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bug report where git-annex-copy fails with "thread blocked indefinitely in an STM transaction"

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Ilya_Shlyakhter 2019-09-02 18:26:28 +00:00 • committed by admin
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### Please describe the problem.
`git-annex-copy` fails after a short time with the message "thread blocked indefinitely in an STM transaction". Re-running it brings the same problem.
### What steps will reproduce the problem?
See below
### What version of git-annex are you using? On what operating system?
[[!format sh """
(master_env_v156_py36) 14:22 [viral-ngs-benchmarks] $ git annex version
git-annex version: 7.20190819-ge4cecf8
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-8.6.5 http-client-0.5.14 persistent-sql\
ite-2.9.3 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 BLAKE2BP512E BLAKE2BP512 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 git-lfs 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_v156_py36) 14:24 [viral-ngs-benchmarks] $ uname -a
Linux ip-172-31-81-103.ec2.internal 4.14.138-114.102.amzn2.x86_64 #1 SMP Thu Aug 15 15:29:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
(master_env_v156_py36) 14:24 [viral-ngs-benchmarks] $
"""]]
### Please provide any additional information below.
[[!format sh """
# 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
(master_env_v156_py36) 14:18 [viral-ngs-benchmarks] $ git annex --debug --verbose copy -J1 --not --in dnanexus --and --not --in mygs \
--to viral-ngs-benchmarks-s3 --json --json-error-messages > tmp/copy.out.txt 2> tmp/copy.err.txt
C-c C-c
(master_env_v156_py36) 14:22 [viral-ngs-benchmarks] $ git annex copy -J1 --not --in dnanexus --and --not --in mygs --to viral-ngs-ben\
chmarks-s3 --json --json-error-messages > tmp/copy.out.txt 2> tmp/copy.err.txt
(master_env_v156_py36) 14:22 [viral-ngs-benchmarks] $ echo $?
1
(master_env_v156_py36) 14:22 [viral-ngs-benchmarks] $ cat tmp/copy.err.txt
git-annex: thread blocked indefinitely in an STM transaction
git-annex: thread blocked indefinitely in an STM transaction
(
# 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)