Please describe the problem.

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?

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.

What steps will reproduce the problem?

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.

What version of git-annex are you using? On what operating system?

(master_env_v142_py36) 17:29  [v1.23.0-rc29] $ git annex version
git-annex version: 7.20190626-g85db42d
build flags: Assistant Webapp Pairing S3 WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
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\
ite-2.9.2 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_2\
24 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE\
2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256\
 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar hook external
operating system: linux x86_64
supported repository versions: 5 7
upgrade supported from repository versions: 0 1 2 3 4 5 6
local repository version: 5
(master_env_v142_py36) 17:32  [v1.23.0-rc29] $ uname -a
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
(master_env_v142_py36) 17:32  [v1.23.0-rc29] $

# End of transcript or log.

Please provide any additional information below.

# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log

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\
/crogrun_190703_162305_36571/viral-ngs-benchmarks kw={'cwd': '/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks/benchmarks/rab\
ies200/analysis-FK7B7p00761bfq2516zQb58F/benchmark_variants/v1.23.0-rc29'}
copy assemble_denovo.wdl (checking viral-ngs-benchmarks-s3...) ok
copy input-spec.json (checking viral-ngs-benchmarks-s3...) ok
copy analysis_labels.json (checking viral-ngs-benchmarks-s3...) (to viral-ngs-benchmarks-s3...) ok
copy inputs-git-links.json (checking viral-ngs-benchmarks-s3...) (to viral-ngs-benchmarks-s3...) ok
copy inputs-local.json (checking viral-ngs-benchmarks-s3...) (to viral-ngs-benchmarks-s3...) ok
copy inputs-orig.json (checking viral-ngs-benchmarks-s3...) (to viral-ngs-benchmarks-s3...) ok
copy imports.zip (checking viral-ngs-benchmarks-s3...) (to viral-ngs-benchmarks-s3...) ok
(recording state in git...)
error: git-annex died of signal 11
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\
-benchmarks, kw={'cwd': '/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks/benchmarks/rabies200/analysis-FK7B7p00761bfq2516zQb\
58F/benchmark_variants/v1.23.0-rc29'}) in 1.063608169555664s: git annex copy . --to=viral-ngs-benchmarks-s3 exception Command 'git ann\
ex copy . --to=viral-ngs-benchmarks-s3' returned non-zero exit status 139.
2019-07-03 17:30:27,434 - workflow_utils:312:_run - INFO - command (cwd=/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks, kw=\
{'cwd': '/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks/benchmarks/rabies200/analysis-FK7B7p00761bfq2516zQb58F/benchmark_va\
riants/v1.23.0-rc29'}) FAILED in 5.06814980506897s: git annex copy . --to=viral-ngs-benchmarks-s3
copy assemble_denovo.wdl (checking viral-ngs-benchmarks-s3...) ok
copy analysis_labels.json (checking viral-ngs-benchmarks-s3...) ok
copy inputs-local.json (checking viral-ngs-benchmarks-s3...) ok
copy inputs-orig.json (checking viral-ngs-benchmarks-s3...) ok
copy input-spec.json (checking viral-ngs-benchmarks-s3...) ok
copy imports.zip (checking viral-ngs-benchmarks-s3...) ok
copy inputs-git-links.json (checking viral-ngs-benchmarks-s3...) ok
2019-07-03 17:30:27,952 - workflow_utils:312:_run - INFO - command (cwd=/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks, kw=\
{'cwd': '/dev/shm/crogrun_190703_162305_36571/viral-ngs-benchmarks/benchmarks/rabies200/analysis-FK7B7p00761bfq2516zQb58F/benchmark_va\
riants/v1.23.0-rc29'}) SUCCEEDED in 5.586166620254517s: git annex copy . --to=viral-ngs-benchmarks-s3
2


# End of transcript or log.

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)