galaxyproject / galaxyproject/galaxy

job scheduling slowdown with large collections

Open
#9,871 3 comments 1 reaction 0 assignees View on GitHub
Dominant language
Python
Stars
1.9k
Forks
1.2k
Avg merge
2d 16h
Merged PRs (30d)
169

Description

```
Jun 12 10:32:47 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:47,111 Handled output named text_param for tool param_value_from_file (1.651 ms)
Jun 12 10:32:47 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:47,718 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (5.053 ms)
Jun 12 10:32:47 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:47,983 Flushed transaction for Job[id=8868738,tool_id=param_value_from_file] (264.129 ms)
Jun 12 10:32:47 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:47,983 (Job[id=8868738,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 10:32:47 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 10:32:47,984 Tool [param_value_from_file] created job [8868738] (968.590 ms)
Jun 12 10:32:48 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:48,928 Handled output named text_param for tool param_value_from_file (3.310 ms)
Jun 12 10:32:49 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:49,496 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (5.110 ms)
Jun 12 10:32:49 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:49,735 Flushed transaction for Job[id=8868739,tool_id=param_value_from_file] (238.781 ms)
Jun 12 10:32:49 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:49,736 (Job[id=8868739,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 10:32:49 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 10:32:49,736 Tool [param_value_from_file] created job [8868739] (830.289 ms)
Jun 12 10:32:50 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:50,398 Handled output named text_param for tool param_value_from_file (1.982 ms)
Jun 12 10:32:51 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:51,014 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (4.166 ms)
Jun 12 10:32:51 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:51,203 Flushed transaction for Job[id=8868740,tool_id=param_value_from_file] (189.218 ms)
Jun 12 10:32:51 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:51,203 (Job[id=8868740,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 10:32:51 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 10:32:51,203 Tool [param_value_from_file] created job [8868740] (821.507 ms)
Jun 12 10:32:51 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:51,858 Handled output named text_param for tool param_value_from_file (2.766 ms)
Jun 12 10:32:52 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:52,372 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (4.681 ms)
Jun 12 10:32:52 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:52,584 Flushed transaction for Job[id=8868741,tool_id=param_value_from_file] (211.955 ms)
Jun 12 10:32:52 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:52,585 (Job[id=8868741,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 10:32:52 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 10:32:52,585 Tool [param_value_from_file] created job [8868741] (743.449 ms)
Jun 12 10:32:53 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:53,216 Handled output named text_param for tool param_value_from_file (1.398 ms)
Jun 12 10:32:53 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:53,804 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (4.110 ms)
Jun 12 10:32:54 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:54,053 Flushed transaction for Job[id=8868742,tool_id=param_value_from_file] (249.284 ms)
Jun 12 10:32:54 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:54,053 (Job[id=8868742,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 10:32:54 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 10:32:54,054 Tool [param_value_from_file] created job [8868742] (860.431 ms)
Jun 12 10:32:54 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:54,697 Handled output named text_param for tool param_value_from_file (1.622 ms)
Jun 12 10:32:55 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:55,235 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (3.673 ms)
Jun 12 10:32:55 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:55,473 Flushed transaction for Job[id=8868744,tool_id=param_value_from_file] (238.238 ms)
Jun 12 10:32:55 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:55,473 (Job[id=8868744,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 10:32:55 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 10:32:55,474 Tool [param_value_from_file] created job [8868744] (793.490 ms)
Jun 12 10:32:56 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:56,104 Handled output named text_param for tool param_value_from_file (2.392 ms)
Jun 12 10:32:56 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 10:32:56,732 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (5.798 ms)
Jun 12 10:32:57 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:56,999 Flushed transaction for Job[id=8868745,tool_id=param_value_from_file] (266.167 ms)
Jun 12 10:32:57 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 10:32:56,999 (Job[id=8868745,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 10:32:57 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 10:32:57,000 Tool [param_value_from_file] created job [8868745] (914.839 ms)

```

```
Jun 12 13:39:37 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:39:37,530 (Job[id=8875906,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:39:37 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:39:37,530 Tool [param_value_from_file] created job [8875906] (1921.552 ms)
Jun 12 13:39:38 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:39:38,177 Handled output named text_param for tool param_value_from_file (1.322 ms)
Jun 12 13:39:39 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:39:39,402 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (2.623 ms)
Jun 12 13:39:39 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:39:39,913 Flushed transaction for Job[id=8875908,tool_id=param_value_from_file] (511.465 ms)
Jun 12 13:39:39 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:39:39,914 (Job[id=8875908,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:39:39 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:39:39,914 Tool [param_value_from_file] created job [8875908] (1754.798 ms)
Jun 12 13:39:51 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:39:51,137 Handled output named text_param for tool param_value_from_file (2.663 ms)
Jun 12 13:39:52 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:39:52,330 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (5.243 ms)
Jun 12 13:39:52 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:39:52,925 Flushed transaction for Job[id=8875909,tool_id=param_value_from_file] (594.712 ms)
Jun 12 13:39:52 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:39:52,925 (Job[id=8875909,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:39:52 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:39:52,925 Tool [param_value_from_file] created job [8875909] (1811.061 ms)
Jun 12 13:39:53 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:39:53,646 Handled output named text_param for tool param_value_from_file (1.625 ms)
Jun 12 13:39:54 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:39:54,999 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (3.816 ms)
Jun 12 13:39:55 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:39:55,672 Flushed transaction for Job[id=8875910,tool_id=param_value_from_file] (673.198 ms)
Jun 12 13:39:55 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:39:55,672 (Job[id=8875910,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:39:55 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:39:55,673 Tool [param_value_from_file] created job [8875910] (2041.287 ms)
Jun 12 13:39:56 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:39:56,321 Handled output named text_param for tool param_value_from_file (2.014 ms)
Jun 12 13:39:57 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:39:57,542 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (5.077 ms)
Jun 12 13:39:58 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:39:58,034 Flushed transaction for Job[id=8875911,tool_id=param_value_from_file] (491.628 ms)
Jun 12 13:39:58 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:39:58,034 (Job[id=8875911,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:39:58 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:39:58,034 Tool [param_value_from_file] created job [8875911] (1732.490 ms)
Jun 12 13:39:58 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:39:58,691 Handled output named text_param for tool param_value_from_file (2.748 ms)
Jun 12 13:39:59 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:39:59,844 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (5.151 ms)
Jun 12 13:40:00 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:00,446 Flushed transaction for Job[id=8875912,tool_id=param_value_from_file] (601.024 ms)
Jun 12 13:40:00 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:00,446 (Job[id=8875912,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:40:00 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:40:00,446 Tool [param_value_from_file] created job [8875912] (1775.768 ms)
Jun 12 13:40:01 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:01,180 Handled output named text_param for tool param_value_from_file (2.068 ms)
Jun 12 13:40:02 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:02,421 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (2.803 ms)
Jun 12 13:40:03 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:03,008 Flushed transaction for Job[id=8875913,tool_id=param_value_from_file] (586.881 ms)
Jun 12 13:40:03 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:03,009 (Job[id=8875913,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:40:03 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:40:03,009 Tool [param_value_from_file] created job [8875913] (1850.211 ms)
Jun 12 13:40:03 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:03,665 Handled output named text_param for tool param_value_from_file (1.510 ms)
Jun 12 13:40:04 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:04,892 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (4.042 ms)
Jun 12 13:40:05 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:05,356 Flushed transaction for Job[id=8875914,tool_id=param_value_from_file] (464.443 ms)
Jun 12 13:40:05 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:05,357 (Job[id=8875914,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:40:05 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:40:05,357 Tool [param_value_from_file] created job [8875914] (1711.221 ms)
Jun 12 13:40:06 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:06,038 Handled output named text_param for tool param_value_from_file (2.165 ms)
Jun 12 13:40:07 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:07,269 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (3.750 ms)
Jun 12 13:40:07 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:07,813 Flushed transaction for Job[id=8875915,tool_id=param_value_from_file] (543.879 ms)
Jun 12 13:40:07 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:07,814 (Job[id=8875915,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:40:07 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:40:07,814 Tool [param_value_from_file] created job [8875915] (1797.988 ms)
Jun 12 13:40:08 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:08,547 Handled output named text_param for tool param_value_from_file (2.609 ms)
Jun 12 13:40:09 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:09,710 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (5.829 ms)
Jun 12 13:40:10 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:10,226 Flushed transaction for Job[id=8875916,tool_id=param_value_from_file] (515.631 ms)
Jun 12 13:40:10 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:10,227 (Job[id=8875916,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:40:10 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:40:10,227 Tool [param_value_from_file] created job [8875916] (1696.763 ms)
Jun 12 13:40:10 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:10,859 Handled output named text_param for tool param_value_from_file (1.352 ms)
Jun 12 13:40:12 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:12,096 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (6.153 ms)
Jun 12 13:40:12 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:12,619 Flushed transaction for Job[id=8875917,tool_id=param_value_from_file] (522.185 ms)
Jun 12 13:40:12 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:12,619 (Job[id=8875917,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:40:12 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:40:12,619 Tool [param_value_from_file] created job [8875917] (1774.229 ms)
Jun 12 13:40:13 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:13,272 Handled output named text_param for tool param_value_from_file (2.403 ms)
Jun 12 13:40:14 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:14,590 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (4.939 ms)
Jun 12 13:40:15 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:15,127 Flushed transaction for Job[id=8875918,tool_id=param_value_from_file] (536.763 ms)
Jun 12 13:40:15 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:15,128 (Job[id=8875918,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:40:15 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:40:15,128 Tool [param_value_from_file] created job [8875918] (1875.143 ms)
Jun 12 13:40:15 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:15,804 Handled output named text_param for tool param_value_from_file (3.156 ms)
Jun 12 13:40:17 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:17,101 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (3.926 ms)
Jun 12 13:40:17 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:17,714 Flushed transaction for Job[id=8875919,tool_id=param_value_from_file] (611.952 ms)
Jun 12 13:40:17 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:17,714 (Job[id=8875919,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:40:17 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:40:17,714 Tool [param_value_from_file] created job [8875919] (1926.184 ms)
Jun 12 13:40:18 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:18,339 Handled output named text_param for tool param_value_from_file (1.774 ms)
Jun 12 13:40:19 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:19,706 Setup for job Job[unflushed,tool_id=param_value_from_file] complete, ready to be enqueued (5.566 ms)
Jun 12 13:40:20 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:20,265 Flushed transaction for Job[id=8875920,tool_id=param_value_from_file] (558.842 ms)
Jun 12 13:40:20 sn04.bi.uni-freiburg.de python[707952]: galaxy.web_stack.handlers INFO 2020-06-12 13:40:20,265 (Job[id=8875920,tool_id=param_value_from_file]) Handler '_default_' assigned using 'db-skip-locked' assignment method
Jun 12 13:40:20 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.execute DEBUG 2020-06-12 13:40:20,265 Tool [param_value_from_file] created job [8875920] (1944.239 ms)
Jun 12 13:40:20 sn04.bi.uni-freiburg.de python[707952]: galaxy.tools.actions INFO 2020-06-12 13:40:20,928 Handled output named text_param for tool param_value_from_file (1.647 ms)
root@sn04:~$

```

Same collection, same run with 6,150 elements. This is now ~10x slower for single job creation than 3h ago. The schduler is not the problem, the queue is empty and jobs are immediately processed once they are on htcondor.

Contributor guide

Open the contributing guide

Research direction

The issue provides timing logs for param_value_from_file job creation, including galaxy.tools.actions, galaxy.web_stack.handlers, and galaxy.tools.execute. Start by locating the entry points that emit these messages and compare job-creation timings for small and large collections. Done means the slowdown is explained and a measurable improvement is demonstrated without regressing job scheduling.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend, performance
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.