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Read hdfs file hit exception during the read process #14909

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Nizifan opened this issue Jan 25, 2022 · 7 comments
Open

Read hdfs file hit exception during the read process #14909

Nizifan opened this issue Jan 25, 2022 · 7 comments
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area-fuse Alluxio fuse integration priority-medium stale The PR/Issue does not have recent activities and will be closed automatically type-bug This issue is about a bug

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@Nizifan
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Nizifan commented Jan 25, 2022

Alluxio Version:
2.7

Describe the bug
When try to read ~2G file from hdfs through Alluxio, command hit IO error and log indicate Java exception is hit.
And it read out correct but partial result

[root@jssz-aiinf-ml-gpu-04 alluxio-2.7.2]# cp /runtime-mnt/alluxio/ogv/ogv-hdfs/alluxio-fuse/ogv-hdfs/log_date=20220117/part-00000-ed2f54f4-90f1-4551-a05b-96345174ad5f.c000 ./temp.out
cp: error reading '/runtime-mnt/alluxio/ogv/ogv-hdfs/alluxio-fuse/ogv-hdfs/log_date=20220117/part-00000-ed2f54f4-90f1-4551-a05b-96345174ad5f.c000': Input/output error
cp: failed to extend './temp.out': Input/output error
[root@jssz-aiinf-ml-gpu-04 alluxio-2.7.2]# cp /runtime-mnt/alluxio/ogv/ogv-hdfs/alluxio-fuse/ogv-hdfs/log_date=20220120/part-00000-aaec8d8d-aa5b-4562-ba70-319e47380d64.c000 ./temp1.out
cp: error reading '/runtime-mnt/alluxio/ogv/ogv-hdfs/alluxio-fuse/ogv-hdfs/log_date=20220120/part-00000-aaec8d8d-aa5b-4562-ba70-319e47380d64.c000': Input/output error
cp: failed to extend './temp1.out': Input/output error
[root@jssz-aiinf-ml-gpu-04 alluxio-2.7.2]# ls -lh
-rw-r--r-- 1 root root 2.2M Jan 25 10:46 temp.out
-rw-r--r-- 1 root root 1.1G Jan 25 10:47 temp1.out

original files are around 2.4g
[root@jssz-aiinf-ml-gpu-04 alluxio-2.7.2]# ls -lh /runtime-mnt/alluxio/ogv/ogv-hdfs/alluxio-fuse/ogv-hdfs/log_date=20220120/part-00000-aaec8d8d-aa5b-4562-ba70-319e47380d64.c000
-rw-r--r-- 1 root root 2.4G Jan 21 06:45 /runtime-mnt/alluxio/ogv/ogv-hdfs/alluxio-fuse/ogv-hdfs/log_date=20220120/part-00000-aaec8d8d-aa5b-4562-ba70-319e47380d64.c000

Logs:
2022-01-25 08:54:49,852 ERROR AlluxioJniFuseFileSystem - Failed to read, path: /ogv-hdfs/log_date=20220117/part-00000-ed2f54f4-90f1-4551-a05b-96345174ad5f.c000 size: 131072 offset: 2228224
java.lang.IllegalArgumentException
at java.nio.Buffer.position(Buffer.java:244)
at alluxio.client.block.stream.SharedGrpcDataReader.readChunk(SharedGrpcDataReader.java:115)
at alluxio.client.block.stream.BlockInStream.readChunk(BlockInStream.java:489)
at alluxio.client.block.stream.BlockInStream.read(BlockInStream.java:316)
at alluxio.client.file.AlluxioFileInStream.read(AlluxioFileInStream.java:184)
at alluxio.fuse.AlluxioJniFuseFileSystem.readInternal(AlluxioJniFuseFileSystem.java:408)
at alluxio.fuse.AlluxioJniFuseFileSystem.lambda$read$5(AlluxioJniFuseFileSystem.java:383)
at alluxio.fuse.AlluxioFuseUtils.call(AlluxioFuseUtils.java:318)
at alluxio.fuse.AlluxioJniFuseFileSystem.read(AlluxioJniFuseFileSystem.java:383)
at alluxio.jnifuse.AbstractFuseFileSystem.readCallback(AbstractFuseFileSystem.java:180)

If use hdfs client, it can read out correct result correctly.

@Nizifan Nizifan added the type-bug This issue is about a bug label Jan 25, 2022
@LuQQiu LuQQiu added area-fuse Alluxio fuse integration priority-medium labels Jan 25, 2022
@LuQQiu
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LuQQiu commented Jan 25, 2022

@Nizifan why enabling alluxio.fuse.shared.caching.reader.enabled to use SharedGrpcDataReader?
@apc999 did we plan to remove SharedGrpcDataReader and what's the reason for us to plan to remove that class?

@apc999
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apc999 commented Jan 25, 2022

to @LuQQiu No concrete plan to remove SharedGrpcDataReader until we figure out more efficient way to reuse transport

to @Nizifan flag alluxio.fuse.shared.caching.reader.enabled is experimental, we do not recommend turning on this flag

@Nizifan
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Nizifan commented Jan 26, 2022

Thanks @apc999 and @LuQQiu
Disabling this setting solve the problem, and it is not a 100% bug, we try several hdfs read but only 1 instance hit this issue but it is 100% repro in this case.

The config is copy-paste from fluid from fluid default. Do you suggest to turn it off in fluid?
setDefaultProperties(runtime, value, "alluxio.fuse.shared.caching.reader.enabled", "true")

@Nizifan Nizifan closed this as completed Jan 26, 2022
@cheyang
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cheyang commented Jan 26, 2022

@apc999 @LuQQiu The properties are for the same blocks concurrent access from #12453 which is from Microsoft. Could you make double check?

@cheyang cheyang reopened this Jan 26, 2022
@Nizifan
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Nizifan commented Jan 26, 2022

If this config will greatly impact read performance should we dig a bit more on while shared reader will cause read failure?

@LuQQiu
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LuQQiu commented Jan 27, 2022

We will take a deeper look into the issue and see how to handle the multiple threads/processes read same big file issue

cheyang pushed a commit to fluid-cloudnative/fluid that referenced this issue Feb 14, 2022
zwwhdls pushed a commit to ldd91/fluid that referenced this issue Mar 18, 2022
cheyang added a commit to fluid-cloudnative/fluid that referenced this issue Mar 22, 2022
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* Support fuse sidecar injection (#1401)

* Support serverless, To #38946668

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Fix ut, To #38946668

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* Signed-off-by: cheyang <[email protected]>

Add mountPropagationHostToContainer, To #37688693

Add testcase, To #37688693

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Fix building docker image for init user (#1408)

* Fix docker build for cento8, To #37688693

Signed-off-by: cheyang <[email protected]>

* Fix docker build for cento8, To #37688693

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Build docker image (#1409)

* Build docker image, To #37688693

Signed-off-by: cheyang <[email protected]>

* Build docker image, To #37688693

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Make  AlluxioRuntime support serverless (#1411)

* Support Alluxio, To #37688693

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* Support Alluxio, To #37688693

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* Support Alluxio, To #37688693

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Support pod's namespace is empty in webhook (#1413)

* Support namespace is empty, To #37688693

Signed-off-by: cheyang <[email protected]>

* Support namespace is empty, To #37688693

Signed-off-by: cheyang <[email protected]>

* Support namespace is empty, To #37688693

Signed-off-by: cheyang <[email protected]>

* Support namespace is empty, To #37688693

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* Support namespace is empty, To #37688693

Signed-off-by: cheyang <[email protected]>

* Support namespace is empty, To #37688693

Signed-off-by: cheyang <[email protected]>

* Support namespace is empty, To #37688693

Signed-off-by: cheyang <[email protected]>

* Support namespace is empty, To #37688693

Signed-off-by: cheyang <[email protected]>

* Support namespace is empty, To #37688693

Signed-off-by: cheyang <[email protected]>

* Support namespace is empty, To #37688693

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* Support namespace is empty, To #37688693

Signed-off-by: cheyang <[email protected]>

* Support namespace is empty, To #37688693

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

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Signed-off-by: zwwhdls <[email protected]>

* Fix redundant type from array, slice, or map composite literal (#1417)

* Fix redundant type from array, slice, or map composite literal, To #37688693

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* Fix redundant type from array, slice, or map composite literal, To #37688693

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* Fix dataload cannot be cleaned up bug (#1421)

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* update goosefs default image to 1.2.0

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* Fix update dataload status error (#1433)

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* Fix some incorrect usage of `ctx.Name`

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* Fix update dataload status error, To #37688693 (#1437)

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Signed-off-by: zwwhdls <[email protected]>

* disable fuse.shared.caching.reader.enabled for alluxio and goosefs, see Alluxio/alluxio#14909 (#1400)

Signed-off-by: nizifan <[email protected]>

Co-authored-by: nizifan <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Update ADOPTERS.md (#1440)

Pxing AI training platform is testing fluid.

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* Remove the removed watermark configure key (#1439)

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Signed-off-by: zwwhdls <[email protected]>

* add feature gate to csi (#1444)

* add feature gate to csi

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* update period to time.Duration & delete period in config

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* Make controllers handle deprecated runtime workers (#1447)

* Handle deprecated worker daemonset

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* Record events to runtime when detecting deprecated runtimes

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* More detailed event message

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* Add ut for Alluxio and GooseFs

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Signed-off-by: zwwhdls <[email protected]>

* Docs for serverless (#1443)

* Add doc, To #37688693

Signed-off-by: cheyang <[email protected]>

* Build docker image, To #39482462

Signed-off-by: cheyang <[email protected]>

* Build docker image, To #39482462

Signed-off-by: cheyang <[email protected]>

* Build docker image, To #39482462

Signed-off-by: cheyang <[email protected]>

* Fluid for serverless, To #37688693

Signed-off-by: cheyang <[email protected]>

* Fluid for serverless, To #37688693

Signed-off-by: cheyang <[email protected]>

* Fluid for serverless, To #37688693

Signed-off-by: cheyang <[email protected]>

* Fluid for serverless, To #37688693

Signed-off-by: cheyang <[email protected]>

* Fluid for serverless, To #37688693

Signed-off-by: cheyang <[email protected]>

* Fix update dataload status error, To #37688693

Signed-off-by: cheyang <[email protected]>

* Build docker image, To #39482462

Signed-off-by: cheyang <[email protected]>

* Build docker image, To #39482462

Signed-off-by: cheyang <[email protected]>

* Build docker image, To #39482462

Signed-off-by: cheyang <[email protected]>

* Fluid for serverless, To #37688693

Signed-off-by: cheyang <[email protected]>

* Fluid for serverless, To #37688693

Signed-off-by: cheyang <[email protected]>

* Fluid for serverless, To #37688693

Signed-off-by: cheyang <[email protected]>

* Fluid for serverless, To #37688693

Signed-off-by: cheyang <[email protected]>

* Add volume, To #38946668

Signed-off-by: cheyang <[email protected]>

* Add volume, To #38946668

Signed-off-by: cheyang <[email protected]>

* Add doc, To #38946668

Signed-off-by: cheyang <[email protected]>

* Add doc, To #38946668

Signed-off-by: cheyang <[email protected]>

* Fluid for serverless, To #37688693

Signed-off-by: cheyang <[email protected]>

* Add doc, To #38946668

Signed-off-by: cheyang <[email protected]>

* Fix ut, To #38946668

Signed-off-by: cheyang <[email protected]>

* Fix ut, To #38946668

Signed-off-by: cheyang <[email protected]>

* Update docs, To #39482462

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Build docker image, To #39482462 (#1449)

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Use less job worker threads (#1450)

Signed-off-by: ssz1997 <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Build for GROMACS, To #26045127 (#1452)

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Fix csi daemonset template typo (#1454)

Signed-off-by: TrafalgarZZZ <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Update Fluid documents (#1455)

* Update Fluid docs

Signed-off-by: TrafalgarZZZ <[email protected]>

* Update Fluid docs

Signed-off-by: TrafalgarZZZ <[email protected]>

* Update Fluid docs

Signed-off-by: TrafalgarZZZ <[email protected]>

* Update Fluid docs

Signed-off-by: TrafalgarZZZ <[email protected]>

* Update Fluid docs

Signed-off-by: TrafalgarZZZ <[email protected]>

* Update Fluid docs

Signed-off-by: TrafalgarZZZ <[email protected]>

* Update Fluid docs

Signed-off-by: TrafalgarZZZ <[email protected]>

* Update Fluid docs

Signed-off-by: TrafalgarZZZ <[email protected]>

* Update Fluid docs(en)

Signed-off-by: TrafalgarZZZ <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* fix gen_sdk.sh (#1457)

* fix gen_sdk.sh

Signed-off-by: zwwhdls <[email protected]>

* fix swagger url & delete useless env

Signed-off-by: zwwhdls <[email protected]>

* keep swagger-codegen-cli.jar in project

Signed-off-by: zwwhdls <[email protected]>

* Archive deprecated Fluid documents (#1458)

* Archive deprecated documents

Signed-off-by: TrafalgarZZZ <[email protected]>

* Update data colocality document

Signed-off-by: TrafalgarZZZ <[email protected]>

* Update pod schedule document

Signed-off-by: TrafalgarZZZ <[email protected]>

* Refactor table of contents

Signed-off-by: TrafalgarZZZ <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Remove cache dir from sidecar pod (#1462)

* Remove cache dir, To #39482462

Signed-off-by: cheyang <[email protected]>

* Remove cache dir, To #39482462

Signed-off-by: cheyang <[email protected]>

* Remove cache dir, To #39482462

Signed-off-by: cheyang <[email protected]>

* Add Fuse container sidecar test, To #37688693

Signed-off-by: cheyang <[email protected]>

* Add Fuse container sidecar test, To #37688693

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Add Docker image for fuse without cachedir, To #37688693 (#1464)

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Disable timezone hostpath for jindoruntime, To #37688693 (#1466)

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Build docker image for disabling timezone hostpath for jindoruntime, To #37688693 (#1468)

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* remove duplicates in Makefile (#1472)

Signed-off-by: wangxu <[email protected]>

Co-authored-by: wangxu <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Add community meeting information (#1471)

Add community meeting information

Signed-off-by: zwwhdls <[email protected]>

* Update docs for enabling cache dir (#1474)

* Add samples, To #26045127

Signed-off-by: cheyang <[email protected]>

* Docs for knative, To #37688693

Signed-off-by: cheyang <[email protected]>

* Docs for knative, To #37688693

Signed-off-by: cheyang <[email protected]>

* Add samples, To #26045127

Signed-off-by: cheyang <[email protected]>

* Add samples, To #26045127

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Update install document (#1475)

* Update install document (zhCN)

Signed-off-by: TrafalgarZZZ <[email protected]>

* Update install document (en)

Signed-off-by: TrafalgarZZZ <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* enable run jindo dataload synchronously (#1477)

Signed-off-by: frankleaf <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* fix jindo some parameter to bool (#1480)

* enable run jindo dataload synchronously

Signed-off-by: frankleaf <[email protected]>

* fix digit to ture/false

Signed-off-by: frankleaf <[email protected]>

* fix test

Signed-off-by: frankleaf <[email protected]>

* fix test

Signed-off-by: frankleaf <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Build docker image for release v0.7.0, To #39482692 (#1484)

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Fix typo in install document (#1486)

Signed-off-by: TrafalgarZZZ <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* modify bug : clean cache in Alluxio due to unknown linux release version  (#1487)

* remove duplicates in Makefile

Signed-off-by: wangxu <[email protected]>

* deal with issue 1476

Signed-off-by: wangxu <[email protected]>

Co-authored-by: wangxu <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Build docker image for 0.7.0 release, To #37688693 (#1488)

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Added what's new for v0.7 release (#1489)

Added what's new for v0.7 release

Signed-off-by: zwwhdls <[email protected]>

* Branch v0.8.0 (#1491)

* Update for v0.8.0, To #39858484

Signed-off-by: cheyang <[email protected]>

* Update for v0.8.0, To #39858484

Signed-off-by: cheyang <[email protected]>

* Update for v0.8.0, To #39858484

Signed-off-by: cheyang <[email protected]>

* Update for v0.8.0, To #39858484

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Update CHANGELOG.md for 0.7 (#1493)

Signed-off-by: TrafalgarZZZ <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* modify userguide faq zh & en documents (#1502)

Signed-off-by: Javy <[email protected]>

Co-authored-by: Javy <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Default csi fuse recovery to false (#1501)

Signed-off-by: TrafalgarZZZ <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* add s3 example (#1494)

* add s3 example

Signed-off-by: ssz1997 <[email protected]>

* Update s3 doc

Signed-off-by: ssz1997 <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Fix misleading logging in csi plugin (#1499)

* Fix logging for init opts, To #39858484

Signed-off-by: cheyang <[email protected]>

* Fix logging for init opts, To #39858484

Signed-off-by: cheyang <[email protected]>

* Fix logging for init opts, To #39858484

Signed-off-by: cheyang <[email protected]>

* Fix logging for init opts, To #39858484

Signed-off-by: cheyang <[email protected]>

* Fix logging for init opts, To #39858484

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* add dmetasoul.com in adopters documents (#1506)

Signed-off-by: Javy <[email protected]>

Co-authored-by: Javy <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Updated the Chinese version of the S3 configuration document and added the English version of the S3 configuration document (#1507)

Signed-off-by: Javy <[email protected]>

Co-authored-by: Javy <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Build docker image for env in csi plugin, To #37688693 (#1509)

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* Build docker image for env in csi plugin, To #37688693 (#1510)

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* fix update JindoRuntime doc link (#1512)

Signed-off-by: frankleaf <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* update data_warm_up's document (#1513)

* Updated the Chinese version of the S3 configuration document and added the English version of the S3 configuration document

Signed-off-by: Javy <[email protected]>

* update data_warm_up's document

Signed-off-by: Javy <[email protected]>

Co-authored-by: Javy <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* add fluid app controller (#1481)

* add fluid app controller

Signed-off-by: zwwhdls <[email protected]>

* fix ci-lint

Signed-off-by: zwwhdls <[email protected]>

* add watch func in fluid app controller

Signed-off-by: zwwhdls <[email protected]>

* fix chart lint

Signed-off-by: zwwhdls <[email protected]>

* reduce rbac

Signed-off-by: zwwhdls <[email protected]>

* use util instead

Signed-off-by: zwwhdls <[email protected]>

* update rbac

Signed-off-by: zwwhdls <[email protected]>

* update rbac

Signed-off-by: zwwhdls <[email protected]>

* Update committer name list. (#1517)

* update committer and maintainer file

Signed-off-by: RongGu <[email protected]>

* update Governance file to add committer list file

Signed-off-by: RongGu <[email protected]>

* fix typo

Signed-off-by: RongGu <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* fix pod/exec rbac in application controller (#1518)

Signed-off-by: zwwhdls <[email protected]>

* Build docker image for fluid app controller (#1516)

* Add samples, To #40056722

Signed-off-by: cheyang <[email protected]>

* Add samples, To #40056722

Signed-off-by: cheyang <[email protected]>

* Update dockerfile, To #40056722

Signed-off-by: cheyang <[email protected]>

* Update dockerfile, To #40056722

Signed-off-by: cheyang <[email protected]>

* Build docker image for env in csi plugin, To #37688693

Signed-off-by: cheyang <[email protected]>
Signed-off-by: zwwhdls <[email protected]>

* fix application controller image (#1519)

Signed-off-by: zwwhdls <[email protected]>

* warmup in each fuse pod

Signed-off-by: zwwhdls <[email protected]>

* fix test

Signed-off-by: zwwhdls <[email protected]>

* update default fuse image

Signed-off-by: zwwhdls <[email protected]>

* add label in job

Signed-off-by: zwwhdls <[email protected]>

* fix DCO

Signed-off-by: zwwhdls <[email protected]>

* update typo

Signed-off-by: zwwhdls <[email protected]>

* update dataload rbac to juicefs controller

Signed-off-by: zwwhdls <[email protected]>

* update warmup to worker

Signed-off-by: zwwhdls <[email protected]>

* add timeout & deal with error

Signed-off-by: zwwhdls <[email protected]>

* set timeout in dataload options

Signed-off-by: zwwhdls <[email protected]>

* update configmap volume mode 0755 & add unit test

Signed-off-by: zwwhdls <[email protected]>

Co-authored-by: TzZtzt <[email protected]>
Co-authored-by: zwwhdls <[email protected]>
Co-authored-by: cheyang <[email protected]>
Co-authored-by: Nizifan <[email protected]>
Co-authored-by: nizifan <[email protected]>
Co-authored-by: frankleaf <[email protected]>
Co-authored-by: Allen <[email protected]>
Co-authored-by: Shawn Sun <[email protected]>
Co-authored-by: xieydd <[email protected]>
Co-authored-by: Ruofeng Lei <[email protected]>
Co-authored-by: peterchenhc <[email protected]>
Co-authored-by: maobaolong <[email protected]>
Co-authored-by: haoeeeee <[email protected]>
Co-authored-by: wangxu <[email protected]>
Co-authored-by: Rong Gu <[email protected]>
Co-authored-by: Javy <[email protected]>
Co-authored-by: Javy <[email protected]>
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This issue has been automatically marked as stale because it has not had recent activity. It will be closed in two weeks if no further activity occurs. Thank you for your contributions.

@github-actions github-actions bot added the stale The PR/Issue does not have recent activities and will be closed automatically label Jan 28, 2023
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area-fuse Alluxio fuse integration priority-medium stale The PR/Issue does not have recent activities and will be closed automatically type-bug This issue is about a bug
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