Posts Tagged ‘empty space’

Linux: Delete empty lines from text file with sed, awk, grep and vim

Saturday, March 23rd, 2013

Reading Time: < 1minute

As a system administrator, sometimes is necessary to do basic plain text processing for various sysadmin tasks. One very common task I do to remove empty lines in file. There are plenty of ways to do it i.e. – with grep, sed, awk, bash, perl etc.

1. Deleting empty file lines with sed

The most standard way to do it is with sed, as sed was written to do in shell quick regexp. Here is how;

sed '/^\s*$/d' file_with_empty_lines.txt > output_no_empty_lines.txt

2. Deleting empty file lines with awk

It is less of writting with awk, but I always forget the syntax and thus I like more sed, anyways here is how with awk;

cat file_with_empty_lines.txt | awk 'NF' >
output_no_empty_lines.txt

3. Deleting empty lines with grep

Grep  regular expression can be used. Here is grep cmd to cut off empty lines from file;

grep -v '^\s*$' file_with_empty_lines.txt >
output_no_empty_lines.txt

4. Delete empty files with vi / vim text editor

Open vi / vim text editor

$ vim

Press Esc+: and if empty lines doesn't have empty space characters use command

g/^$/d

Whether, empty lines contain " " – space characters (which are not visible in most text editors), use vi cmd:
g/^ $/d

How to solve “Incorrect key file for table ‘/tmp/#sql_9315.MYI’; try to repair it” mysql start up error

Saturday, April 28th, 2012

Reading Time: 2minutes

When a server hard disk scape gets filled its common that Apache returns empty (no content) pages…
This just happened in one server I administer. To restore the normal server operation I freed some space by deleting old obsolete backups.
Actually the whole reasons for this mess was an enormous backup files, which on the last monthly backup overfilled the disk empty space.

Though, I freed about 400GB of space on the the root filesystem and on a first glimpse the system had plenty of free hard drive space, still restarting the MySQL server refused to start up properly and spit error:

Incorrect key file for table '/tmp/#sql_9315.MYI'; try to repair it" mysql start up error

Besides that there have been corrupted (crashed) tables, which reported next to above error.
Checking in /tmp/#sql_9315.MYI, I couldn't see any MYI – (MyISAM) format file. A quick google look up revealed that this error is caused by not enough disk space. This was puzzling as I can see both /var and / partitions had plenty of space so this shouldn't be a problem. Also manally creating the file /tmp/#sql_9315.MYI with:

server:~# touch /tmp/#sql_9315.MYI

Didn't help it, though the file created fine. Anyways a bit of a closer examination I've noticed a /tmp filesystem mounted besides with the other file system mounts ????
You can guess my great amazement to find this 1 Megabyte only /tmp filesystem hanging on the server mounted on the server.

I didn't mounted this 1 Megabyte filesystem, so it was either an intruder or some kind of "weird" bug…
I digged in Googling to see, if I can find more on the error and found actually the whole mess with this 1 mb mounted /tmp partition is caused by, just recently introduced Debian init script /etc/init.d/mountoverflowtmp.
It seems this script was introduced in Debian newer releases. mountoverflowtmp is some kind of emergency script, which is triggered in case if the root filesystem/ space gets filled.
The script has only two options:

# /etc/init.d/mountoverflowtmp
Usage: mountoverflowtmp [start|stop]

Once started what it does it remounts the /tmp to be 1 megabyte in size and stops its execution like it never run. Well maybe, the developers had something in mind with introducing this script I will not argue. What I should complain though is the script design is completely broken. Once the script gets "activated" and does its job. This 1MB mount stays like this, even if hard disk space is freed on the root partition – / ….

Hence to cope with this unhandy situation, once I had freed disk space on the root partition for some reason mountoverflowtmp stop option was not working,
So I had to initiate "hard" unmount:

server:~# mount -l /tmp

Also as I had a bunch of crashed tables and to fix them, also issued on each of the broken tables reported on /etc/init.d/mysql start start-up.

server:~# mysql -u root -p
mysql> use Database_Name;
mysql> repair table Table_Name extended;
....

Then to finally solve the stupid Incorrect key file for table '/tmp/#sql_XXYYZZ33444.MYI'; try to repair it error, I had to restart once again the SQL server:

Stopping MySQL database server: mysqld.
Starting MySQL database server: mysqld.
Checking for corrupt, not cleanly closed and upgrade needing tables..
root@server:/etc/init.d#

Tadadadadam!, SQL now loads and works back as before!