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Posted to reviews@spark.apache.org by GitBox <gi...@apache.org> on 2021/03/22 07:51:56 UTC
[GitHub] [spark] Yikun opened a new pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Yikun opened a new pull request #31923:
URL: https://github.com/apache/spark/pull/31923
### What changes were proposed in this pull request?
We added the gnupg installation in https://github.com/apache/spark/pull/30130 , we should do apt update before gnupg isntallation, otherwise we will get a fetch error when package is updated.
### Why are the changes needed?
add a apt-update cmd before gnupg installation to avoid invaild package cache list.
### Does this PR introduce _any_ user-facing change?
No
### How was this patch tested?
K8s Integration test passed
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[GitHub] [spark] Yikun commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
Yikun commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-804017917
```shell
Step 6/12 : RUN apt-get update && apt install -y gnupg && echo "deb http://cloud.r-project.org/bin/linux/debian buster-cran35/" >> /etc/apt/sources.list && (apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF' || apt-key adv --keyserver keys.openpgp.org --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF') && apt-get update && apt install -y -t buster-cran35 r-base r-base-dev && rm -rf /var/cache/apt/*
---> Running in 890d910fdc12
... ...
---> 6fc29805545e
Step 7/12 : COPY R ${SPARK_HOME}/R
---> 98781dd121aa
Step 8/12 : ENV R_HOME /usr/lib/R
```
From [1] (Step 6/12 succeed), we can see the failed fetch problem of [SPARK-34820](https://issues.apache.org/jira/browse/SPARK-34820) had been fixed.
[1] https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder-K8s/40920/consoleFull
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Can one of the admins verify this patch?
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[GitHub] [spark] shaneknapp commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
shaneknapp commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-804161577
thanks for doing this!
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[GitHub] [spark] Ngone51 commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
Ngone51 commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-806304063
Hi all, I'd like to get your continued attention on the K8s integration test issue. After this PR fixed the gnupg installation issue, another issue shows up, which is almost a constant failure:
```shell
- Run SparkR on simple dataframe.R example *** FAILED ***
io.fabric8.kubernetes.client.KubernetesClientException: Failure executing: GET at: https://192.168.39.219:8443/api/v1/namespaces/b80cb1250aba4d92a99fc87b609b2328/pods/spark-test-app-411d038edc8b4e9b8e3761052cd44bd8/log?pretty=false. Message: container "spark-kubernetes-driver" in pod "spark-test-app-411d038edc8b4e9b8e3761052cd44bd8" is waiting to start: trying and failing to pull image. Received status: Status(apiVersion=v1, code=400, details=null, kind=Status, message=container "spark-kubernetes-driver" in pod "spark-test-app-411d038edc8b4e9b8e3761052cd44bd8" is waiting to start: trying and failing to pull image, metadata=ListMeta(_continue=null, remainingItemCount=null, resourceVersion=null, selfLink=null, additionalProperties={}), reason=BadRequest, status=Failure, additionalProperties={}).
at io.fabric8.kubernetes.client.dsl.base.OperationSupport.requestFailure(OperationSupport.java:570)
at io.fabric8.kubernetes.client.dsl.base.OperationSupport.assertResponseCode(OperationSupport.java:509)
at io.fabric8.kubernetes.client.dsl.internal.core.v1.PodOperationsImpl.doGetLog(PodOperationsImpl.java:189)
at io.fabric8.kubernetes.client.dsl.internal.core.v1.PodOperationsImpl.getLog(PodOperationsImpl.java:198)
at io.fabric8.kubernetes.client.dsl.internal.core.v1.PodOperationsImpl.getLog(PodOperationsImpl.java:85)
at org.apache.spark.deploy.k8s.integrationtest.KubernetesSuite.$anonfun$logForFailedTest$3(KubernetesSuite.scala:89)
at org.apache.spark.internal.Logging.logInfo(Logging.scala:57)
at org.apache.spark.internal.Logging.logInfo$(Logging.scala:56)
at org.apache.spark.SparkFunSuite.logInfo(SparkFunSuite.scala:61)
at org.apache.spark.deploy.k8s.integrationtest.KubernetesSuite.$anonfun$logForFailedTest$2(KubernetesSuite.scala:86)
```
And here is [PR](https://github.com/apache/spark/pull/31102) that has tried K8s integration test multiple times but all failed.
Could someone please help take a look? Thanks!
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[GitHub] [spark] SparkQA commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
SparkQA commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-803918760
Kubernetes integration test status failure
URL: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder-K8s/40920/
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[GitHub] [spark] Yikun commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
Yikun commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-803851097
cc @Ngone51
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[GitHub] [spark] Ngone51 commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
Ngone51 commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-809346172
Thanks for the effort @attilapiros
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Posted by GitBox <gi...@apache.org>.
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URL: https://github.com/apache/spark/pull/31923#issuecomment-804066208
**[Test build #136345 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/136345/testReport)** for PR 31923 at commit [`7418fdb`](https://github.com/apache/spark/commit/7418fdb5059b7dc7f94d0b5eef5635c48f6d36e7).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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Posted by GitBox <gi...@apache.org>.
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URL: https://github.com/apache/spark/pull/31923#issuecomment-803864620
**[Test build #136335 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/136335/testReport)** for PR 31923 at commit [`7418fdb`](https://github.com/apache/spark/commit/7418fdb5059b7dc7f94d0b5eef5635c48f6d36e7).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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Can one of the admins verify this patch?
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Can one of the admins verify this patch?
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[GitHub] [spark] Ngone51 commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
Ngone51 commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-804054259
retest this please
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[GitHub] [spark] Ngone51 commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
Ngone51 commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-804054496
Let's retry test see if it's flaky
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Kubernetes integration test status success
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[GitHub] [spark] attilapiros commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
attilapiros commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-807006483
I hope this will help to troubleshoot this and similar errors:
https://github.com/apache/spark/pull/31962
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[GitHub] [spark] attilapiros commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
attilapiros commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-806706204
It would be wonderful to see `kubectl describe pod <pod>` output.
Actually I think I can do this in one of my PR...
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Kubernetes integration test starting
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[GitHub] [spark] dongjoon-hyun closed pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
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dongjoon-hyun closed pull request #31923:
URL: https://github.com/apache/spark/pull/31923
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[GitHub] [spark] attilapiros commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
attilapiros commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-806885852
Of course locally all the tests passed:
```
All tests passed.
...
[INFO] Spark Project Kubernetes Integration Tests ......... SUCCESS [25:12 min]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
```
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[GitHub] [spark] Yikun commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
Yikun commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-804130717
![image](https://user-images.githubusercontent.com/1736354/112010075-f006d400-8b61-11eb-97c0-d48851d09ce4.png)
The SparkPullRequestBuilder-K8s (Kubernetes integration test) back to green again, I think the PR is ready to merge.
[1] https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder-K8s/
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[GitHub] [spark] shaneknapp commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
shaneknapp commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-809801068
fwiw the k8s and minikube installs on the workers haven't changed... i
went through earlier today and ensured that we didn't have any dangling
minikube processes on the workers, and killed any leftover build procs as
well. i'm not sure why this is happening...
also, we'll be upgrading both k8s and mk in the next week or so.
On Mon, Mar 29, 2021 at 5:43 AM wuyi ***@***.***> wrote:
> Thanks for the effort @attilapiros <https://github.com/attilapiros>
>
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[GitHub] [spark] SparkQA commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
SparkQA commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-804056880
**[Test build #136345 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/136345/testReport)** for PR 31923 at commit [`7418fdb`](https://github.com/apache/spark/commit/7418fdb5059b7dc7f94d0b5eef5635c48f6d36e7).
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[GitHub] [spark] SparkQA removed a comment on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
SparkQA removed a comment on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-803855605
**[Test build #136335 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/136335/testReport)** for PR 31923 at commit [`7418fdb`](https://github.com/apache/spark/commit/7418fdb5059b7dc7f94d0b5eef5635c48f6d36e7).
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[GitHub] [spark] attilapiros commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
attilapiros commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-806654897
@Ngone51 I checked the PR you mentioned.
My findings based on [the last failure](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder-K8s/41014/consoleFull).
Here the first error is:
```
- Launcher client dependencies
- SPARK-33615: Launcher client archives *** FAILED ***
io.fabric8.kubernetes.client.KubernetesClientException: Failure executing: GET at: https://192.168.39.147:8443/api/v1/namespaces/09e9c94160d543c1a338f364722d49a6/pods/spark-test-app-c80c78f512574b36b2608f7d92c24503/log?pretty=false. Message: container "spark-kubernetes-driver" in pod "spark-test-app-c80c78f512574b36b2608f7d92c24503" is waiting to start: trying and failing to pull image. Received status: Status(apiVersion=v1, code=400, details=null, kind=Status, message=container "spark-kubernetes-driver" in pod "spark-test-app-c80c78f512574b36b2608f7d92c24503" is waiting to start: trying and failing to pull image, metadata=ListMeta(_continue=null, remainingItemCount=null, resourceVersion=null, selfLink=null, additionalProperties={}), reason=BadRequest, status=Failure, additionalProperties={}).
at io.fabric8.kubernetes.client.dsl.base.OperationSupport.requestFailure(OperationSupport.java:570)
at io.fabric8.kubernetes.client.dsl.base.OperationSupport.assertResponseCode(OperationSupport.java:509)
at io.fabric8.kubernetes.client.dsl.internal.core.v1.PodOperationsImpl.doGetLog(PodOperationsImpl.java:189)
at io.fabric8.kubernetes.client.dsl.internal.core.v1.PodOperationsImpl.getLog(PodOperationsImpl.java:198)
at io.fabric8.kubernetes.client.dsl.internal.core.v1.PodOperationsImpl.getLog(PodOperationsImpl.java:85)
at org.apache.spark.deploy.k8s.integrationtest.KubernetesSuite.$anonfun$logForFailedTest$3(KubernetesSuite.scala:89)
at org.apache.spark.internal.Logging.logInfo(Logging.scala:57)
at org.apache.spark.internal.Logging.logInfo$(Logging.scala:56)
at org.apache.spark.SparkFunSuite.logInfo(SparkFunSuite.scala:61)
at org.apache.spark.deploy.k8s.integrationtest.KubernetesSuite.$anonfun$logForFailedTest$2(KubernetesSuite.scala:86)
...
```
Checking the last successful and first failed ones we can see just a very few differences in the code: the failed one uses a `--archives` and the successful uses `--files`.
I do not think this difference could lead to an error such "is waiting to start: trying and failing to pull image."
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[GitHub] [spark] AmplabJenkins commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
AmplabJenkins commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-803855382
Can one of the admins verify this patch?
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[GitHub] [spark] Ngone51 commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
Ngone51 commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-803854699
ok to test
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[GitHub] [spark] SparkQA commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
SparkQA commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-803855605
**[Test build #136335 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/136335/testReport)** for PR 31923 at commit [`7418fdb`](https://github.com/apache/spark/commit/7418fdb5059b7dc7f94d0b5eef5635c48f6d36e7).
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[GitHub] [spark] AmplabJenkins commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
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[GitHub] [spark] Ngone51 commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
Ngone51 commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-803852696
@Yikun thanks for the quick fix. cc @dongjoon-hyun @holdenk
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Can one of the admins verify this patch?
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[GitHub] [spark] Yikun commented on pull request #31923: [SPARK-34820][K8S][R] add apt-update before gnupg install
Posted by GitBox <gi...@apache.org>.
Yikun commented on pull request #31923:
URL: https://github.com/apache/spark/pull/31923#issuecomment-804023215
```
- Run SparkR on simple dataframe.R example *** FAILED ***
io.fabric8.kubernetes.client.KubernetesClientException: Failure executing: GET at: https://192.168.39.219:8443/api/v1/namespaces/5b12a03f6e2c40308f8c12bf4d9ea3e3/pods/spark-test-app-f99d40879bc94e569c8ae32b79a88970/log?pretty=false. Message: container "spark-kubernetes-driver" in pod "spark-test-app-f99d40879bc94e569c8ae32b79a88970" is waiting to start: trying and failing to pull image. Received status: Status(apiVersion=v1, code=400, details=null, kind=Status, message=container "spark-kubernetes-driver" in pod "spark-test-app-f99d40879bc94e569c8ae32b79a88970" is waiting to start: trying and failing to pull image, metadata=ListMeta(_continue=null, remainingItemCount=null, resourceVersion=null, selfLink=null, additionalProperties={}), reason=BadRequest, status=Failure, additionalProperties={}).
at io.fabric8.kubernetes.client.dsl.base.OperationSupport.requestFailure(OperationSupport.java:570)
at io.fabric8.kubernetes.client.dsl.base.OperationSupport.assertResponseCode(OperationSupport.java:509)
at io.fabric8.kubernetes.client.dsl.internal.core.v1.PodOperationsImpl.doGetLog(PodOperationsImpl.java:189)
at io.fabric8.kubernetes.client.dsl.internal.core.v1.PodOperationsImpl.getLog(PodOperationsImpl.java:198)
at io.fabric8.kubernetes.client.dsl.internal.core.v1.PodOperationsImpl.getLog(PodOperationsImpl.java:85)
at org.apache.spark.deploy.k8s.integrationtest.KubernetesSuite.$anonfun$logForFailedTest$3(KubernetesSuite.scala:89)
at org.apache.spark.internal.Logging.logInfo(Logging.scala:57)
at org.apache.spark.internal.Logging.logInfo$(Logging.scala:56)
at org.apache.spark.SparkFunSuite.logInfo(SparkFunSuite.scala:61)
at org.apache.spark.deploy.k8s.integrationtest.KubernetesSuite.$anonfun$logForFailedTest$2(KubernetesSuite.scala:86)
...
```
and there are still some other errors triggerd, looks like unrelated.
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