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In a huge file, Delete duplicate lines leaving unique lines

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# 1  
Old 08-02-2011
In a huge file, Delete duplicate lines leaving unique lines

Hi All,

I have a very huge file (4GB) which has duplicate lines. I want to delete duplicate lines leaving unique lines. Sort, uniq, awk '!x[$0]++' are not working as its running out of buffer space.

I dont know if this works : I want to read each line of the File in a For Loop, and want to delete all the matching lines leaving 1 line. This way I think it will not use any buffer space.
PS: Idea is not use any second file.
Suggestions please.

input data:

output data:


Last edited by radoulov; 08-02-2011 at 11:07 AM.. Reason: Code tags!
# 2  
Old 08-02-2011
What's the exact error message returned by the awk command?

awk '!x[$0]++' infile

# 3  
Old 08-02-2011
awk: cmd. line:1: (FILENAME=result FNR=6094197) fatal: assoc_lookup: bucket->ahname_str: can't allocate 423 bytes of memory (Cannot allocate memory)

---------- Post updated at 09:21 AM ---------- Previous update was at 09:19 AM ----------

command i tried:
awk '!x[$0]++' result > result_new

Last edited by radoulov; 08-02-2011 at 11:22 AM.. Reason: Code tags.
# 4  
Old 08-02-2011
Try with Perl:

perl -ne'
  print unless $_{$_}++ 
  ' infile

# 5  
Old 08-02-2011
You can split the file (with "split" command), then "sort -u" the chunks separately and then merge them with "sort -m". (Of course whether you need it depends on the memory size of your system).
This User Gave Thanks to yazu For This Post:
# 6  
Old 08-02-2011
Sorry not the mention .. "thanks for your prompt replies".

Now I am running ..
perl -ne'print unless $_{$_}++' result > result_new2

I am getting the error messge - Segmentation fault

Last edited by radoulov; 08-02-2011 at 11:35 AM.. Reason: Code tags.
# 7  
Old 08-02-2011
Try the solution suggested by yazu:

split -l 1000000 infile

for f in x*; do
  sort -u "$f" > "$f"_sorted

sort -u x*_sorted > final.out

I believe the final sort should be with -u (not -m).

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