[med-svn] [Git][med-team/kmc][master] 4 commits: Add cap-default-thread-count.patch

[Étienne Mollier]

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 <etienne.mollier at mailoo.org>  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 <etienne.mollier at mailoo.org>
+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
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