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single: Fsck
Fsck
=====
This section describles how the internal file system consystency checks (FSCK) are configured and work.
Enable FST Scan
---------------
To enable the FST scan you have to set the variable **scaninterval** on the space and
on all file systems:
.. code-block:: bash
# set it on the space to inherit a value for all new filesystems in this space every 14 days (time has to be in seconds)
space config default space.scaninterval=1209600
# set it on an existing filesystem (fsid 23) to 14 days (time has to be in seconds)
fs config 23 space.scaninterval=1209600
# set the scaninterval for all the existing file systems already registered in the given space
space config default fs.scaninterval=1209601
.. note::
The *scaninterval* time has to be given in seconds!
Caveats
-------
For FSCK engine to function correctly, FSTs must be able to connect to QuarkDB directly (and to the MGM).
Overview
--------
High level summary
------------------
#) error collection happens in the FST in defined intervals, no action/trigger by MGM is required for this
#) the locally saved results will be collected by the fsck collection thread of fsck engine
#) if the fsck repair thread is enabled, the mgm will trigger repair actions (i.e. create / delete replica)
as required (based on collected error data)
Intervals and config parameters for file systems(FS)
-----------------------------------------------------
These values are set as global defaults on the space. A file system should get the values from the space when it is newly created.
Below you can find a brief description of the parameters influencing the scanning procedure.
=================== =============== ===========================================================
Name Default Description
=================== =============== ===========================================================
scan_disk_interval 14400 [s] (4h) interval at which files in the FS should be scanned, by the FST itself
scan_ns_interval 259200 [s] (3d) interval at which files in the FS are compares against the
namespace information from QuarkDB
scaninterval 604800 [s] (7d) target interval at which all file should be scanned
scan_ns_rate 50 [Hz] rate limit the requests to QuarkDB for the namespace scans
scanrate 100 [MB/s] rate limit bandwidth used by the scanner when reading files
from disk
=================== =============== ===========================================================
**scan_disk_interval** and **scan_ns_interval** are skewed by a random factor per FS so that not all disks become busy at the same time.
The scan jobs are started with a lower IO priority class (using Linux ioprio_set) within EOS to decrease the impact on normal filesystem access, i.e. check logs for set io priority to 7 (lowest best-effort).
.. code-block:: bash
210211 12:41:40 time=1613043700.017295 func=RunDiskScan level=NOTE
logid=1af8cd9e-6c5e-11eb-ae37-3868dd2a6fb0 unit=fst@fst-9.eos.grid.vbc.ac.at:1095 tid=00007f98bebff700 source=ScanDir:446
tident=<service> sec= uid=0 gid=0 name= geo="" msg="set io priority to 7(lowest best-effort)" pid=221712
Scan duration
-------------
The first scan of a larger (fuller) FS can take several hours. Following scans will be much faster, within minutes (10-30min).
Subsequent scans will only look at file that have not been scanned since scaninterval . i.e. each scan iteration will only look at a fraction of the files on disk, compare the logs for such a scan. (see the last line “scannedfiles†vs “skippedfiles†and the scanduration of 293s.)
.. code-block:: bash
210211 12:49:44 time=1613044184.957472 func=RunDiskScan level=NOTE logid=1827f5ea-6c5e-11eb-ae37-3868dd2a6fb0 unit=fst@fst-9.eos.grid.vbc.ac.at:1095 tid=00007f993afff700 source=ScanDir:504 tident=<service> sec= uid=0 gid=0 name= geo="" [ScanDir] Directory: /srv/data/data.01 files=147957 scanduration=293 [s] scansize=23732973568 [Bytes] [ 23733 MB ] scannedfiles=391 corruptedfiles=0 hwcorrupted=0 skippedfiles=147557
Error types detected by fsck
-----------------------------
(in decreasing priority)
============= ==================================================== ==============
Error Description Fixed by
============= ==================================================== =============
d_mem_sz_diff disk and reference size mismatch FsckRepairJob
m_mem_sz_diff MGM and reference size mismatch inspecting all the replicas or saved for manual inspection
d_cx_diff disk and reference checksum mismatch FsckRepairJob
m_cx_diff MGM and reference checksum mismatch inspecting all the replicas or saved for manual inspection
unreg_n unregistered file / replica (i.e. file on FS that has no entry in MGM) register replica if metadata match or drop if not needed
rep_missing_n missing replica for a file replica is registered on mgm but not on disk - FsckRepairJob
rep_diff_n replica count is not nominal (too high or too low) fixed by dropping replicas or creating new ones through FsckRepairJob
orphans_n orphan files (no record for replica/file in mgm) no action at the MGM, files not referenced by MGM at all, moved to to .eosorphans directory on FS mountpoint
============= ==================================================== ========
Configuration
--------------
space
-----
Some config items on the space are global, some are defaults (i.e. for newly created filesystems), see https://eos-docs.web.cern.ch/configuration/autorepair.html
To enable the FST scan you have to set the variable **scaninterval** on the space and on all file systems.
The intervals other than `scaninterval` are defaults for newly created filesystems. For an explanation. of the intervals see above.
.. code-block:: bash
[root@mgm-1 ~]# eos space status default
# ------------------------------------------------------------------------------------
# Space Variables
# ....................................................................................
autorepair := on
[...]
scan_disk_interval := 14400
scan_ns_interval := 259200
scan_ns_rate := 50
scaninterval := 604800
scanrate := 100
[...]
filesystem / FS
---------------
To enable the FST scan you have to set the variable `scaninterval` on the space and on all file systems
.. code-block:: bash
[root@mgm-1 ~]# eos fs status 1
# ------------------------------------------------------------------------------------
# FileSystem Variables
# ------------------------------------------------------------------------------------
bootcheck := 0
bootsenttime := 1612456466
configstatus := rw
host := fst-1.eos.grid.vbc.ac.at
hostport := fst-1.eos.grid.vbc.ac.at:1095
id := 1
local.drain := nodrain
path := /srv/data/data.00
port := 1095
queue := /eos/fst-1.eos.grid.vbc.ac.at:1095/fst
queuepath := /eos/fst-1.eos.grid.vbc.ac.at:1095/fst/srv/data/data.00
[...] defaults for these are taken from MGM, scanterval must be set!
scan_disk_interval := 14400
scan_ns_interval := 259200
scan_ns_rate := 50
scaninterval := 604800
scanrate := 100
[...] various stat values reported back by the FST
stat.fsck.blockxs_err := 1
stat.fsck.d_cx_diff := 0
stat.fsck.d_mem_sz_diff := 0
stat.fsck.d_sync_n := 148520
stat.fsck.m_cx_diff := 0
stat.fsck.m_mem_sz_diff := 0
stat.fsck.m_sync_n := 148025
stat.fsck.mem_n := 148526
stat.fsck.orphans_n := 497
stat.fsck.rep_diff_n := 5006
stat.fsck.rep_missing_n := 0
stat.fsck.unreg_n := 5003
[...]
Ffsck settings
-------------
With the settings above, stats are collected on the FST (and reported in fs status) but no further action is taken. To setup of the fsck mechanism, see the eos fsck subcommands:
`fsck stat`
-----------
Gives a quick status of error stats collection and if the repair thread is active. The `eos fsck toggle-repair` and `toggle-collect` are really toggles. Use **eos fsck stat** to verify the correctness of your settings!
.. code-block:: bash
[root@mgm-1 ~]# eos fsck stat
Info: collection thread status -> enabled
Info: repair thread status -> enabled
210211 15:54:09 1613055249.712603 Start error collection
210211 15:54:09 1613055249.712635 Filesystems to check: 252
210211 15:54:10 1613055250.769177 blockxs_err : 118
210211 15:54:10 1613055250.769208 orphans_n : 92906
210211 15:54:10 1613055250.769221 rep_diff_n : 1226274
210211 15:54:10 1613055250.769224 rep_missing_n : 6
210211 15:54:10 1613055250.769231 unreg_n : 1221521
210211 15:54:10 1613055250.769235 Finished error collection
210211 15:54:10 1613055250.769237 Next run in 30 minutes
The collection thread will interrogate the FSTs for locally collected error stats at configured intervals (default: 30 minutes).
`fsck report`
-------------
For a more comprehensive error report, use **eos fsck report** this will only contain data once the error collection has started (also note the switch -a to show errors per filesystem FS)
.. code-block:: bash
[root@mgm-1 ~]# eos fsck report
timestamp=1613055250 tag="blockxs_err" count=43
timestamp=1613055250 tag="orphans_n" count=29399
timestamp=1613055250 tag="rep_diff_n" count=181913
timestamp=1613055250 tag="rep_missing_n" count=4
timestamp=1613055250 tag="unreg_n" count=180971
Repair
-------
Most of the repair operations are implemented using the DrainTransferJob functionality.
Operations
-----------
Inspect FST local error stats
-----------------------------
Use **eos-leveldb-inspect** command to inspect the contents of the local database on the FSTs.
The local database contains all information (fxid, error type, etc) that will be collected
by the mgm (compare the eos fs status <fsid> output).
.. code-block:: bash
[root@fst-9 ~]# eos-leveldb-inspect --dbpath /var/eos/md/fmd.0225.LevelDB --fsck
Num. entries in DB[mem_n]: 148152
Num. files synced from disk[d_sync_n]: 148150
Num, files synced from MGM[m_sync_n]: 147723
Disk/referece size missmatch[d_mem_sz_diff]: 0
MGM/reference size missmatch[m_mem_sz_diff]: 140065
Disk/reference checksum missmatch[d_cx_diff]: 0
MGM/reference checksum missmatch[m_cx_diff]: 0
Num. of orphans[orphans_n]: 427
Num. of unregistered replicas[unreg_n]: 5078
Files with num. replica missmatch[rep_diff_n]: 5081
Files missing on disk[rep_missing_n]: 0
Check fsck repair activity
--------------------------
See if the fsck repair thread is active and how log its work queue is (cross check with log activity on mgm):
.. code-block:: bash
[root@mgm-1 ~]# eos ns | grep fsck
ALL fsck info thread_pool=fsck min=2 max=20 size=20 queue_size=562
ALL tracker info tracker=fsck size=582
compare namespace stats for total count of fsck operations:
[root@mgm-1 ~]# eos ns stat | grep -i fsck
ALL fsck info thread_pool=fsck min=2 max=20 size=20 queue_size=168
ALL tracker info tracker=fsck size=188
all FsckRepairFailed 71.58 K 0.00 0.03 1.35 0.87 -NA- -NA-
all FsckRepairStarted 63.19 M 857.75 1107.25 1112.05 918.32 -NA- -NA-
all FsckRepairSuccessful 63.12 M 857.75 1106.88 1110.64 917.44 -NA- -NA-
Log examples
------------
Startup of FST service and initializing fsck threads:
.. code-block:: bash
210211 12:41:39 time=1613043699.997897 func=ConfigScanner level=INFO logid=1af5b7a8-6c5e-11eb-ae37-3868dd2a6fb0
unit=fst@fst-9.eos.grid.vbc.ac.at:1095 tid=00007f99497ff700 source=FileSystem:159 tident=<service> sec= uid=0 gid=0
name= geo="" msg="started ScanDir thread with default parameters" fsid=238
# NS scanner thread with random skew
210211 12:41:50 time=1613043710.000322 func=RunNsScan level=INFO logid=1af62382-6c5e-11eb-ae37-3868dd2a6fb0
unit=fst@fst-9.eos.grid.vbc.ac.at:1095 tid=00007f98e6bfe700 source=ScanDir:224 tident=<service> sec= uid=0 gid=0
name= geo="" msg="delay ns scan thread by 38889 seconds" fsid=239 dirpath="/srv/data/data.14"
systemd ScanDir results
-----------------------
These logs are also written to /var/log/eos/fst/xrdlog.fst
.. code-block:: bash
Feb 11 12:41:33 fst-9.eos.grid.vbc.ac.at eos_start.sh[220738]: Using xrootd binary: /opt/eos/xrootd/bin/xrootd
Feb 11 12:49:44 fst-9.eos.grid.vbc.ac.at scandir[220738]: skipping scan w-open file: localpath=/srv/data/data.01/000006e3/010d045d fsid=226 fxid=010d045d
Feb 11 12:49:44 fst-9.eos.grid.vbc.ac.at scandir[220738]: [ScanDir] Directory: /srv/data/data.01 files=147957 scanduration=293 [s] scansize=23732973568 [Bytes] [ 23733 MB ] scanned...iles=147557
Feb 11 13:07:55 fst-9.eos.grid.vbc.ac.at scandir[220738]: [ScanDir] Directory: /srv/data/data.18 files=148074 scanduration=263 [s] scansize=17977114624 [Bytes] [ 17977.1 MB ] scann...iles=147730
Feb 11 13:08:36 fst-9.eos.grid.vbc.ac.at scandir[220738]: [ScanDir] Directory: /srv/data/data.22 files=147905 scanduration=258 [s] scansize=19978055680 [Bytes] [ 19978.1 MB ] scann...iles=147498
Feb 11 13:14:56 fst-9.eos.grid.vbc.ac.at scandir[220738]: [ScanDir] Directory: /srv/data/data.27 files=147445 scanduration=249 [s] scansize=15998377984 [Bytes] [ 15998.4 MB ] scann...iles=147119
fsck repairs. success/failure on MGM
210211 13:58:17 time=1613048297.294157 func=RepairReplicaInconsistencies level=INFO logid=cf14c90e-6c68-11eb-becb-3868dd28d0c0 unit=mgm@mgm-1.eos.grid.vbc.ac.at:1094 tid=00007efd53bff700 source=FsckEntry:689 tident=<service> sec= uid=0 gid=0 name= geo="" msg="file replicas consistent" fxid=0028819b
210211 13:58:17 time=1613048297.294294 func=RepairReplicaInconsistencies level=INFO logid=cf14c54e-6c68-11eb-becb-3868dd28d0c0 unit=mgm@mgm-1.eos.grid.vbc.ac.at:1094 tid=00007efd51bfb700 source=FsckEntry:689 tident=<service> sec= uid=0 gid=0 name= geo="" msg="file replicas consistent" fxid=00ef5955
210211 13:59:18 time=1613048358.345753 func=RepairReplicaInconsistencies level=ERROR logid=cf14c7ce-6c68-11eb-becb-3868dd28d0c0 unit=mgm@mgm-1.eos.grid.vbc.ac.at:1094 tid=00007efd523fc700 source=FsckEntry:663 tident=<service> sec= uid=0 gid=0 name= geo="" msg="replica inconsistency repair failed" fxid=0079b4d0 src_fsid=244
No repair action, file is being deleted
---------------------------------------
The file has an FsckEntry i.e. is marked from repair, and was previously listed on the collected errors, but
.. code-block:: bash
210211 16:27:45 time=1613057265.418302 func=Repair level=INFO logid=b077de7c-6c7d-11eb-becb-3868dd28d0c0 unit=mgm@mgm-1.eos.grid.vbc.ac.at:1094 tid=00007efd95bff700 source=FsckEntry:773 tident=<service> sec= uid=0 gid=0 name= geo=""
msg="no repair action, file is being deleted" fxid=00033673
The file is noted as “being deleted†as its container (directory) does not exist anymore, i.e.
[root@mgm-1 ~]# eos fileinfo fxid:00033673
File: 'fxid:00033673' Flags: 0600 Clock: 1662bb7c74f01d9f
Size: 0
Modify: Fri Jul 24 11:32:15 2020 Timestamp: 1595583135.037235673
Change: Fri Jul 24 11:32:15 2020 Timestamp: 1595583135.037235673
Birth: Fri Jul 24 11:32:15 2020 Timestamp: 1595583135.037235673
CUid: 12111 CGid: 11788 Fxid: 00033673 Fid: 210547 Pid: 0 Pxid: 00000000
XStype: adler XS: 00 00 00 00 ETAGs: "56518279954432:00000000"
Layout: raid6 Stripes: 7 Blocksize: 1M LayoutId: 20640642 Redundancy: d0::t0
#Rep: 0
*******
error: cannot retrieve file meta data - Container #0 not found (errc=0) (Success)
Discrepancy reported errors
----------------------------
... between fsck report summary / per filesystem and fsck stat.
EOS fsck report is giving different numbers for total report and per filesystem summary. This is expected.
Per filesystem reports may contain error counts for individual replicas of a single file stored in EOS.
**eos fsck stat** will reflect the per replica count, **eos fsck report** will show lower numbers,
not counting per each replica of a file.
**example script**
.. code-block:: bash
echo "summed up by filesystem"
ERR_TYPES="blockxs_err orphans_n rep_diff_n rep_missing_n unreg_n"
for ETYPE in $ERR_TYPES; do
echo -n "$ETYPE: "
eos fsck report -a | grep $ETYPE | awk '{print $4;}' | awk 'BEGIN{ FS="="; total=0}; { total=total+$2; } END{print total;}'
done
echo ""
echo "eos fsck summary report"
eos fsck report
**output example**
.. code-block:: bash
[root@mgm-1 ~]# ./eos_fsck_miscount.sh
summed up by filesystem
blockxs_err: 115
orphans_n: 95056
rep_diff_n: 1251566
rep_missing_n: 30
unreg_n: 1246475
eos fsck summary report
timestamp=1613069473 tag="blockxs_err" count=43
timestamp=1613069473 tag="orphans_n" count=29602
timestamp=1613069473 tag="rep_diff_n" count=181913
timestamp=1613069473 tag="rep_missing_n" count=28
timestamp=1613069473 tag="unreg_n" count=180998