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Initial report on export -J6 to S3 failing due to "transfer already in progress"

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yarikoptic 2020-12-10 21:16:56 +00:00 committed by admin
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<details>
<summary>git annex version</summary>
```shell
git-annex version: 8.20201127-ga19b48c
build flags: Assistant Webapp Pairing Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite S3 WebDAV
dependency versions: aws-0.22 bloomfilter-2.0.1.0 cryptonite-0.26 DAV-1.3.4 feed-1.3.0.1 ghc-8.8.4 http-client-0.6.4.1 persistent-sqlite-2.10.6.2 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.1.0
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2BP512E BLAKE2BP512 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL X*
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar git-lfs httpalso hook external
operating system: linux x86_64
supported repository versions: 8
upgrade supported from repository versions: 0 1 2 3 4 5 6 7
local repository version: 8
```
</details>
<details>
<summary>git annex info on the repo</summary>
```shell
trusted repositories: 0
semitrusted repositories: 5
00000000-0000-0000-0000-000000000001 -- web
00000000-0000-0000-0000-000000000002 -- bittorrent
4d79a724-9e8c-4cce-b030-f712eed3e131 -- snastase@scotty.pni.Princeton.EDU:/mnt/bucket/labs/hasson/snastase/smaug/narratives/derivatives/fmriprep
5f96664f-23ba-4c25-8e75-9ca24fcd46f5 -- nastase@smaug:/mnt/datasets/incoming/nastase/narratives/derivatives/fmriprep [here]
bf6f56f3-f6b7-4df8-9898-a4226dc71400 -- [fcp-indi]
untrusted repositories: 0
transfers in progress: none
available local disk space: 34.8 terabytes (+1 megabyte reserved)
local annex keys: 40135
local annex size: 1.83 terabytes
annexed files in working tree: 50622
size of annexed files in working tree: 1.81 terabytes
bloom filter size: 32 mebibytes (8% full)
backend usage:
MD5E: 50622
```
</details>
```
$ git show git-annex:remote.log | grep indi
bf6f56f3-f6b7-4df8-9898-a4226dc71400 autoenable=true bucket=fcp-indi datacenter=US encryption=none exporttree=yes fileprefix=data/Projects/narratives/derivatives/fmriprep/ host=s3.amazonaws.com name=fcp-indi partsize=1GiB port=80 public=yes publicurl=https://s3.amazonaws.com/fcp-indi storageclass=STANDARD type=S3 versioning=yes timestamp=1607616182.971041s
```
the invocation `git annex export --to "$srname" --jobs 6 master` within our [script](https://github.com/datalad/datalad/issues/5227) ended with `git-annex: export: 360 failed`. Scrolling back through the terminal (in screen) session I saw
```
export fcp-indi sub-345/func/sub-345_task-notthefallintact_space-MNI152NLin2009cAsym_res-native_desc-aseg_dseg.nii.gz ok
export fcp-indi sub-345/func/sub-345_task-notthefallintact_space-MNI152NLin2009cAsym_res-native_desc-preproc_bold.json (transfer already in progress, or unable to take transfer lock) failed
export fcp-indi sub-345/anat/sub-345_hemi-L_pial.surf.gii ok
```
and alike for a few other files (until ran out of history, output was not `tee`-ed into a file).
looking at that specific file
```
/mnt/datasets/incoming/nastase/narratives/derivatives/fmriprep$ ls -l sub-345/func/sub-345_task-notthefallintact_space-MNI152NLin2009cAsym_res-native_desc-preproc_bold.json
lrwxrwxrwx 1 nastase nastase 126 Jul 16 16:33 sub-345/func/sub-345_task-notthefallintact_space-MNI152NLin2009cAsym_res-native_desc-preproc_bold.json -> ../../.git/annex/objects/45/xZ/MD5E-s87--c4e21e8310450e816749d8bd7541292f.json/MD5E-s87--c4e21e8310450e816749d8bd7541292f.json
```
and the content (key) is not unique: there is a good number of files for that key:
```
$ find -lname *MD5E-s87--c4e21e8310450e816749d8bd7541292f.json | nl | tail
215 ./sub-343/func/sub-343_task-notthefallintact_space-MNI152NLin6Asym_res-native_desc-preproc_bold.json
216 ./sub-343/func/sub-343_task-notthefallintact_space-T1w_desc-preproc_bold.json
217 ./sub-344/func/sub-344_task-notthefallintact_desc-preproc_bold.json
218 ./sub-344/func/sub-344_task-notthefallintact_space-MNI152NLin2009cAsym_res-native_desc-preproc_bold.json
219 ./sub-344/func/sub-344_task-notthefallintact_space-MNI152NLin6Asym_res-native_desc-preproc_bold.json
220 ./sub-344/func/sub-344_task-notthefallintact_space-T1w_desc-preproc_bold.json
221 ./sub-345/func/sub-345_task-notthefallintact_desc-preproc_bold.json
222 ./sub-345/func/sub-345_task-notthefallintact_space-MNI152NLin2009cAsym_res-native_desc-preproc_bold.json
223 ./sub-345/func/sub-345_task-notthefallintact_space-MNI152NLin6Asym_res-native_desc-preproc_bold.json
224 ./sub-345/func/sub-345_task-notthefallintact_space-T1w_desc-preproc_bold.json
```
so I guess it is the reason for the "issue".
Note: some of those "duplicate"s were successfully exported, but not the one for which error was reported:
```
nastase@smaug:/mnt/datasets/incoming/nastase/narratives/derivatives/fmriprep$ s3cmd ls s3://fcp-indi/data/Projects/narratives/derivatives/fmriprep/sub-343/func/sub-343_task-notthefallintact_space-MNI152NLin6Asym_res-native_desc-preproc_bold.json
2020-12-10 18:24 87 s3://fcp-indi/data/Projects/narratives/derivatives/fmriprep/sub-343/func/sub-343_task-notthefallintact_space-MNI152NLin6Asym_res-native_desc-preproc_bold.json
nastase@smaug:/mnt/datasets/incoming/nastase/narratives/derivatives/fmriprep$ s3cmd ls s3://fcp-indi/data/Projects/narratives/derivatives/fmriprep/sub-345/func/sub-345_task-notthefallintact_space-MNI152NLin2009cAsym_res-native_desc-preproc_bold.json
<no output was produced>
```
Besides reporting the issue, I also have a question: could I just rerun `export` and it should be "safe/efficient" (not reupload what was already uploaded, thus producing DeleteMarkers, new versionIds etc)? or I would need to manually fixup somehow to avoid heavy/lengthy re-upload?
[[!meta author=yoh]]
[[!tag projects/datalad]]