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Empty rootfs and VolGroup-lv_root

asked 2012-03-22 15:44:02 -0500

KFerraro gravatar image

updated 2014-09-29 00:12:16 -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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2 Answers

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answered 2012-03-22 17:31:37 -0500

skytux gravatar image

Maybe you need more room in your /, and you can do that by decreasing the size of your /home and increasing / using logical volumes tools.

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answered 2012-03-22 17:14:03 -0500

KevinA gravatar image

My typical process for finding what is taking space is the following:

cd / #change to the root of the filesystem 
du -sxh * #calculate the size of the top level folders including all the contents below

Once that completes it will look something like this:

11M  bin
44M  boot
4.0K    cgroup
0   dev
52M etc
68G home
397M    lib
31M lib64
16K lost+found 
0   media
12K mnt
281M    opt
0   proc
123M    root
19M run
20M sbin
8.0K    selinux
4.0K    srv
0   sys
192K    tmp

After that you can see what directory is claiming all of the space. When you find the culprit you can cd in to that directory and issue the same commands to find the exact files.

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Asked: 2012-03-22 15:44:02 -0500

Seen: 803 times

Last updated: Mar 22 '12