Posts Tagged Scripting

Clustercomputing with mpirun and torque

Posted by on Wednesday, 18 July, 2012

Some time ago I wrote about Clustercomputing with Torque, with a focus on discrete event simulations (using the method of independent replications). Turns out that method was not really efficient, so we try something else. Read the rest of this entry »

Finding duplicate files

Posted by on Wednesday, 23 May, 2012

You have a bunch of files (for instance, jpegs). Over time they get moved around, you get a bunch from some family members and before you know it you have a situation where you have the same file multiple times. Of course you can manually sort out these duplicates, but you can also automate duplicate detection.

After a short search, I found this solution on LinuxQuestions.org:

tmp=$(mktemp)
find . -type f |xargs md5sum > $tmp
awk '{ print $1 }' $tmp |sort |uniq -d |while read f; do 
    grep "^$f" $tmp
    echo ""
done

This outputs a list of duplicate files once it has run to completion.

However, it borks when it encounters whitespaces, special characters like the apostrophe etc. A solution:

#!/bin/bash
tmp=$(mktemp)
find . -type f | sed -e "s/'/\\\'/g" |xargs  -I{} md5sum {} > $tmp
awk '{ print $1 }' $tmp |sort |uniq -d | while read f; do 
    grep "^$f" $tmp
    echo ""
done

Use the -I{} and {} to make sure the input to md5sum is not terminated by whitespaces, but only by endlines. Also, the “| sed -e “s/’/\\\’/g”” part replaces every occurence of the apostrophe “‘” with its escaped version “\'” as you would when entering it on the commandeline.

This is able to traverse deep into directory structures, and also accepts any filename I encountered in my dataset. It is however quite CPU intensive, as it calculates the MD5 hash for every file. If you only want to compare based on filename, the whole operation becomes a lot more lightweight.

Duplicate detection with locate/mlocate.db

Actually, it is not necessary to manually index all files, good chance this is already being done by the updatedb cronjob. For instance,

skidder@@spetznas:~$ locate fstab
/etc/fstab

and it also finds some other files containing the string fstab. Unfortunately, mlocate.db is a very simple list of filenames only – a file size and an MD5 would greatly ease the detection of duplicates. So far I have not found a way to do this more efficiently than the shellscript posted above.

Getting grip on eventlogs in OMNeT++

Posted by on Monday, 12 December, 2011

OMNeT++ simulations can export an eventlog. Though the manual is pretty complete about it, I’ll summarise it here. Read the rest of this entry »

OMNeT++: Error during startup: No user interface (Cmdenv, Tkenv, etc.) found

Posted by on Wednesday, 7 December, 2011

After an update of GCC (on Kubuntu 11.10) this error shows up when running simulations after recompilation.
Read the rest of this entry »

PHP Script for Calculating Confidence Intervals

Posted by on Tuesday, 29 November, 2011

Some time ago I wrote about a Shell Script for calculating confidence intervals. Since I also do a lot of number crunching with PHP (hey, it’s web-based and works great with an SQL server for the data!) I wrote a PHP script to get the job done. Here’s how. Read the rest of this entry »