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 <[email protected]> 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 <[email protected]> +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 -- View it on GitLab: https://salsa.debian.org/med-team/simka/-/compare/80cc29378d7f4275d7804dcb8133b2e7ab7ea826...f83093f768e596efc2cdf57bd593f7a977eed375 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
