TES Backend Prototype. Closes #1294 #1979

adamstruck · 2017-02-13T18:55:54Z

Picking up from #1816.

Setup for Centaur testing. The current TES schema doesn't allow for changing the default user, so centaur fails on:

non_root_specified_user

Is there a way to configure Centaur to skip specific tests?

kshakir · 2017-02-13T22:25:36Z

Try sbt 'testOnly -- -l localdockertest'

kshakir · 2017-02-13T22:34:40Z

src/bin/travis/testCentaurTes.sh

+# because pulling the image during some of the tests would cause them to fail 
+# (specifically output_redirection which expects a specific value in stderr)
+docker pull ubuntu:latest
+centaur/test_cromwell.sh -j"${CROMWELL_JAR}" -c${TES_CENTAUR_CONF}


Until we figure out excluding these local tests by default, change:

centaur/test_cromwell.sh -j"${CROMWELL_JAR}" -c${TES_CENTAUR_CONF}

to:

centaur/test_cromwell.sh -j"${CROMWELL_JAR}" -c${TES_CENTAUR_CONF} -elocaldockertest

adamstruck · 2017-02-14T17:42:38Z

@kshakir adding -elocaldockertest addressed the issue when I ran the tests locally. In Travis CI, the non_root_default_user test is failing with:

Status: Downloaded newer image for mcovarr/notroot:v1
bin/bash: /cromwell-executions/woot/148f812b-028b-4264-82bd-ab2f089efe98/call-notroot/execution/script: Permission denied

This test passes when I run it locally. Any ideas?

mcovarr · 2017-02-14T21:55:17Z

@adamstruck That test tries to run a Docker image which has a default user which is not root (the test was created based on this ticket). That error looks like the non-root user in the container doesn't have execute permission on the script that was created by Cromwell running as a different user.

kshakir · 2017-02-15T00:36:44Z

...Backends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala

+  def createTaskMessage(): TesTaskMessage = {
+    val task = TesTask(jobDescriptor, configurationDescriptor, jobLogger, tesJobPaths, runtimeAttributes, commandDirectory, backendEngineFunctions)
+
+    tesJobPaths.script.write(commandScriptContents)


Perhaps, as Miguel pointed out, changing the permissions might help, specifically here?

tesJobPaths.script.write(commandScriptContents).chmod("rwxrwxrwx")

I haven't tried running this myself yet though. I'm assuming that this is the right spot to fix permissions, based on the error message in the logs producing the exit code 126:

/bin/bash: /cromwell-executions/woot/a2c488a2-e2a0-46f4-8714-47ac3a89bc2b/call-notroot/execution/script: Permission denied

I'm not 100% sure at the moment where/why the permissions on the script are not-as-expected though. The local backend gets around permissions errors by telling docker to run /bin/bash /path/to/script, that seems to work even if the file is rw-rw-r--.

If you really are running into problems and don't want to support this test and the "running as non-root" functionality for whatever reason, let us know, and we can figure out a way to exclude it.

This was an issue on the TES side of things. I am resolving this today.

adamstruck · 2017-02-16T19:02:07Z

@kshakir all TES Centaur tests are now passing.

kshakir · 2017-02-17T18:26:23Z

src/bin/travis/testCentaurTes.sh

+cd ..
+
+TES_CONF="$(pwd)/src/bin/travis/resources/tes.conf"
+git clone https://github.com/ohsu-comp-bio/funnel.git


@adamstruck Can you change this to https://github.com/broadinstitute/funnel.git? I've forked the repo.

kshakir · 2017-02-17T18:30:58Z

supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendFileHashing.scala

+    } get
+
+    tryWithResource(() => path.newInputStream) { inputStream =>
+      org.apache.commons.codec.digest.DigestUtils.md5Hex(inputStream)


ToL: Note for the future, this is fine for passing centaur tests, but takes too long on real BAM files. Hopefully whenever #1843 is implemented it will be reusable by this backend also.

kshakir · 2017-02-17T18:34:08Z

👍 once centaur isn't downloading from an external repo

mcovarr · 2017-02-17T18:36:54Z

README.md

@@ -75,7 +80,8 @@ A [Workflow Management System](https://en.wikipedia.org/wiki/Workflow_management
  * [Local Filesystem Options](#local-filesystem-options)
 * [Imports](#imports)
 * [Sub Workflows](#sub-workflows)
-* [Meta blocks](#meta-blocks)
+  * [Execution](#execution)
+  * [Metadata](#metadata)


oops thanks for fixing this!

mcovarr · 2017-02-17T18:52:44Z

supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala

+  private val MemoryDefaultValue = "2 GB"
+
+  val DiskSizeKey = "disk"
+  private val DiskSizeDefaultValue = "2 GB"


These default values are not consistent with the README

mcovarr · 2017-02-17T19:06:37Z

README.md

@@ -1392,6 +1399,65 @@ In order to monitor metrics (CPU, Memory, Disk usage...) about the VM during Cal

 The output of this script will be written to a `monitoring.log` file that will be available in the call gcs bucket when the call completes.  This feature is meant to run a script in the background during long-running processes.  It's possible that if the task is very short that the log file does not flush before de-localization happens and you will end up with a zero byte file.

+## GA4GH TES Backend
+The TES backend submit jobs to a server that complies with the protocol described by the [GA4GH schema](https://github.com/ga4gh/task-execution-schemas).


submit jobs => submits jobs

mcovarr · 2017-02-17T19:27:34Z

👍

geoffjentry · 2017-02-17T20:48:15Z

Pretty cool, thanks @adamstruck

adamstruck · 2017-02-17T21:42:47Z

Thanks for the comments. I pushed the README changes and Funnel is now being downloaded from the broad's fork.

It looks like both the Local and Tes Centaur build are failing now though?

added -elocaldockertest to centaur command print TES logs after run fixed unmarshalling bug inputs in read-only volume; matched TES case classes to schema address final PR comments

kshakir · 2017-02-18T02:34:29Z

The Local build did fail, due to an unrelated hiccup. A restart of the build cleared the error.

Meanwhile, JES Centaur failed due to #1717, but TES passed just fine.

Everything looking great. Thanks again for all of your contributions!

adamstruck mentioned this pull request Feb 13, 2017

TES Backend Prototype. Closes #1294 #1816

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kshakir reviewed Feb 13, 2017

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adamstruck force-pushed the tes_backend_prototype branch 3 times, most recently from 1a87c5e to 0e02f81 Compare February 14, 2017 19:01

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adamstruck force-pushed the tes_backend_prototype branch from 01c2e2e to b9faa69 Compare February 16, 2017 18:46

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kshakir assigned mcovarr Feb 17, 2017

mcovarr approved these changes Feb 17, 2017

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adamstruck force-pushed the tes_backend_prototype branch from b9faa69 to 97b2116 Compare February 17, 2017 20:53

tes backend prototype with centuar setup

d7adb19

added -elocaldockertest to centaur command print TES logs after run fixed unmarshalling bug inputs in read-only volume; matched TES case classes to schema address final PR comments

adamstruck force-pushed the tes_backend_prototype branch from 97b2116 to d7adb19 Compare February 17, 2017 22:14

kshakir merged commit 1524f3d into broadinstitute:develop Feb 18, 2017

adamstruck deleted the tes_backend_prototype branch May 12, 2017 21:45

aednichols mentioned this pull request Mar 28, 2024

WX-1535 Change Docker root on Azure to match GCP #7395

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TES Backend Prototype. Closes #1294 #1979

TES Backend Prototype. Closes #1294 #1979

adamstruck commented Feb 13, 2017

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kshakir commented Feb 18, 2017

TES Backend Prototype. Closes #1294 #1979

TES Backend Prototype. Closes #1294 #1979

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