79 lines
5.4 KiB
Markdown
79 lines
5.4 KiB
Markdown
### Please describe the problem.
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I keep encountering situations where git-annex fails on parallel operations. Retrying the operation several times sometimes resolves the issue -- it would be better if git-annex could be configured to do the retrying. I have set `annex.retry` and `annex.retry-delay`, but these don't seem to be enough. Maybe, these config vars could apply to all idempotent operations?
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I have also seen a parallel copy operation, copying to an S3 remote, hang indefinitely. Killing and retrying fixed the problem; it would be better if git-annex could have a timeout for operations, and kill and retry them automatically. This especially matters when building scripts on top of git-annex.
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### What steps will reproduce the problem?
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I have included the log below. I think repeatedly trying to copy from a local repo to an S3 bucket (non-export-tree) should eventually reproduce the problem.
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### What version of git-annex are you using? On what operating system?
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[[!format sh """
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(master_env_v142_py36) 17:29 [v1.23.0-rc29] $ git annex version
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git-annex version: 7.20190626-g85db42d
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build flags: Assistant Webapp Pairing S3 WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
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dependency versions: aws-0.21.1 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.1.0 ghc-8.4.2 http-client-0.5.14 persistent-sql\
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ite-2.9.2 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0
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key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_2\
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24 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE\
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2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256\
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BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL
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remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar hook external
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operating system: linux x86_64
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supported repository versions: 5 7
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upgrade supported from repository versions: 0 1 2 3 4 5 6
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local repository version: 5
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(master_env_v142_py36) 17:32 [v1.23.0-rc29] $ uname -a
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Linux ip-172-31-81-187.ec2.internal 4.14.128-112.105.amzn2.x86_64 #1 SMP Wed Jun 19 16:53:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
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(master_env_v142_py36) 17:32 [v1.23.0-rc29] $
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# End of transcript or log.
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"""]]
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### Please provide any additional information below.
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[[!format sh """
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# If you can, paste a complete transcript of the problem occurring here.
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# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
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2019-07-03 17:30:22,365 - workflow_utils:289:_run - INFO - running command: git annex copy . --to=viral-ngs-benchmarks-s3 cwd=/dev/shm\
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/crogrun_190703_162305_36571/viral-ngs-benchmarks kw={'cwd': '/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks/benchmarks/rab\
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ies200/analysis-FK7B7p00761bfq2516zQb58F/benchmark_variants/v1.23.0-rc29'}
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copy assemble_denovo.wdl (checking viral-ngs-benchmarks-s3...) ok
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copy input-spec.json (checking viral-ngs-benchmarks-s3...) ok
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copy analysis_labels.json (checking viral-ngs-benchmarks-s3...) (to viral-ngs-benchmarks-s3...) ok
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copy inputs-git-links.json (checking viral-ngs-benchmarks-s3...) (to viral-ngs-benchmarks-s3...) ok
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copy inputs-local.json (checking viral-ngs-benchmarks-s3...) (to viral-ngs-benchmarks-s3...) ok
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copy inputs-orig.json (checking viral-ngs-benchmarks-s3...) (to viral-ngs-benchmarks-s3...) ok
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copy imports.zip (checking viral-ngs-benchmarks-s3...) (to viral-ngs-benchmarks-s3...) ok
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(recording state in git...)
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error: git-annex died of signal 11
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2019-07-03 17:30:23,429 - workflow_utils:303:_run - INFO - RETRY 2 sleep 4 command (cwd=/dev/shm/crogrun_190703_162305_36571/viral-ngs\
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-benchmarks, kw={'cwd': '/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks/benchmarks/rabies200/analysis-FK7B7p00761bfq2516zQb\
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58F/benchmark_variants/v1.23.0-rc29'}) in 1.063608169555664s: git annex copy . --to=viral-ngs-benchmarks-s3 exception Command 'git ann\
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ex copy . --to=viral-ngs-benchmarks-s3' returned non-zero exit status 139.
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2019-07-03 17:30:27,434 - workflow_utils:312:_run - INFO - command (cwd=/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks, kw=\
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{'cwd': '/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks/benchmarks/rabies200/analysis-FK7B7p00761bfq2516zQb58F/benchmark_va\
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riants/v1.23.0-rc29'}) FAILED in 5.06814980506897s: git annex copy . --to=viral-ngs-benchmarks-s3
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copy assemble_denovo.wdl (checking viral-ngs-benchmarks-s3...) ok
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copy analysis_labels.json (checking viral-ngs-benchmarks-s3...) ok
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copy inputs-local.json (checking viral-ngs-benchmarks-s3...) ok
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copy inputs-orig.json (checking viral-ngs-benchmarks-s3...) ok
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copy input-spec.json (checking viral-ngs-benchmarks-s3...) ok
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copy imports.zip (checking viral-ngs-benchmarks-s3...) ok
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copy inputs-git-links.json (checking viral-ngs-benchmarks-s3...) ok
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2019-07-03 17:30:27,952 - workflow_utils:312:_run - INFO - command (cwd=/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks, kw=\
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{'cwd': '/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks/benchmarks/rabies200/analysis-FK7B7p00761bfq2516zQb58F/benchmark_va\
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riants/v1.23.0-rc29'}) SUCCEEDED in 5.586166620254517s: git annex copy . --to=viral-ngs-benchmarks-s3
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2
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# End of transcript or log.
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"""]]
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### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
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