Étienne Mollier pushed to branch master at Debian Med / kmc
Commits: 2c774fae by Étienne Mollier at 2020-12-08T21:05:27+01:00 Add cap-default-thread-count.patch - - - - - 21a8986a by Étienne Mollier at 2020-12-08T21:07:06+01:00 Fix d/watch to find newer upstream versions - - - - - 887d06e8 by Étienne Mollier at 2020-12-08T21:17:12+01:00 update autopkgtest The idea is to test both single-threaded and multi-threaded runs of kmc. This should allow one to rule out threading specific issues. There is also a test explicitly specifying a higher thread count, which is known to break, using kmc 2.3, but which is fixed in kmc 3.1.1. This test is commented out with a fixme marker for the moment. The problem for now with kmc 3.1.1 is that it dropped support for almost all architectures, except x86_64, hence not having updated right away. - - - - - 34231fb9 by Étienne Mollier at 2020-12-08T21:22:19+01:00 ready to upload to unstable - - - - - 5 changed files: - debian/changelog - + debian/patches/cap-default-thread-count.patch - debian/patches/series - debian/tests/build-lib - debian/watch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +kmc (2.3+dfsg-10) unstable; urgency=medium + + * Add cap-default-thread-count.patch. (Closes: #954270) + * Fix d/watch to find newer upstream versions. + * Update autopkgtest: test single-threaded and default option independently. + + -- Étienne Mollier <[email protected]> Tue, 08 Dec 2020 21:21:51 +0100 + kmc (2.3+dfsg-9) unstable; urgency=medium * Team upload. ===================================== debian/patches/cap-default-thread-count.patch ===================================== @@ -0,0 +1,25 @@ +Description: cap default thread count to 24 threads + New upstream versions fix this issue more appropriately, and past kmc 3 this + patch should be dropped. Update to kmc 3 is not obvious due to the new version + being heavily optimized against x86_64, and failing to build from source on any + other architecture sadly. +Author: Étienne Mollier <[email protected]> +Bug: https://github.com/refresh-bio/KMC/issues/82#issuecomment-451616129 +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=954270 +Forwarded: not-needed +Applied-Upstream: 3.1.1 +Last-Update: 2020-12-08 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- kmc.orig/kmc_tools/parameters_parser.cpp ++++ kmc/kmc_tools/parameters_parser.cpp +@@ -60,6 +60,9 @@ + { + //defaults + config.avaiable_threads = thread::hardware_concurrency(); ++ //cap defaults to 24 threads due to Debian Bug#954270 ++ if ( config.avaiable_threads > 24 ) ++ config.avaiable_threads = 24; + + //override defaults if specified + for( ; pos < argc && argv[pos][0] == '-' ; ++pos) ===================================== debian/patches/series ===================================== @@ -5,3 +5,4 @@ hardening 0007-Use-standard-compiler-environment-variables.patch spelling newish_gcc_build_fix.patch +cap-default-thread-count.patch ===================================== debian/tests/build-lib ===================================== @@ -13,12 +13,32 @@ g++ kmc_dump/*cpp -std=c++11 -lkmc -o $WORKDIR/my_kmcdump echo "build: OK" cd $WORKDIR -kmc -ci1 -m1 -k28 $ORIGDIR/debian/tests/sample_6.fastq.gz 1 . +echo 'Running kmc (single threaded)' +kmc -ci1 -m1 -k28 -t1 $ORIGDIR/debian/tests/sample_6.fastq.gz 1 . ls -Al [ -s 1.kmc_suf ] [ -s 1.kmc_pre ] -echo "kmc: OK" +echo "kmc (single threaded): OK" ./my_kmcdump 1 out [ -s out ] echo "run: OK" + +# FIXME: uncomment the below test once kmc is updated to version 3.1.1 or more. +## Multi-threaded runs have been known to be faulty (#954270). +#echo 'Running kmc (32 threads)' +#rm -f 1.kmc_suf 1.kmc_pre +#kmc -ci1 -m1 -k28 -t32 $ORIGDIR/debian/tests/sample_6.fastq.gz 1 . +#ls -Al +#[ -s 1.kmc_suf ] +#[ -s 1.kmc_pre ] +#echo "kmc (32 threads): OK" + +# In the end, default options should, ideally, work on any configuration.. +echo 'Running kmc (default thread count)' +rm -f 1.kmc_suf 1.kmc_pre +kmc -ci1 -m1 -k28 $ORIGDIR/debian/tests/sample_6.fastq.gz 1 . +ls -Al +[ -s 1.kmc_suf ] +[ -s 1.kmc_pre ] +echo "kmc (default thread count): OK" ===================================== debian/watch ===================================== @@ -2,4 +2,4 @@ version=4 opts="repacksuffix=+dfsg,dversionmangle=auto,filenamemangle=s/(?:.*?)?v?(\d[\d.]*)\.tar\.gz/kmc_$1.tar.gz/" \ https://github.com/marekkokot/KMC/releases \ - .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) + .*/archive/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) View it on GitLab: https://salsa.debian.org/med-team/kmc/-/compare/090409638404d0682d00f03cb8478d0caac64a4c...34231fb9309ff6967bc1e93a34a0fe6f0d5334b4 -- View it on GitLab: https://salsa.debian.org/med-team/kmc/-/compare/090409638404d0682d00f03cb8478d0caac64a4c...34231fb9309ff6967bc1e93a34a0fe6f0d5334b4 You're receiving this email because of your account on salsa.debian.org.
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