we are using git since may and all is working fine for all of us (almost 20 people) on our workstations. However, when we clone our repositories to the cluster, only and only there we are having many problems similiar to this post: What filesystem tests have you run on lustre? I would run every test you can find, and lustre should have a robust test suite. It's really hard to be certain, but given how many filesystems git is used with, your experience points to a lustre bug. I would also suggest using ktrace/ktruss/strace and perhaps poring over the logs to see if you can spot any bad behavior.
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