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df shows 100% full partition even when there is space on the disk

Now this is a situation where I got stucked into the other day where df -h showed me the partition was 100% full disrupting many of the the applications using that partition.

# df -h /var/
Filesystem            Size  Used Avail Use% Mounted on
/dev/mapper/VolGroup00-var
3.9G  3.9G     0 100% /var

But when I went into the partition and checked the size using du, I saw the partition is only 80% full occupying 2.9G data out of 3.9G

[root@server1 var]# du -sh
2.9G    .

So where are the other files inside /var occupying the size on the hard disk?

To check that lets see the process using /var which can be checked using lsof

# lsof /var

 

Explanation:

While going through the list of processes I saw a long list of deleted files which were still occupied by the PID.

What are these deleted files?
These are the files which were being used by the command as shown in first column which in our case is rhn_check. But once the steps were completed the files were deleted as a part of the command procedure but since the command is still executing these files are locked and will be in the same state unless the PID is released or the command is executed completely.

# lsof /var | grep -i deleted
rhn_check 31261    root    8u   REG  253,2   22082560 327733 /var/cache/yum/prod-03-epel-x86_64-server-5-rhel5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root    9u   REG  253,2      78848 327737 /var/cache/yum/prod-03-likewise-x86_64-client-5-rhel5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root   10u   REG  253,2     144384 327741 /var/cache/yum/prod-03-mssb-x86_64-server-5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root   11u   REG  253,2   54056960 327748 /var/cache/yum/prod-03-rhel-x86_64-server-5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root   12u   REG  253,2    9275392 327752 /var/cache/yum/prod-03-rhel-x86_64-server-supplementary-5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root   13u   REG  253,2     582656 327756 /var/cache/yum/prod-03-rhn-tools-rhel-x86_64-server-5-rhel5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root   14u   REG  253,2   34002944 327758 /var/cache/yum/prod-03-epel-x86_64-server-5-rhel5/filelists.xml.gz.sqlite (deleted)
rhn_check 31261    root   15u   REG  253,2   33857536 327760 /var/cache/yum/prod-03-epel-x86_64-server-5-rhel5/other.xml.gz.sqlite (deleted)
rhn_check 31261    root   16u   REG  253,2      23552 327762 /var/cache/yum/prod-03-likewise-x86_64-client-5-rhel5/filelists.xml.gz.sqlite (deleted)
rhn_check 31261    root   17u   REG  253,2       6144 327765 /var/cache/yum/prod-03-likewise-x86_64-client-5-rhel5/other.xml.gz.sqlite (deleted)
rhn_check 31261    root   18u   REG  253,2      98304 327767 /var/cache/yum/prod-03-mssb-x86_64-server-5/filelists.xml.gz.sqlite (deleted)
rhn_check 31261    root   19u   REG  253,2      68608 327769 /var/cache/yum/prod-03-mssb-x86_64-server-5/other.xml.gz.sqlite (deleted)
rhn_check 31261    root   20u   REG  253,2  227818496 327772 /var/cache/yum/prod-03-rhel-x86_64-server-5/filelists.xml.gz.sqlite (deleted)
rhn_check 31261    root   21uw  REG  253,2  489109504 327774 /var/cache/yum/prod-03-rhel-x86_64-server-5/other.xml.gz.sqlite (deleted)
rhn_check 31261    root   22r   REG  253,2  135095452 327773 /var/cache/yum/prod-03-rhel-x86_64-server-5/other.xml.gz (deleted)

You can also view these deleted files using the below command

Syntax:

lsof +aL1 /file-system
# lsof +aL1 /var
COMMAND   PID     USER    FD   TYPE DEVICE      SIZE NLINK   NODE   NAME
rhn_check 31261    root    8u   REG  253,2   22082560 0 327733 /var/cache/yum/prod-03-epel-x86_64-server-5-rhel5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root    9u   REG  253,2      78848  0 327737 /var/cache/yum/prod-03-likewise-x86_64-client-5-rhel5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root   10u   REG  253,2     144384  0 327741 /var/cache/yum/prod-03-mssb-x86_64-server-5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root   11u   REG  253,2   54056960  0 327748 /var/cache/yum/prod-03-rhel-x86_64-server-5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root   12u   REG  253,2    9275392  0 327752 /var/cache/yum/prod-03-rhel-x86_64-server-supplementary-5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root   13u   REG  253,2     582656  0 327756 /var/cache/yum/prod-03-rhn-tools-rhel-x86_64-server-5-rhel5/primary.xml.gz.sqlite (deleted)
rhn_check 31261    root   14u   REG  253,2   34002944  0 327758 /var/cache/yum/prod-03-epel-x86_64-server-5-rhel5/filelists.xml.gz.sqlite (deleted)
rhn_check 31261    root   15u   REG  253,2   33857536  0 327760 /var/cache/yum/prod-03-epel-x86_64-server-5-rhel5/other.xml.gz.sqlite (deleted)
rhn_check 31261    root   16u   REG  253,2      23552  0 327762 /var/cache/yum/prod-03-likewise-x86_64-client-5-rhel5/filelists.xml.gz.sqlite (deleted)
rhn_check 31261    root   17u   REG  253,2       6144  0 327765 /var/cache/yum/prod-03-likewise-x86_64-client-5-rhel5/other.xml.gz.sqlite (deleted)
rhn_check 31261    root   18u   REG  253,2      98304  0 327767 /var/cache/yum/prod-03-mssb-x86_64-server-5/filelists.xml.gz.sqlite (deleted)
rhn_check 31261    root   19u   REG  253,2      68608  0 327769 /var/cache/yum/prod-03-mssb-x86_64-server-5/other.xml.gz.sqlite (deleted)
rhn_check 31261    root   20u   REG  253,2  227818496  0 327772 /var/cache/yum/prod-03-rhel-x86_64-server-5/filelists.xml.gz.sqlite (deleted)
rhn_check 31261    root   21uw  REG  253,2  489109504  0 327774 /var/cache/yum/prod-03-rhel-x86_64-server-5/other.xml.gz.sqlite (deleted)
rhn_check 31261    root   22r   REG  253,2  135095452  0 327773 /var/cache/yum/prod-03-rhel-x86_64-server-5/other.xml.gz (deleted)

Check the total size locked by the deleted files( for first command)

# lsof /var | gawk -F” ” ‘{ print $7}’ |sort| uniq| awk ‘{ sum += $1} END { print sum/(1024*1024*1024) }’
0.937209

So around 0.94 GB size of files are locked. Now I hope I make myself clear the reason for the size difference between du and df command.

For the second command

# lsof +aL1 /var | awk -F ” ” ‘{print $7}’ | sort | uniq | awk ‘{ sum += $1} END { print sum/(1024*1024*1024*1024) }’
0.937209

 

Solution:

Let us check other files used by this PID (I have trimmed the o/p as it was a long one)

# lsof -p 31261
rhn_check 31261 root  mem    REG              253,0    143144    557343 /lib64/libexpat.so.0.5.0
rhn_check 31261 root  mem    REG              253,0    372912    950724 /usr/lib64/python2.4/site-packages/M2Crypto/__m2crypto.so
rhn_check 31261 root  mem    REG              253,0      7120    918933 /usr/lib64/python2.4/lib-dynload/_weakref.so
rhn_check 31261 root  mem    REG              253,0     34184    919549 /usr/lib64/python2.4/site-packages/_sqlite.so
rhn_check 31261 root  mem    REG              253,0     41784    919601 /usr/lib64/python2.4/site-packages/_sqlitecache.so
rhn_check 31261 root  mem    REG              253,0    647608    557099 /lib64/libglib-2.0.so.0.1200.3
rhn_check 31261 root  mem    REG              253,0   1297104    763802 /usr/lib64/libxml2.so.2.6.26
rhn_check 31261 root  mem    REG              253,0     25104    920528 /usr/lib64/python2.4/lib-dynload/termios.so
rhn_check 31261 root  mem    REG              253,0      7280    920527 /usr/lib64/python2.4/lib-dynload/syslog.so
rhn_check 31261 root    0uW  REG              253,2         5    163893 /var/run/rhn_check.pid
rhn_check 31261 root    1w  FIFO                0,6           901384192 pipe
rhn_check 31261 root    2w  FIFO                0,6           901384192 pipe
rhn_check 31261 root    3r   REG              253,2  32641024    622598 /var/lib/rpm/Packages
rhn_check 31261 root    4r   REG              253,2    344064    622601 /var/lib/rpm/Providename
rhn_check 31261 root    5r   REG              253,0     19517    920332 /usr/share/rhn/actions/packages.py
rhn_check 31261 root    6u  unix 0xffff8106770ba980           901384670 socket
rhn_check 31261 root    7w   REG              253,2       107     32851 /var/log/yum.log

As you see there are many other files which are still in use and the command rhn_check still seems to be executing. Now at this point of time you need to decide if the space is important or the service/command executing. Because if you go ahead and kill that PID then the service responsible with this PID would be dead affecting your applications and usage.

In my case the rhn_check command is not of very much importance at this point of time so I can go ahead and kill it

# kill -9 31261

 

$ df -h /var/
Filesystem            Size  Used Avail Use% Mounted on
/dev/mapper/VolGroup00-var
3.9G  3.0G  703M  82% /var

The other better option for this problem is restart the required service. For example if any of your service like named, httpd etc are locking any deleted files so it is better to restart the service. With this all the locked deleted files would be released. So instead of killing the PID this can be a better option.

Source :
https://www.golinuxhub.com/2014/06/df-shows-100-full-partition-even-when.html