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GIT checkout failed with lfs enabled

Hi,

 

since yesterday I am having a problem checking out branches in a repository where lfs support is enabled and in use. I tried a fresh clone as well and when checking out the requested branch GIT reports a "fatal: Out of memory, realloc failed":

 

This is the output from Sourcetree:

 

it -c filter.lfs.smudge= -c filter.lfs.required=false -c diff.mnemonicprefix=false -c core.quotepath=false --no-optional-locks clone --branch VDG_development https://______.git D:\________
Cloning into 'D:\____________'...
Filtering content: 12% (2/16)
Filtering content: 12% (2/16), 113.50 MiB | 100.22 MiB/s
Filtering content: 18% (3/16), 113.50 MiB | 100.22 MiB/s
Filtering content: 18% (3/16), 123.34 MiB | 13.38 MiB/s
Filtering content: 25% (4/16), 123.34 MiB | 13.38 MiB/s
Filtering content: 25% (4/16), 137.22 MiB | 11.40 MiB/s
Filtering content: 31% (5/16), 137.22 MiB | 11.40 MiB/s
Filtering content: 37% (6/16), 137.22 MiB | 11.40 MiB/s
Filtering content: 37% (6/16), 257.65 MiB | 22.64 MiB/s
Filtering content: 43% (7/16), 257.65 MiB | 22.64 MiB/s
Filtering content: 43% (7/16), 399.13 MiB | 32.09 MiB/s
Filtering content: 50% (8/16), 399.13 MiB | 32.09 MiB/s
Filtering content: 56% (9/16), 399.48 MiB | 29.89 MiB/s
Filtering content: 62% (10/16), 399.48 MiB | 29.89 MiB/s
Filtering content: 68% (11/16), 399.48 MiB | 29.89 MiB/s
Filtering content: 75% (12/16), 399.48 MiB | 29.89 MiB/s
Filtering content: 75% (12/16), 402.46 MiB | 26.79 MiB/s
Filtering content: 81% (13/16), 402.46 MiB | 26.79 MiB/s
Filtering content: 81% (13/16), 607.22 MiB | 32.76 MiB/s
Filtering content: 87% (14/16), 607.22 MiB | 32.76 MiB/s
Filtering content: 87% (14/16), 1.48 GiB | 27.44 MiB/s
Filtering content: 93% (15/16), 1.48 GiB | 27.44 MiB/s
fatal: Out of memory, realloc failed
Error downloading object: CAD/451300000_vrml_3_mm.wrl (e01f42e): Smudge error: Error reading from media file: write /dev/stdout: The pipe is being closed.: write /dev/stdout: The pipe is being closed.
Errors logged to D:\d______________________\.git\lfs\logs\20220301T151014.8058504.log
Use `git lfs logs last` to view the log.

warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry with 'git restore --source=HEAD :/'

 

Completed with errors, see above.

 

The suggested git lfs logs last gives:

$ git lfs logs last
git-lfs/2.13.2 (GitHub; windows 386; go 1.14.13; git fc664697)
git version 2.30.2.windows.1

$ git-lfs.exe filter-process
Error downloading object: CAD/451300000_vrml_3_mm.wrl (e01f42e): Smudge error: Error reading from media file: write /dev/stdout: The pipe is being closed.: write /dev/stdout: The pipe is being closed.

write /dev/stdout: The pipe is being closed.
Error reading from media file: write /dev/stdout: The pipe is being closed.
github.com/git-lfs/git-lfs/errors.newWrappedError
D:/a/git-lfs/git-lfs/errors/types.go:198
github.com/git-lfs/git-lfs/errors.Wrapf
D:/a/git-lfs/git-lfs/errors/errors.go:85
github.com/git-lfs/git-lfs/lfs.(*GitFilter).readLocalFile
D:/a/git-lfs/git-lfs/lfs/gitfilter_smudge.go:200
github.com/git-lfs/git-lfs/lfs.(*GitFilter).Smudge
D:/a/git-lfs/git-lfs/lfs/gitfilter_smudge.go:81
github.com/git-lfs/git-lfs/commands.smudge
D:/a/git-lfs/git-lfs/commands/command_smudge.go:127
github.com/git-lfs/git-lfs/commands.filterCommand
D:/a/git-lfs/git-lfs/commands/command_filter_process.go:120
github.com/spf13/cobra.(*Command).execute
go/pkg/mod/github.com/spf13/cobra@v0.0.3/command.go:766
github.com/spf13/cobra.(*Command).ExecuteC
go/pkg/mod/github.com/spf13/cobra@v0.0.3/command.go:852
github.com/spf13/cobra.(*Command).Execute
go/pkg/mod/github.com/spf13/cobra@v0.0.3/command.go:800
github.com/git-lfs/git-lfs/commands.Run
D:/a/git-lfs/git-lfs/commands/run.go:105
main.main
D:/a/git-lfs/git-lfs/git-lfs.go:33
runtime.main
go/src/runtime/proc.go:203
runtime.goexit
go/src/runtime/asm_386.s:1337
Smudge error
github.com/git-lfs/git-lfs/errors.newWrappedError
D:/a/git-lfs/git-lfs/errors/types.go:198
github.com/git-lfs/git-lfs/errors.NewSmudgeError
D:/a/git-lfs/git-lfs/errors/types.go:284
github.com/git-lfs/git-lfs/lfs.(*GitFilter).Smudge
D:/a/git-lfs/git-lfs/lfs/gitfilter_smudge.go:85
github.com/git-lfs/git-lfs/commands.smudge
D:/a/git-lfs/git-lfs/commands/command_smudge.go:127
github.com/git-lfs/git-lfs/commands.filterCommand
D:/a/git-lfs/git-lfs/commands/command_filter_process.go:120
github.com/spf13/cobra.(*Command).execute
go/pkg/mod/github.com/spf13/cobra@v0.0.3/command.go:766
github.com/spf13/cobra.(*Command).ExecuteC
go/pkg/mod/github.com/spf13/cobra@v0.0.3/command.go:852
github.com/spf13/cobra.(*Command).Execute
go/pkg/mod/github.com/spf13/cobra@v0.0.3/command.go:800
github.com/git-lfs/git-lfs/commands.Run
D:/a/git-lfs/git-lfs/commands/run.go:105
main.main
D:/a/git-lfs/git-lfs/git-lfs.go:33
runtime.main
go/src/runtime/proc.go:203
runtime.goexit
go/src/runtime/asm_386.s:1337

Current time in UTC:
2022-03-01 14:10:14

ENV:
LocalWorkingDir=D:\___________________
LocalGitDir=D:\________________.git
LocalGitStorageDir=D:\_______________x_\.git
LocalMediaDir=D:\____________________\.git\lfs\objects
LocalReferenceDirs=
TempDir=D:\_________________________\.git\lfs\tmp
ConcurrentTransfers=8
TusTransfers=false
BasicTransfersOnly=false
SkipDownloadErrors=false
FetchRecentAlways=false
FetchRecentRefsDays=7
FetchRecentCommitsDays=0
FetchRecentRefsIncludeRemotes=true
PruneOffsetDays=3
PruneVerifyRemoteAlways=false
PruneRemoteName=origin
LfsStorageDir=D:\______________________________\.git\lfs
AccessDownload=none
AccessUpload=none
DownloadTransfers=basic,lfs-standalone-file
UploadTransfers=basic,lfs-standalone-file
GIT_CONFIG_PARAMETERS='filter.lfs.smudge=' 'filter.lfs.required=false' 'color.branch=false' 'color.diff=false' 'color.status=false' 'diff.mnemonicprefix=false' 'core.quotepath=false'
GIT_DIR=D:/________________________________/.git
GIT_EXEC_PATH=C:/Users/vdg/AppData/Local/Atlassian/SourceTree/git_local/mingw32/libexec/git-core
GIT_LFS_PATH=C:\Program Files\Git LFS
GIT_OPTIONAL_LOCKS=0
GIT_PAGER=cat

Client IP addresses:
fe80::8838:f2c9:60f7:8060 192.168.1.250

 

I assume it has something to do with a CAD file that cannot be downloaded due to a reason I do not see. The destination drive has >50GB available and the sfile is <2GB in size. 

 

Any help is very appreciated.

1 answer

0 votes
Caroline R Atlassian Team Mar 03, 2022

Hi, @vdg, thank you for reaching out to Atlassian Community.

I saw that you created a ticket with our support related to the same question and they have already answered you and resolved the issue.

So in case someone else faces the same issue, I will share the steps we need to follow to fix this problem:

// Skip smudge - We'll download binary files later in a faster batch
git lfs install --skip-smudge

// Do git clone here
git clone ...

// Fetch all the binary files in the new clone
git lfs pull

// Reinstate smudge
git lfs install --force

Kind regards,
Caroline

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