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Posted to reviews@spark.apache.org by felixcheung <gi...@git.apache.org> on 2017/01/16 08:00:28 UTC
[GitHub] spark pull request #16596: [SPARK-19237][SPARKR] R should check for java whe...
GitHub user felixcheung opened a pull request:
https://github.com/apache/spark/pull/16596
[SPARK-19237][SPARKR] R should check for java when installed as a package
## What changes were proposed in this pull request?
When SparkR is installed as a R package there might not be any java runtime.
If it is not there spark-submit will just hang, hanging the R IDE/shell.
## How was this patch tested?
manually
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/felixcheung/spark rcheckjava
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/16596.patch
To close this pull request, make a commit to your master/trunk branch
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This closes #16596
----
commit e6bc65dec702c3358c9d730c0fe6c2be305a04ce
Author: Felix Cheung <fe...@hotmail.com>
Date: 2017-01-16T07:51:46Z
check for java
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/16596
Ah we are only changing this on Windows - I see. This is a lower risk change then. LGTM. Merging this to master, branch-2.1
cc @HyukjinKwon
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
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https://github.com/apache/spark/pull/16596
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR] R should check for java when insta...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/16596
`spark-submit` eventually finds java from https://github.com/apache/spark/blob/a115a54399cd4bedb1a5086943a88af6339fbe85/bin/spark-class#L26 and uses the bash builtin `command` - In fact it looks like using `which` is discouraged (http://stackoverflow.com/a/677212/4577954) but I'm not sure if we have a better thing to call from R.
So another way to do this might be to have a `find-java` shell script that is part of the R package (and thus always available) and call that. But handling windows support etc. becomes a pain then ?
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
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**[Test build #74799 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/74799/testReport)** for PR 16596 at commit [`1821e21`](https://github.com/apache/spark/commit/1821e21483904cf2890e9c7ba420d72a20623a74).
* This patch passes all tests.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
retest this please
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR] R should check for java when insta...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/16596
Hmm thinking more about it isn't it better to have a way to handle spark-submit not starting or capturing its error message ? i.e. lack of java could be one of a few reasons why spark-submit might not start and hanging shouldn't be the response to any of that.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR] R should check for java when insta...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
We certainly could - since we never had this before, my thought was to constraint this to only the point where we are installing on presumably a new machine.
If we have it in `launchBackend` we would be doing that check every time? But I wasn't completely sure if there was any other way spark-submit could have run before where `java` was not in path or JAVA_HOME (sym lnk in current directory??)
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR] R should check for java when insta...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
That's what I have been thinking as well. We should probably investigate why the absence of java doesn't result in an error immediately (1), and also look into adding a timeout when we are launching the backend (might be tricker on the R side?).
I do think having a fast, upfront check wouldn't hurt - but obviously better if getting error back immediately (from (1)). I'll dig deeper, I speculate this might be related to the use of `shell` on Windows.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE][WIP] spark-submit should han...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
I've updated the PR title/description and JIRA to reflect what needs to be changed.
Will work on this today.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR] R should check for java when insta...
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https://github.com/apache/spark/pull/16596
**[Test build #71428 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71428/testReport)** for PR 16596 at commit [`e6bc65d`](https://github.com/apache/spark/commit/e6bc65dec702c3358c9d730c0fe6c2be305a04ce).
* This patch passes all tests.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR] R should check for java when insta...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
Yes, this is a but messy. Even `Sys.which` is said to behave differently on Windows, and I haven't found a convenient way to search through path etc. otherwise.
That's remind me - I wanted to test this on Windows first.
But yea, this is why I wasn't sure about putting it in the main flow - if it is only at the very end of `install.spark` even when the user is stuck the first time he would be able to workaround it (restarting, which skip `install.spark`)
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
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updated. pretty sure this is an issue on Windows only
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][WIP] R should check for java when ...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/16596
@felixcheung Any update on this ? Looking through the list of PRs I thought this might be a good one to add to a CRAN submission
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][WIP] R should check for java when ...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
right, i think we could either leave it as-is, or
- check for java like this PR was trying to do originally; or
- check that it resolved to an empty string in spark-submit, and echo an error message - this won't solve the wait with R but it's better than nothing for 1 minute
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][WIP] R should check for java when ...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
so what I found earlier was that when java is not there spark-submit would attempt to launch an empty string, which would not do anything.
the issue is that since we are doing fire-and-wait-to-connect, on the R-side we don't know that nothing is being run, and we keep waiting until it times out. I think we need to change to launch and poll for status, so that we can tell if the command has failed immediately.
but from a preliminary look that seems somewhat challenging to do in R - `shell` doesn't provide this capability to check on the child process.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][WIP] R should check for java when ...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
I've found the root cause, from investigations, but need to test cross platform for the fix.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
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Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/16596
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE][WIP] spark-submit should han...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/16596
Ok sounds good. Since this touches spark-submit scripts that are shared across all languages it would be good to get loop in some other reviewers as well. I can do that once we have the new diff
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][WIP] R should check for java when ...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
@shivaram what do you think about https://github.com/apache/spark/pull/16596#issuecomment-286015752?
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/16596
**[Test build #74801 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/74801/testReport)** for PR 16596 at commit [`e33b50a`](https://github.com/apache/spark/commit/e33b50aae78c79a425ab1e935498919eb0350c97).
* This patch **fails Spark unit tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
Jenkins, retest this please
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by SparkQA <gi...@git.apache.org>.
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https://github.com/apache/spark/pull/16596
**[Test build #74801 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/74801/testReport)** for PR 16596 at commit [`e33b50a`](https://github.com/apache/spark/commit/e33b50aae78c79a425ab1e935498919eb0350c97).
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by HyukjinKwon <gi...@git.apache.org>.
Github user HyukjinKwon commented on the issue:
https://github.com/apache/spark/pull/16596
Thanks for cc'ing me. I just ran a build against branch-2.1.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
Jenkins, retest this please
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by SparkQA <gi...@git.apache.org>.
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https://github.com/apache/spark/pull/16596
**[Test build #74795 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/74795/testReport)** for PR 16596 at commit [`f37c891`](https://github.com/apache/spark/commit/f37c891a8f38c244c8be7c452581778d1e2e180f).
* This patch passes all tests.
* This patch **does not merge cleanly**.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR] R should check for java when insta...
Posted by AmplabJenkins <gi...@git.apache.org>.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
Jenkins, AppVeyor are both passing.
Tested manually on Windows - this change matches the behavior on *nix
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/16596
**[Test build #74833 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/74833/testReport)** for PR 16596 at commit [`e33b50a`](https://github.com/apache/spark/commit/e33b50aae78c79a425ab1e935498919eb0350c97).
* This patch passes all tests.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][WIP] R should check for java when ...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/16596
I think echoing an error message earlier than 1 minute would be useful. What would be the files we'd need to change for that ?
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][WIP] R should check for java when ...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
@shivaram the change would need to be in spark-submit & spark-submit.cmd - that's where JAVA is resolved (and if it's not there, to empty string)
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][WIP] R should check for java when ...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/16596
Ok. That sounds like a bigger change then. I guess we could leave this out of branch-2.1 and do this for 2.2
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/16596
Jenkins, retest this please
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/16596
**[Test build #74812 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/74812/testReport)** for PR 16596 at commit [`e33b50a`](https://github.com/apache/spark/commit/e33b50aae78c79a425ab1e935498919eb0350c97).
* This patch **fails PySpark unit tests**.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
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**[Test build #74833 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/74833/testReport)** for PR 16596 at commit [`e33b50a`](https://github.com/apache/spark/commit/e33b50aae78c79a425ab1e935498919eb0350c97).
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[GitHub] spark pull request #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-subm...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/16596
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR] R should check for java when insta...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/16596
I think having a check for Java is a good idea, but I'm not sure if we should do this inside the install.spark function ? Why not do this before we call `launchBackend` at https://github.com/apache/spark/blob/a115a54399cd4bedb1a5086943a88af6339fbe85/R/pkg/R/sparkR.R#L169
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
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https://github.com/apache/spark/pull/16596
**[Test build #74797 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/74797/testReport)** for PR 16596 at commit [`cc44ae5`](https://github.com/apache/spark/commit/cc44ae577a972c26623e26d349aa2990d33b5b28).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/16596
**[Test build #74796 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/74796/testReport)** for PR 16596 at commit [`61d6ba6`](https://github.com/apache/spark/commit/61d6ba64774b4c65a4c05f69e1a97f4f978464db).
* This patch **fails Spark unit tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #16596: [SPARK-19237][SPARKR][CORE] On Windows spark-submit shou...
Posted by HyukjinKwon <gi...@git.apache.org>.
Github user HyukjinKwon commented on the issue:
https://github.com/apache/spark/pull/16596
Build started: [SparkR][BRANCH-2.1] [](https://ci.appveyor.com/project/spark-test/spark/build/646-PR-16596)
Diff: https://github.com/apache/spark/compare/branch-2.1...spark-test:PR-16596
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