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Cleaning out rootfs and VolGroup-lv_root

asked 2012-03-22 15:45:26 -0500

KFerraro gravatar image

updated 2014-09-29 00:11:16 -0500

mether gravatar image


Hoping someone can help me out a bit. I'm new to linux and am using the OS to run DNA sequence assembly software. After an overnight run I noticed that the program failed due to insufficient memory. A little internet reading and command prompt toying led me to this:

Filesystem                    Size  Used Avail Use% Mounted on
rootfs                         50G   48G     0 100% /
devtmpfs                       20G     0   20G   0% /dev
tmpfs                          20G  8.0K   20G   1% /dev/shm
/dev/mapper/VolGroup-lv_root   50G   48G     0 100% /
tmpfs                          20G   49M   20G   1% /run
tmpfs                          20G     0   20G   0% /sys/fs/cgroup
tmpfs                          20G     0   20G   0% /media
/dev/sdb3                     497M   96M  377M  21% /boot
/dev/mapper/VolGroup-lv_home  344G   36G  291G  12% /home

I did see another thread about this type of a problem but the responses seemed focused on finding the cause. In this case, I'm aware of the cause (Trinity RNA-Seq software max memory not set) but cannot figure out how to clear rootfs and VolGroup-lv_root.

Thanks in advance

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answered 2012-03-23 08:13:29 -0500

René Rask gravatar image

You most likely have a lot of temporary files somewhere on your root filesystem. In this case rootfs and VolGroup-lv_root are the same thing.

Check size of /tmp and /var/tmp by running this command: du -hs /tmp /var/tmp

Otherwise check the /var directories with: du -hs /var/* If you run your program as root it could be somewhere in /root.

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answered 2012-03-23 15:28:49 -0500

mooninite gravatar image

You can use a program called "baobab" to find the largest files in your rootfs and move them or delete them.

Configure your DNA sequence app to store its files on your home partition. You may need to create a symbolic link to your lv_home LVM volume so that your root file system keeps its free space if the app cannot be configured.

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Asked: 2012-03-22 15:45:26 -0500

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Last updated: Mar 23 '12