[med-svn] [Git][med-team/simka][master] 5 commits: initialize changelog

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / simka


Commits:
d246e494 by Étienne Mollier at 2021-04-07T22:58:21+02:00
initialize changelog

- - - - -
397541bf by Étienne Mollier at 2021-04-07T22:58:45+02:00
d/t/run-unit-test: remove argument from py script

The python script does not take arguments, so its use in the d/t/r
script is misleading.  However the bash test script takes it properly
into account.

- - - - -
ce9d0261 by Étienne Mollier at 2021-04-07T23:02:16+02:00
add high_cores_count.patch

- - - - -
44be76b1 by Étienne Mollier at 2021-04-07T23:08:35+02:00
high_cores_count.patch dep3 header

- - - - -
f83093f7 by Étienne Mollier at 2021-04-07T23:12:10+02:00
update changelog

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/high_cores_count.patch
- debian/patches/series
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+simka (1.5.3-4) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * debian/tests/run-unit-test: remove misleading argument from Python script.
+  * Add high_cores_count.patch to fix deadlock with Python test script.
+    (Closes: #986256)
+
+ -- Étienne Mollier <etienne.mollier at mailoo.org>  Wed, 07 Apr 2021 23:08:57 +0200
+
 simka (1.5.3-3) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/high_cores_count.patch
=====================================
@@ -0,0 +1,67 @@
+Description: run tests on a single core
+ On very high cores count machines, simka may deadlock if left to using as many
+ threads as there are cores available.  Parallel runs are kept for tests which
+ explicitly test the parallel aspect of the program.
+ .
+ Additional flush=True are for better readability of the autopkgtest output.
+Author: Étienne Mollier <etienne.mollier at mailoo.org>
+Bug: https://github.com/GATB/simka/issues/20
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=986256
+Last-Update: 2021-04-07
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- simka.orig/tests/simple_test.py
++++ simka/tests/simple_test.py
+@@ -90,39 +90,39 @@
+ 
+ #test k=31 t=0
+ clear()
+-print("TESTING k=31 t=0")
+-command = "simka -in simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0"
+-print(command)
++print("TESTING k=31 t=0", flush=True)
++command = "simka -in simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0 -nb-cores 1"
++print(command, flush=True)
+ os.system(command + suffix)
+ test_dists("results_k31_t0")
+ 
+ #test k=21 t=0
+ clear()
+-print("TESTING k=21 t=0")
+-command = "simka -in simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0"
+-print(command)
++print("TESTING k=21 t=0", flush=True)
++command = "simka -in simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0 -nb-cores 1"
++print(command, flush=True)
+ os.system(command + suffix)
+ test_dists("results_k21_t0")
+ 
+ #test k=31 t=2
+ clear()
+-print("TESTING k=31 t=2")
+-command = "simka -in simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0"
+-print(command)
++print("TESTING k=31 t=2", flush=True)
++command = "simka -in simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0 -nb-cores 1"
++print(command, flush=True)
+ os.system(command + suffix)
+ test_dists("results_k31_t2")
+ 
+ #test k=21 t=2
+ clear()
+-print("TESTING k=21 t=2")
+-command = "simka -in simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0"
+-print(command)
++print("TESTING k=21 t=2", flush=True)
++command = "simka -in simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0 -nb-cores 1"
++print(command, flush=True)
+ os.system(command + suffix)
+ test_dists("results_k21_t2")
+ 
+ #test resources 1
+ clear()
+-print("TESTING parallelization")
++print("TESTING parallelization", flush=True)
+ command = "simka -in simka_input.txt -out ./__results__/results_resources1 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 20 -max-memory 4000  -verbose 0"
+ os.system(command + suffix)
+ command = "simka -in simka_input.txt -out ./__results__/results_resources2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 2 -max-memory 2000  -verbose 0"


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ fix_binary_path.patch
 fix_test_path.patch
 2to3.patch
 use_debian_packaged_libraries.patch
+high_cores_count.patch


=====================================
debian/tests/run-unit-test
=====================================
@@ -28,7 +28,7 @@ then
 	NR_CPUS=8
 fi
 bash simple_test.sh -nb-cores "$NR_CPUS"
-python3 simple_test.py -nb-cores "$NR_CPUS"
+python3 simple_test.py
 echo "FIXME: Testing simkaMin does not work - needs more investigation"
 echo "FIXME: The test suite slows dramatically down when exceeding 8 cores."
 # python3 simkaMin/test_simkaMin.py



View it on GitLab: https://salsa.debian.org/med-team/simka/-/compare/80cc29378d7f4275d7804dcb8133b2e7ab7ea826...f83093f768e596efc2cdf57bd593f7a977eed375

-- 
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