Clone freezes at Compressing objects: 96%

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Platform notice: Server and Data Center only. This article only applies to Atlassian products on the Server and Data Center platforms.

Support for Server* products ended on February 15th 2024. If you are running a Server product, you can visit the Atlassian Server end of support announcement to review your migration options.

*Except Fisheye and Crucible

Summary

Performing a clone operation freezes at "Compressing objects: 96%" on the client side.

> git clone <bitbucket base url>/scm/<project>/<repository>.git
...
Cloning into '.'...
remote: Counting objects: 453, done.
remote: Compressing objects:  96% (381/396)

Environment

Bitbucket Data Center 6.10.1
Linux Kernel 2.6.32-573.el6.x86_64

Diagnosis

  • The same clone operation also fails when executed from Sourcetree and locally on the server.
  • Navigating to the repository on Bitbucket UI shows a 500 error

  • Using GNU Debugger the following entries are found pointing to threads blocked in lock_wait_private()


Click here to expand... 
Attaching to process 14670
Reading symbols from /usr/local/git/libexec/git-core/git...done.
Reading symbols from /lib64/libz.so.1...(no debugging symbols found)...done.
Loaded symbols for /lib64/libz.so.1
Reading symbols from /lib64/libpthread.so.0...(no debugging symbols found)...done.
[New LWP 14679]
[New LWP 14678]
[New LWP 14673]
[Thread debugging using libthread_db enabled]
Loaded symbols for /lib64/libpthread.so.0
Reading symbols from /lib64/librt.so.1...(no debugging symbols found)...done.
Loaded symbols for /lib64/librt.so.1
Reading symbols from /lib64/libc.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/libc.so.6
Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/ld-linux-x86-64.so.2
0x0000003e988f80ce in __lll_lock_wait_private () from /lib64/libc.so.6
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.166.el6.x86_64 zlib-1.2.3-29.el6.x86_64

Thread 4 (Thread 0x7fa31cc78700 (LWP 14673)):
#0  0x0000003e988f80ce in __lll_lock_wait_private () from /lib64/libc.so.6
#1  0x0000003e9887cf7e in _L_lock_5746 () from /lib64/libc.so.6
#2  0x0000003e98878a8b in _int_free () from /lib64/libc.so.6
#3  0x00000000004b203d in create_delta_index (buf=0x7fa23385b010, bufsize=206161280) at diff-delta.c:253
#4  0x00000000004533de in try_delta (list=0x2395f10, list_size=0x238cf54, window=11, depth=50, processed=0x7ffc59af8adc) at builtin/pack-objects.c:1901
#5  find_deltas (list=0x2395f10, list_size=0x238cf54, window=11, depth=50, processed=0x7ffc59af8adc) at builtin/pack-objects.c:2044
#6  0x0000000000453673 in threaded_find_deltas (arg=0x238cf40) at builtin/pack-objects.c:2178
#7  0x0000003e98c07a51 in start_thread () from /lib64/libpthread.so.0
#8  0x0000003e988e896d in clone () from /lib64/libc.so.6

Thread 3 (Thread 0x7fa31a474700 (LWP 14678)):
#0  0x0000003e988f80ce in __lll_lock_wait_private () from /lib64/libc.so.6
#1  0x0000003e9887d313 in _L_lock_10110 () from /lib64/libc.so.6
#2  0x0000003e9887abbf in malloc () from /lib64/libc.so.6
#3  0x0000003e9887c0f8 in realloc () from /lib64/libc.so.6
#4  0x00000000004b1c5e in create_delta (index=0x7fa305efc820, trg_buf=<value optimized out>, trg_size=<value optimized out>, delta_size=0x7fa31a473e40, max_size=11611521) at diff-delta.c:476
#5  0x0000000000453102 in try_delta (list=0x2396448, list_size=0x238d1fc, window=11, depth=50, processed=0x7ffc59af8adc) at builtin/pack-objects.c:1911
#6  find_deltas (list=0x2396448, list_size=0x238d1fc, window=11, depth=50, processed=0x7ffc59af8adc) at builtin/pack-objects.c:2044
#7  0x0000000000453673 in threaded_find_deltas (arg=0x238d1e8) at builtin/pack-objects.c:2178
#8  0x0000003e98c07a51 in start_thread () from /lib64/libpthread.so.0
#9  0x0000003e988e896d in clone () from /lib64/libc.so.6

Thread 2 (Thread 0x7fa319a73700 (LWP 14679)):
#0  0x0000003e98c0b63c in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
#1  0x00000000004536bb in threaded_find_deltas (arg=0x238d270) at builtin/pack-objects.c:2196
#2  0x0000003e98c07a51 in start_thread () from /lib64/libpthread.so.0
#3  0x0000003e988e896d in clone () from /lib64/libc.so.6

Thread 1 (Thread 0x7fa326627700 (LWP 14670)):
#0  0x0000003e988f80ce in __lll_lock_wait_private () from /lib64/libc.so.6
#1  0x0000003e9887cf7e in _L_lock_5746 () from /lib64/libc.so.6
#2  0x0000003e98878a8b in _int_free () from /lib64/libc.so.6
#3  0x0000003e98011197 in _dl_deallocate_tls () from /lib64/ld-linux-x86-64.so.2
#4  0x0000003e98c0675d in __free_stacks () from /lib64/libpthread.so.0
#5  0x0000003e98c0796a in __free_tcb () from /lib64/libpthread.so.0
#6  0x0000003e98c08274 in pthread_join () from /lib64/libpthread.so.0
#7  0x0000000000455c14 in ll_find_deltas (window=396, depth=4) at builtin/pack-objects.c:2326
#8  prepare_pack (window=396, depth=4) at builtin/pack-objects.c:2443
#9  0x0000000000456ef7 in cmd_pack_objects (argc=<value optimized out>, argv=<value optimized out>, prefix=<value optimized out>) at builtin/pack-objects.c:3096
#10 0x000000000040514b in run_builtin (argc=6, argv=0x7ffc59afabd0) at git.c:346
#11 handle_builtin (argc=6, argv=0x7ffc59afabd0) at git.c:554
#12 0x0000000000405391 in run_argv (argc=6, argv=0x7ffc59afabd0) at git.c:606
#13 cmd_main (argc=6, argv=0x7ffc59afabd0) at git.c:683
#14 0x0000000000481faf in main (argc=7, argv=0x7ffc59afabc8) at common-main.c:43
A debugging session is active.

In the example above threads 0x7fa31cc78700, 0x7fa31a474700 and 0x7fa326627700 are blocked on that method.

Cause

This issue is caused by the bug below reported on older versions of the GLIBC library

Solution

  1. Update the GLIBC library to glibc-2.12-1.166.el6_7.1 or greater
  2. Update the OS to a newer version of the kernel


Last modified on Apr 20, 2021

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