timestamp:0.
Many more GNU ld options are now supported, which e.g. allows the lld MinGW frontend to be called by GCC.
The following options are added: --exclude-all-symbols, --appcontainer, --undefined
2019-10-19 14:01:36 +00:00
adam
2f60f054df hwloc: updated to 1.11.3
hwloc (Hardware Locality) 1.11.13

The most important change is support for upcoming Intel processors with
multiple Dies per CPU. hwloc release 2.1 will add a new "Die" object.
In the meantime 1.11.13 and 2.0.4 represent those Dies as "Die" groups.

Summary of the changes since 1.11.12:

* Add support for Linux 5.3 new sysfs cpu topology files with Die information.
* Add support for Intel v2 Extended Topology Enumeration in the x86 backend.
* Tiles, Modules and Dies are exposed as Groups for now.
  + HWLOC_DONT_MERGE_DIE_GROUPS=1 may be set in the environment to prevent
    Die groups from being automatically merged with identical parent or
children.
* Ignore NUMA node information from AMD topoext in the x86 backend,
  unless HWLOC_X86_TOPOEXT_NUMANODES=1 is set in the environment.
* Group objects have a new "dont_merge" attribute to prevent them from
  being automatically merged with identical parent or children.
2019-09-11 13:16:45 +00:00
maya
fa1a41bc02 R-promises: add missing dependency
From Benjamin Lorenz in PR pkg/54518
2019-09-07 13:16:27 +00:00
ryoon
edacf2bbcb Recursive revbump from boost-1.71.0 2019-08-22 12:22:48 +00:00
wiz
84e123ddd2 Bump PKGREVISIONs for perl 5.30.0 2019-08-11 13:17:48 +00:00
brook
7b143976cd R-promises: initial commit
Provides fundamental abstractions for doing asynchronous programming
in R using promises. Asynchronous programming is useful for allowing a
single R process to orchestrate multiple tasks in the background while
also attending to something else. Semantics are similar to
'JavaScript' promises, but with a syntax that is idiomatic R.
2019-08-09 20:25:29 +00:00
adam
b063e5dd0e llvm: updated to 8.0.1
LLVM 8.0.1 is now available! Download it now, or read the release notes.

This release contains bug-fixes for the LLVM 8.0.0 release. This
release is API and ABI compatible with 8.0.0.
2019-08-05 19:06:49 +00:00
wiz
c30c5fbc0b *: recursive bump for nettle 3.5.1 2019-07-20 22:45:58 +00:00
nia
c66ee34855 Follow some http->https redirects. 2019-07-08 10:36:25 +00:00
ryoon
57d0806c39 Recursive revbump from boost-1.70.0 2019-07-01 04:07:44 +00:00
nia
38ae6917f0 Use https for sourceforge project links. 2019-06-22 11:52:31 +00:00
adam
e1f76177cc openmp: added version 8.0.0
The OpenMP subproject of LLVM contains the components required to build an
executable OpenMP program that are outside the compiler itself.

Here you can find the code for the runtime library against which code compiled
by clang -fopenmp must be linked before it can run.
2019-06-17 16:35:44 +00:00
maya
f34a8c24a3 PKGREVISION bump for anything using python without a PYPKGPREFIX.
This is a semi-manual PKGREVISION bump.
2019-04-25 07:32:34 +00:00
cheusov
f69a45c7e1 Remove mova.org from MASTER_SITES 2019-04-08 21:38:39 +00:00
adam
964776cc40 py-billiard: updated to 3.6.0.0
3.6.0.0:
- Add support of sending parent process death signal.
- Previous fix for handling timeouts caused a problem in warm shutdowns due
  to use of deepcopy.
  We now use a shallow copy of the cache and do so only when it is needed.
- Cleanup old checks and workarounds for Python versions we no longer support.
2019-04-05 13:03:11 +00:00
wiz
2efdb6ad16 pvm3: remove Xp dependency.
Not used here.
Bump PKGREVISION.
2019-03-20 10:55:21 +00:00
cheusov
be20516bd2 Update to paexec-1.1.1
Fix build using clang
  Verify snprintf didn't truncate the output
2019-02-15 19:31:24 +00:00
wiz
1e9caac440 *: update email for fhajny 2018-12-15 21:12:18 +00:00
adam
5b12b7b592 revbump for boost 1.69.0 2018-12-13 19:51:31 +00:00
adam
d7d8a749dd hwloc: updated to 1.11.12
Version 1.11.12
* Fix a corner case of hwloc_topology_restrict() where children would
  become out-of-order.
* Fix the return length of export_xmlbuffer() functions to always
  include the ending \0.

Version 1.11.11
* Add support for Hygon Dhyana processors in the x86 backend,
  thanks to Pu Wen for the patch.
* Fix symbol renaming to also rename internal components,
  thanks to Evan Ramos for the patch.
* Fix build on HP-UX, thanks to Richard Lloyd for reporting the issues.
* Detect PCI link speed without being root on Linux >= 4.13.
2018-12-13 19:11:28 +00:00
kleink
f1a683c990 Revbump after cairo 1.16.0 update. 2018-11-14 22:20:58 +00:00