[ARVADOS] updated: 2.1.0-122-gc735c1bbb
Git user
git at public.arvados.org
Fri Mar 19 20:03:31 UTC 2021
Summary of changes:
doc/_config.yml | 1 +
.../cwl/crunchstat-summary.html.textile.liquid | 150 +++++++++++++++++++++
doc/user/cwl/images/crunchstat-summary-html.png | Bin 0 -> 132084 bytes
3 files changed, 151 insertions(+)
create mode 100644 doc/user/cwl/crunchstat-summary.html.textile.liquid
create mode 100644 doc/user/cwl/images/crunchstat-summary-html.png
via c735c1bbbb148c5ced9bad0b4b1894294024c84a (commit)
via 00751bbff726863ad1fe8b6d99043d4d0fa97a02 (commit)
from e94b01699a2ff50e1f39321c305c03e79f94dcf2 (commit)
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commit c735c1bbbb148c5ced9bad0b4b1894294024c84a
Author: Ward Vandewege <ward at curii.com>
Date: Fri Mar 19 16:01:14 2021 -0400
10458: implement review feedback.
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward at curii.com>
diff --git a/doc/user/cwl/crunchstat-summary.html.textile.liquid b/doc/user/cwl/crunchstat-summary.html.textile.liquid
index f2d6391ad..adeb9e7fe 100644
--- a/doc/user/cwl/crunchstat-summary.html.textile.liquid
+++ b/doc/user/cwl/crunchstat-summary.html.textile.liquid
@@ -9,7 +9,7 @@ Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-The @crunchstat-summary@ tool can be used to analyze workflow and container performance. It can be installed from packages (@apt install crunchstat-summary@ or @yum install rh-python36-python-crunchstat-summary@). @crunchstat-summary@ analyzes the crunchstat lines from the logs of a container or workflow and generates a report in text or html format.
+The @crunchstat-summary@ tool can be used to analyze workflow and container performance. It can be installed from packages (@apt install python3-crunchstat-summary@ or @yum install rh-python36-python-crunchstat-summary@). @crunchstat-summary@ analyzes the crunchstat lines from the logs of a container or workflow and generates a report in text or html format.
h2(#syntax). Syntax
commit 00751bbff726863ad1fe8b6d99043d4d0fa97a02
Author: Ward Vandewege <ward at curii.com>
Date: Fri Mar 19 13:07:52 2021 -0400
10458: add some basic documentation for crunchstat-summary.
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward at curii.com>
diff --git a/doc/_config.yml b/doc/_config.yml
index 7e8bd8f12..50a27de93 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -56,6 +56,7 @@ navbar:
- user/cwl/cwl-extensions.html.textile.liquid
- user/cwl/federated-workflows.html.textile.liquid
- user/cwl/cwl-versions.html.textile.liquid
+ - user/cwl/crunchstat-summary.html.textile.liquid
- Working with git repositories:
- user/tutorials/add-new-repository.html.textile.liquid
- user/tutorials/git-arvados-guide.html.textile.liquid
diff --git a/doc/user/cwl/crunchstat-summary.html.textile.liquid b/doc/user/cwl/crunchstat-summary.html.textile.liquid
new file mode 100644
index 000000000..f2d6391ad
--- /dev/null
+++ b/doc/user/cwl/crunchstat-summary.html.textile.liquid
@@ -0,0 +1,150 @@
+---
+layout: default
+navsection: userguide
+title: Analyzing workflow performance
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+The @crunchstat-summary@ tool can be used to analyze workflow and container performance. It can be installed from packages (@apt install crunchstat-summary@ or @yum install rh-python36-python-crunchstat-summary@). @crunchstat-summary@ analyzes the crunchstat lines from the logs of a container or workflow and generates a report in text or html format.
+
+h2(#syntax). Syntax
+
+The @crunchstat-summary@ tool has a number of command line arguments:
+
+<notextile>
+<pre><code>~$ <span class="userinput">crunchstat-summary -h</span>
+usage: crunchstat-summary [-h]
+ [--job UUID | --container UUID | --pipeline-instance UUID | --log-file LOG_FILE]
+ [--skip-child-jobs] [--format {html,text}]
+ [--threads THREADS] [--verbose]
+
+Summarize resource usage of an Arvados Crunch job
+
+optional arguments:
+ -h, --help show this help message and exit
+ --job UUID, --container-request UUID
+ Look up the specified job or container request and
+ read its log data from Keep (or from the Arvados event
+ log, if the job is still running)
+ --container UUID [Deprecated] Look up the specified container find its
+ container request and read its log data from Keep (or
+ from the Arvados event log, if the job is still
+ running)
+ --pipeline-instance UUID
+ [Deprecated] Summarize each component of the given
+ pipeline instance (historical pre-1.4)
+ --log-file LOG_FILE Read log data from a regular file
+ --skip-child-jobs Do not include stats from child jobs/containers
+ --format {html,text} Report format
+ --threads THREADS Maximum worker threads to run
+ --verbose, -v Log more information (once for progress, twice for
+ debug)
+</code></pre>
+</notextile>
+
+h2(#examples). Examples
+
+ at crunchstat-summary@ prints to stdout. The html report, in particular, should be redirected to a file and then loaded in a browser.
+
+An example text report for a single workflow step:
+
+<notextile>
+<pre><code>~$ <span class="userinput">crunchstat-summary --container-request pirca-xvhdp-rs0ef250emtmbj8 --format text</span>
+category metric task_max task_max_rate job_total
+blkio:0:0 read 63067755822 53687091.20 63067755822
+blkio:0:0 write 64484253320 16376234.80 64484253320
+cpu cpus 16 - -
+cpu sys 2147.29 0.60 2147.29
+cpu user 549046.22 15.99 549046.22
+cpu user+sys 551193.51 16.00 551193.51
+fuseop:create count 1 0.10 1
+fuseop:create time 0.01 0.00 0.01
+fuseop:destroy count 0 0 0
+fuseop:destroy time 0 0 0.00
+fuseop:flush count 12 0.70 12
+fuseop:flush time 0.00 0.00 0.00
+fuseop:forget count 0 0 0
+fuseop:forget time 0 0 0.00
+fuseop:getattr count 40 2.70 40
+fuseop:getattr time 0.00 0.00 0.00
+fuseop:lookup count 36 2.90 36
+fuseop:lookup time 0.67 0.07 0.67
+fuseop:mkdir count 0 0 0
+fuseop:mkdir time 0 0 0.00
+fuseop:on_event count 0 0 0
+fuseop:on_event time 0 0 0.00
+fuseop:open count 9 0.30 9
+fuseop:open time 0.00 0.00 0.00
+fuseop:opendir count 0 0 0
+fuseop:opendir time 0 0 0.00
+fuseop:read count 481185 409.60 481185
+fuseop:read time 370.11 2.14 370.11
+fuseop:readdir count 0 0 0
+fuseop:readdir time 0 0 0.00
+fuseop:release count 7 0.30 7
+fuseop:release time 0.00 0.00 0.00
+fuseop:rename count 0 0 0
+fuseop:rename time 0 0 0.00
+fuseop:rmdir count 0 0 0
+fuseop:rmdir time 0 0 0.00
+fuseop:setattr count 0 0 0
+fuseop:setattr time 0 0 0.00
+fuseop:statfs count 0 0 0
+fuseop:statfs time 0 0 0.00
+fuseop:unlink count 0 0 0
+fuseop:unlink time 0 0 0.00
+fuseop:write count 5414406 1123.00 5414406
+fuseop:write time 475.04 0.11 475.04
+fuseops read 481185 409.60 481185
+fuseops write 5414406 1123.00 5414406
+keepcache hit 961402 819.20 961402
+keepcache miss 946 0.90 946
+keepcalls get 962348 820.00 962348
+keepcalls put 961 0.30 961
+mem cache 22748987392 - -
+mem pgmajfault 0 - 0
+mem rss 27185491968 - -
+net:docker0 rx 0 - 0
+net:docker0 tx 0 - 0
+net:docker0 tx+rx 0 - 0
+net:ens5 rx 1100398604 - 1100398604
+net:ens5 tx 1445464 - 1445464
+net:ens5 tx+rx 1101844068 - 1101844068
+net:keep0 rx 63086467386 53687091.20 63086467386
+net:keep0 tx 64482237590 20131128.60 64482237590
+net:keep0 tx+rx 127568704976 53687091.20 127568704976
+statfs available 398721179648 - 398721179648
+statfs total 400289181696 - 400289181696
+statfs used 1568198656 0 1568002048
+time elapsed 34820 - 34820
+# Number of tasks: 1
+# Max CPU time spent by a single task: 551193.51s
+# Max CPU usage in a single interval: 1599.52%
+# Overall CPU usage: 1582.98%
+# Max memory used by a single task: 27.19GB
+# Max network traffic in a single task: 127.57GB
+# Max network speed in a single interval: 53.69MB/s
+# Keep cache miss rate 0.10%
+# Keep cache utilization 99.97%
+# Temp disk utilization 0.39%
+#!! bwamem-samtools-view max RSS was 25927 MiB -- try reducing runtime_constraints to "ram":27541477785
+#!! bwamem-samtools-view max temp disk utilization was 0% of 381746 MiB -- consider reducing "tmpdirMin" and/or "outdirMin"
+</code></pre>
+</notextile>
+
+When @crunchstat-summary@ is given a container or container request uuid for a toplevel workflow runner container, it will generate a report for the whole workflow. If the workflow is big, it can take a long time to generate the report.
+
+The equivalent html report can be generated as follows:
+
+<notextile>
+<pre><code>~$ <span class="userinput">crunchstat-summary --container-request pirca-xvhdp-rs0ef250emtmbj8 --format html > report.html</span>
+</code></pre>
+</notextile>
+
+When loaded in a browser:
+
+!(full-width)images/crunchstat-summary-html.png!
diff --git a/doc/user/cwl/images/crunchstat-summary-html.png b/doc/user/cwl/images/crunchstat-summary-html.png
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index 000000000..488541b3a
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