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sort tmp files closed before removing? #124

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goranrakocevic opened this issue Mar 4, 2015 · 2 comments
Closed

sort tmp files closed before removing? #124

goranrakocevic opened this issue Mar 4, 2015 · 2 comments

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@goranrakocevic
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Hi,

I've tried running sort in a NFS mounted directory (tmp is also in this directory). I sort exists with the error:
sambamba-sort: Failed to remove file ./sambamba-pid30-osbs/.nfs00000000008a005200000003: Device or resource busy

This tends to happen if a process maintains an open handle on a file that is removed. Removing the directory then fails.
Not placing the tmp on the nfs is a way around the issue, but it would be helpful if it could work this way as well.
chapmanb added a commit to chapmanb/homebrew-cbl that referenced this issue Mar 18, 2015
@chapmanb
sambamba: update version with fix to avoid temporary file cleanup err…
458f76a 
…ors with busy NFS shares bcbio/bcbio-nextgen#784 biod/sambamba#124
chapmanb added a commit to chapmanb/sambamba that referenced this issue Mar 19, 2015
@chapmanb
Avoid NFS errors when removing temporary directories after sort
0191fb3 
On busy NFS filesystems, removal of temporary directories can fail due
to NFS having a lock on files. This avoids erroring out in this
situation. (biod#124 bcbio/bcbio-nextgen#784)
@chapmanb chapmanb mentioned this issue Mar 19, 2015
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@lomereiter
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Fixed by Brad.

@cc2qe
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cc2qe commented Apr 29, 2015

thanks for this fix! I was having this problem as well and had no idea how to address it. works great now

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@lomereiter @cc2qe @goranrakocevic