[lustre-discuss] Disk usage / quota discrepancy
Nehring, Shane R [ITS]
snehring at iastate.edu
Thu Dec 11 08:24:47 PST 2025
A pretty naive approach might be to lfs find any file with more than
one component and then compare the results of df and df --apparent-size
for instances where the --apparent-size is significantly smaller than
the regular df size.
On Thu, 2025-12-11 at 15:28 +0100, Rasool Almasikoupaei via lustre-
discuss wrote:
> Hi All,
>
> Just wondering how we can identify the affected files and migrate
> them
> back to the optimal block size (after applying the patch, of course).
> We upgraded to 2.15.7 when it was released (from 2.15.6).
>
> Best,
> Rasool
>
> On 20.11.25 07:05, David Schanzenbach via lustre-discuss wrote:
> > Hi Shane,
> >
> > If you are using Lustre 2.15.7 + zfs with PFL , you are possibly
> > encountering issue LU-19193
> > https://jira.whamcloud.com/browse/LU-19193 .
> >
> > For our site, until we applied the patch provided in LU-19193,
> > we saw newly written files balloon to 4-10 times the uncompressed
> > file
> > size, unless it was written to a single stripe.
> >
> >
> > Thanks,
> > David
> >
> >
> > On 11/19/2025 5:56 AM, Nehring, Shane R [ITS] via lustre-discuss
> > wrote:
> > > Hello All,
> > >
> > > As background this lustre volume is only (currently) 1 mdt and 5
> > > osts, the mdt and osts are using zfs with compression on. We also
> > > have a default PFL defined to stripe any file larger than 1T to 2
> > > osts.
> > >
> > > Recently we had a user create a swath of large files and I had to
> > > reach out to them because the volume was filling up pretty
> > > quickly. The files compress very nicely so they're in the process
> > > of doing that now, which resulted in a very quick reclaiming of
> > > the used space. It all sounds innocuous, but the rate at which
> > > the space was consumed and then freed was somewhat suspicious,
> > > the reported usage was also very much higher than what the user
> > > expected. So I got to looking.
> > >
> > > The usage as reported by lfs quota for the project directory this
> > > is:
> > > # lfs quota -h -p 212496 /lustre/hdd
> > > Disk quotas for prj 212496 (pid 212496):
> > > Filesystem used quota limit grace files quota
> > > limit grace
> > > /lustre/hdd 260.3T 0k 0k - 7205 0
> > > 0 -
> > > At its highest point it was around 660T. The file count isn't too
> > > high so on average the files are quite large.
> > >
> > > A du on the directory reports numbers in line with the quota
> > > report:
> > > # du -sh /lustre/hdd/LAS/<directory>
> > > 261T /lustre/hdd/LAS/<directory>
> > >
> > > The bulk of this space is used by a single directory containing
> > > multiple large (3T+ before compression) files.
> > >
> > > a du from within it looks like:
> > > du -sh .
> > > 253T .
> > >
> > > however that number does not appear realistic when you roughly
> > > sum the sizes of the files reported with ls:
> > > -rw-rw----+ 1 <user> <group> 470G Nov 1 01:34
> > > run2025.ZmChr10.all.vcf.gz
> > > -rw-rw----+ 1 <user> <group> 150K Nov 1 01:34
> > > run2025.ZmChr10.all.vcf.idx
> > > -rw-r-----+ 1 <user> <group> 259G Oct 21 20:10
> > > run2025.ZmChr10.variant.vcf.gz
> > > -rw-r-----+ 1 <user> <group> 150K Oct 21 17:49
> > > run2025.ZmChr10.variant.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 942G Nov 11 20:21
> > > run2025.ZmChr1.all.vcf.gz
> > > -rw-rw----+ 1 <user> <group> 302K Nov 11 20:21
> > > run2025.ZmChr1.all.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 830G Nov 10 01:10
> > > run2025.ZmChr1.variant.vcf.gz
> > > -rw-rw----+ 1 <user> <group> 302K Nov 10 01:10
> > > run2025.ZmChr1.variant.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 736G Nov 10 22:02
> > > run2025.ZmChr2.all.vcf.gz
> > > -rw-rw----+ 1 <user> <group> 239K Nov 10 22:02
> > > run2025.ZmChr2.all.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 407G Oct 31 21:16
> > > run2025.ZmChr2.variant.vcf.gz
> > > -rw-rw----+ 1 <user> <group> 239K Oct 31 21:16
> > > run2025.ZmChr2.variant.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 732G Nov 10 19:34
> > > run2025.ZmChr3.all.vcf.gz
> > > -rw-rw----+ 1 <user> <group> 233K Nov 10 19:34
> > > run2025.ZmChr3.all.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 401G Nov 9 22:45
> > > run2025.ZmChr3.variant.vcf.gz
> > > -rw-rw----+ 1 <user> <group> 233K Nov 9 22:45
> > > run2025.ZmChr3.variant.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 792G Nov 11 06:22
> > > run2025.ZmChr4.all.vcf.gz
> > > -rw-rw----+ 1 <user> <group> 245K Nov 11 06:22
> > > run2025.ZmChr4.all.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 437G Oct 31 21:33
> > > run2025.ZmChr4.variant.vcf.gz
> > > -rw-rw----+ 1 <user> <group> 245K Oct 31 21:33
> > > run2025.ZmChr4.variant.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 6.9T Oct 31 19:36
> > > run2025.ZmChr5.all.vcf
> > > -rw-------+ 1 <user> <group> 295G Nov 19 09:15
> > > run2025.ZmChr5.all.vcf.gz
> > > -rw-rw----+ 1 <user> <group> 222K Oct 31 19:36
> > > run2025.ZmChr5.all.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 3.0T Oct 31 22:47
> > > run2025.ZmChr5.variant.vcf
> > > -rw-rw----+ 1 <user> <group> 222K Oct 31 22:47
> > > run2025.ZmChr5.variant.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 5.5T Nov 9 16:19
> > > run2025.ZmChr6.all.vcf
> > > -rw-rw----+ 1 <user> <group> 178K Nov 9 16:19
> > > run2025.ZmChr6.all.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 2.3T Oct 30 15:51
> > > run2025.ZmChr6.variant.vcf
> > > -rw-rw----+ 1 <user> <group> 178K Oct 30 15:51
> > > run2025.ZmChr6.variant.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 5.7T Nov 9 10:58
> > > run2025.ZmChr7.all.vcf
> > > -rw-rw----+ 1 <user> <group> 182K Nov 9 10:58
> > > run2025.ZmChr7.all.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 2.5T Oct 31 10:04
> > > run2025.ZmChr7.variant.vcf
> > > -rw-rw----+ 1 <user> <group> 182K Oct 31 10:04
> > > run2025.ZmChr7.variant.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 5.6T Oct 29 19:34
> > > run2025.ZmChr8.all.vcf
> > > -rw-rw----+ 1 <user> <group> 179K Oct 29 19:34
> > > run2025.ZmChr8.all.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 2.4T Oct 29 16:11
> > > run2025.ZmChr8.variant.vcf
> > > -rw-rw----+ 1 <user> <group> 179K Oct 29 16:11
> > > run2025.ZmChr8.variant.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 5.0T Oct 30 00:25
> > > run2025.ZmChr9.all.vcf
> > > -rw-rw----+ 1 <user> <group> 160K Oct 30 00:25
> > > run2025.ZmChr9.all.vcf.idx
> > > -rw-rw----+ 1 <user> <group> 2.2T Oct 29 18:05
> > > run2025.ZmChr9.variant.vcf
> > > -rw-rw----+ 1 <user> <group> 160K Oct 29 18:05
> > > run2025.ZmChr9.variant.vcf.idx
> > >
> > > what does more reflect reality is the result of du with --
> > > apparent-size added:
> > > # du -sh --apparent-size .
> > > 47T .
> > >
> > > Looking at an individual file we see similar discrepancies:
> > > # du -sh run2025.ZmChr5.all.vcf
> > > 47T run2025.ZmChr5.all.vcf
> > > # du -sh --apparent-size run2025.ZmChr5.all.vcf
> > > 6.9T run2025.ZmChr5.all.vcf
> > > # ls -lah run2025.ZmChr5.all.vcf
> > > -rw-rw----+ 1 <user> <group> 6.9T Oct 31 19:36
> > > run2025.ZmChr5.all.vcf
> > >
> > > I'm used to this being the reverse, with --apparent-size showing
> > > the 'logical usage' of a file before any transparent compression
> > > that might be in place (we use ZFS a lot).
> > >
> > > This appears to be being caused by the PFL striping to two osts,
> > > as I don't see a discrepancy on files with a single stripe.
> > > Here's one of the files that have been compressed (and are under
> > > 1T so not striped):
> > > # du -h --apparent-size run2025.ZmChr10.all.vcf.gz
> > > 470G run2025.ZmChr10.all.vcf.gz
> > > # du -h run2025.ZmChr10.all.vcf.gz
> > > 470G run2025.ZmChr10.all.vcf.gz
> > >
> > > I had another volume I copied this file to with a different
> > > default striping rule and you can see the discrepancy from
> > > striping:
> > > # du -h run2025.ZmChr10.variant.vcf.gz
> > > 418G run2025.ZmChr10.variant.vcf.gz
> > > # du -h --apparent-size run2025.ZmChr10.variant.vcf.gz
> > > 259G run2025.ZmChr10.variant.vcf.gz
> > >
> > > The same file in the same volume but with the striping set to
> > > only one stripe:
> > > # du -h run2025.ZmChr10.variant.vcf.gz.copy
> > > 259G run2025.ZmChr10.variant.vcf.gz.copy
> > > # du -h --apparent-size run2025.ZmChr10.variant.vcf.gz.copy
> > > 259G run2025.ZmChr10.variant.vcf.gz.copy
> > >
> > > getstripe for the first large striped file:
> > > # lfs getstripe -y run2025.ZmChr5.all.vcf
> > > lcm_layout_gen: 3
> > > lcm_mirror_count: 1
> > > lcm_entry_count: 2
> > > component0:
> > > lcme_id: 1
> > > lcme_mirror_id: 0
> > > lcme_flags: init
> > > lcme_extent.e_start: 0
> > > lcme_extent.e_end: 1099511627776
> > > sub_layout:
> > > lmm_stripe_count: 1
> > > lmm_stripe_size: 1048576
> > > lmm_pattern: raid0
> > > lmm_layout_gen: 0
> > > lmm_stripe_offset: 1
> > > lmm_objects:
> > > - l_ost_idx: 1
> > > l_fid: 0x100010000:0x1869cb06:0x0
> > >
> > > component1:
> > > lcme_id: 2
> > > lcme_mirror_id: 0
> > > lcme_flags: init
> > > lcme_extent.e_start: 1099511627776
> > > lcme_extent.e_end: EOF
> > > sub_layout:
> > > lmm_stripe_count: 2
> > > lmm_stripe_size: 1048576
> > > lmm_pattern: raid0
> > > lmm_layout_gen: 65535
> > > lmm_stripe_offset: 0
> > > lmm_objects:
> > > - l_ost_idx: 0
> > > l_fid: 0x100000000:0x18ad637a:0x0
> > > - l_ost_idx: 1
> > > l_fid: 0x100010000:0x18717a96:0x0
> > >
> > > getstripe for the second single striped file:
> > > # lfs getstripe -y run2025.ZmChr10.all.vcf.gz
> > > lcm_layout_gen: 2
> > > lcm_mirror_count: 1
> > > lcm_entry_count: 2
> > > component0:
> > > lcme_id: 1
> > > lcme_mirror_id: 0
> > > lcme_flags: init
> > > lcme_extent.e_start: 0
> > > lcme_extent.e_end: 1099511627776
> > > sub_layout:
> > > lmm_stripe_count: 1
> > > lmm_stripe_size: 1048576
> > > lmm_pattern: raid0
> > > lmm_layout_gen: 0
> > > lmm_stripe_offset: 1
> > > lmm_objects:
> > > - l_ost_idx: 1
> > > l_fid: 0x100010000:0x18d70b19:0x0
> > >
> > > component1:
> > > lcme_id: 2
> > > lcme_mirror_id: 0
> > > lcme_flags: 0
> > > lcme_extent.e_start: 1099511627776
> > > lcme_extent.e_end: EOF
> > > sub_layout:
> > > lmm_stripe_count: 2
> > > lmm_stripe_size: 1048576
> > > lmm_pattern: raid0
> > > lmm_layout_gen: 0
> > > lmm_stripe_offset: -1
> > >
> > > getstripe of the smaller file copied to another volume with a
> > > smaller striping threshold:
> > > # lfs getstripe -y run2025.ZmChr10.variant.vcf.gz
> > > lcm_layout_gen: 3
> > > lcm_mirror_count: 1
> > > lcm_entry_count: 2
> > > component0:
> > > lcme_id: 1
> > > lcme_mirror_id: 0
> > > lcme_flags: init
> > > lcme_extent.e_start: 0
> > > lcme_extent.e_end: 107374182400
> > > sub_layout:
> > > lmm_stripe_count: 1
> > > lmm_stripe_size: 1048576
> > > lmm_pattern: raid0
> > > lmm_layout_gen: 0
> > > lmm_stripe_offset: 1
> > > lmm_objects:
> > > - l_ost_idx: 1
> > > l_fid: 0x100010000:0x11ae544:0x0
> > >
> > > component1:
> > > lcme_id: 2
> > > lcme_mirror_id: 0
> > > lcme_flags: init
> > > lcme_extent.e_start: 107374182400
> > > lcme_extent.e_end: EOF
> > > sub_layout:
> > > lmm_stripe_count: 2
> > > lmm_stripe_size: 1048576
> > > lmm_pattern: raid0
> > > lmm_layout_gen: 0
> > > lmm_stripe_offset: 0
> > > lmm_objects:
> > > - l_ost_idx: 0
> > > l_fid: 0x100000000:0x1689eaa:0x0
> > > - l_ost_idx: 1
> > > l_fid: 0x100010000:0x11ae545:0x0
> > >
> > > getstripe of the same file copied with the striping disabled:
> > >
> > > # lfs getstripe -y run2025.ZmChr10.variant.vcf.gz.copy
> > > lmm_stripe_count: 1
> > > lmm_stripe_size: 1048576
> > > lmm_pattern: raid0
> > > lmm_layout_gen: 0
> > > lmm_stripe_offset: 0
> > > lmm_objects:
> > > - l_ost_idx: 0
> > > l_fid: 0x100000000:0x1689eab:0x0
> > >
> > > Is this behavior expected or is something strange going on?
> > >
> > > Shane
> > > _______________________________________________
> > > lustre-discuss mailing list
> > > lustre-discuss at lists.lustre.org
> > > https://urldefense.com/v3/__http://lists.lustre.org/listinfo.cgi/lustre-discuss-lustre.org__;!!PvDODwlR4mBZyAb0!RDImgn2BJkk2oqRGAmMCO07TJNyKH7ddP8H_obZ5_WKpVuS9v5UZK3H_URS94t4BwEA9fvLlj1F2rojjojBASBD3hvWS91s$
> > >
> >
> >
> > _______________________________________________
> > lustre-discuss mailing list
> > lustre-discuss at lists.lustre.org
> > http://lists.lustre.org/listinfo.cgi/lustre-discuss-lustre.org
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