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yarikoptic 2022-05-24 21:05:03 +00:00 • committed by admin
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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="comment 3"
date="2022-05-24T21:05:03Z"
content="""
I should have looked above in that stderr where interesting part begins with possibly relevant extra complaints:
```
52 2022-05-20T19:27:59-0400 [INFO ] backups2datalad Downloading files for Dandiset 000026
53 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS10_stain-NeuN_chunk-04_SPIM.ome.tif (from web...)
54 failed to commit changes to sqlite database: Just SQLite3 returned ErrorBusy while attempting to perform step: database is locked
55 CallStack (from HasCallStack):
56 error, called at ./Database/Handle.hs:91:26 in main:Database.Handle
57 (Delaying 1s before retrying....)
58 ok
59 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS10_stain-NeuN_chunk-02_SPIM.ome.tif (from web...)
60 thread blocked indefinitely in an MVar operation
61 (Delaying 1s before retrying....)
62 ok
63 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS12_stain-Calretinin_chunk-00_SPIM.ome.tif (from web...)
64 thread blocked indefinitely in an MVar operation
65 (Delaying 1s before retrying....)
66 ok
67 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS12_stain-NeuN_chunk-01_SPIM.ome.tif (from web...)
68 thread blocked indefinitely in an MVar operation
69 (Delaying 1s before retrying....)
70 ok
71 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS12_stain-Nuclei_chunk-01_SPIM.ome.tif (from web...)
72 thread blocked indefinitely in an MVar operation
73 (Delaying 1s before retrying....)
74 ok
75 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS12_stain-Nuclei_chunk-05_SPIM.ome.tif (from web...)
76 failed to commit changes to sqlite database: Just SQLite3 returned ErrorBusy while attempting to perform step: database is locked
77 CallStack (from HasCallStack):
78 error, called at ./Database/Handle.hs:91:26 in main:Database.Handle
79 (Delaying 1s before retrying....)
80 ok
81 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS12_stain-Nuclei_chunk-06_SPIM.ome.tif (from web...)
82 thread blocked indefinitely in an MVar operation
83 (Delaying 1s before retrying....)
84 ok
85 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS13_stain-NeuN_chunk-02_SPIM.ome.tif (from web...)
86 thread blocked indefinitely in an MVar operation
87 (Delaying 1s before retrying....)
88 ok
89 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS14_stain-Calretinin_chunk-01_SPIM.ome.tif (from web...)
90 thread blocked indefinitely in an MVar operation
91 (Delaying 1s before retrying....)
92 ok
93 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS13_stain-Nuclei_chunk-05_SPIM.ome.tif (from web...)
94 thread blocked indefinitely in an MVar operation
95 (Delaying 1s before retrying....)
96 ok
97 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS14_stain-NeuN_chunk-07_SPIM.ome.tif (from web...)
98 thread blocked indefinitely in an MVar operation
99 (Delaying 1s before retrying....)
100 ok
101 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS13_stain-Nuclei_chunk-08_SPIM.ome.tif (from web...)
102 thread blocked indefinitely in an MVar operation
103 (Delaying 1s before retrying....)
104 ok
105 get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-BrocaAreaS14_stain-NeuN_chunk-10_SPIM.ome.tif (from web...)
106 thread blocked indefinitely in an MVar operation
107 (Delaying 1s before retrying....)
```
`strace -f -p 1683786` ends with
```
[pid 1683799] <... sched_yield resumed>) = 0
[pid 1683798] sched_yield( <unfinished ...>
[pid 1683810] futex(0x7fd5cc000c08, FUTEX_WAIT_PRIVATE, 0, NULL <unfinished ...>
[pid 1683803] futex(0x7fd5c0000be8, FUTEX_WAIT_PRIVATE, 0, NULL <unfinished ...>
[pid 1683799] futex(0x5b180ec, FUTEX_WAIT_PRIVATE, 0, NULL <unfinished ...>
[pid 1683798] <... sched_yield resumed>) = 0
[pid 1683798] futex(0x7fd5d8000bec, FUTEX_WAIT_PRIVATE, 0, NULL <unfinished ...>
[pid 1683787] <... read resumed>\"\1\0\0\0\0\0\0\0\", 8) = 8
[pid 1683787] futex(0x4a4844c, FUTEX_WAIT_PRIVATE, 0, NULL
```
I will now interrupt that process to \"proceed\", knowing what to do next time would be helpful
"""]]