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Getting the sum

 
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# 1  
Old 12-10-2011
Getting the sum
I am trying to get the sum of the first column of a file. When I use the same method for other files it works just fine... for some reason for the file below it gives me an error that I don't understand... I tried looking at different lines of the file and tried different things, but I still don't know what the problem is... any idea?

This is my input:

Code:
awk '{sum+=$1} END {print "The sum for age 4Myr with a reddening of 00 = ",sum}' ResultOfChiNGC1856A.dat

And this is the error I get (and I don't understand!)

Code:
awk(10378)  malloc: *** error for object 0x10086e400: incorrect checksum for freed  object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
Abort trap

The file ResultOfChiNGC1856A.dat is below.

Thank you so much in advance!

(I can't attch/ post the file, it is too big!)
# 2  
Old 12-11-2011
Your last line answered your own question - the file may have too many rows for your version of awk. Or too much data.

Code:
ls -l ResultOfChiNGC1856A.dat
wc -l ResultOfChiNGC1856A.dat

What do these commands show? And important: does wc -l show the number of rows you expected in the file? I am asking in case of file corruption. Barring corruption the file may be REALLY large, hence the ls -l question.

One for you - what is χ NGC 1856a - I can't seem to look up that NGC number 1856?
# 3  
Old 12-11-2011
Quote:
Originally Posted by jim mcnamara
Your last line answered your own question - the file may have too many rows for your version of awk. Or too much data.

Code:
ls -l ResultOfChiNGC1856A.dat
wc -l ResultOfChiNGC1856A.dat

What do these commands show? And important: does wc -l show the number of rows you expected in the file? I am asking in case of file corruption. Barring corruption the file may be REALLY large, hence the ls -l question.

One for you - what is χ NGC 1856a - I can't seem to look up that NGC number 1856?

What confuses me is the 8 files were created in the same exact way (shown below) the sum script works for 6 of them and doesn't work for 2!!
The number of line (wc -l) is 165 as expected. Here is how these files were created (that's why I am not getting what is different about getting the sum of 2 of these ResultChiNGC*): SmilieSmilieSmilie

Code:
awk '{print "awk \47{gsub(\/FileHere\/,\"GALEVw"$2".dat\");print}\47 Step2.dat > ApplyGALEVw"$2".exe"}' ClustersWNames.dat > SpecifyChiSqrt.exe
chmod +x *exe
./SpecifyChiSqrt.exe
awk '{print "./ApplyGALEVw"$2".exe > ResultOfChi"$2".dat"}' ClustersWNames.dat > ApplyChiSqrt.exe
chmod +x *exe
./ApplyChiSqrt.exe

(NGC1985 is a star cluster in the LMC)
# 4  
Old 12-11-2011
$1 should be a number. Correct?
Code:
cut -d ' ' -c 1   ResultOfChiNGC1856A.dat

will show you what column one is. With 165 lines you should be able to see anomalous data.

Sometimes data will have non-printing characters that cause big problems. If that is the case (meaning you saw nothing from try #1 above):

Code:
cut -d ' ' -c 1   ResultOfChiNGC1856A.dat | cat -v

You will see octal numbers like "^037" or "^?" with non-ascii (>127) if there there are problems. The carat precedes a non-printing character.
# 5  
Old 12-11-2011
Also, it looks like you are writing to a compiled intermediate file that you then execute? What exactly is the .exe file?

That is sufficiently off-the-wall to merit looking into as well. JUst because it works sometimes does not allow us to assume it always works correctly.

And what UNIX are you on?
# 6  
Old 12-11-2011
Quote:
Originally Posted by jim mcnamara
Also, it looks like you are writing to a compiled intermediate file that you then execute? What exactly is the .exe file?

That is sufficiently off-the-wall to merit looking into as well. JUst because it works sometimes does not allow us to assume it always works correctly.

And what UNIX are you on?
This is what I get (it looks like something is missing?):


Code:
cut -d ' ' -c 1   ResultOfChiNGC1856A.dat
usage: cut -b list [-n] [file ...]
       cut -c list [file ...]
       cut -f list [-s] [-d delim] [file ...]

---------- Post updated at 12:26 PM ---------- Previous update was at 12:24 PM ----------

This is the *.exe file:

Code:
head -3 SpecifyChiSqrt.exe 
awk '{gsub(/FileHere/,"GALEVwNGC1711all.dat");print}' Step2.dat > ApplyGALEVwNGC1711all.exe
awk '{gsub(/FileHere/,"GALEVwNGC1856A.dat");print}' Step2.dat > ApplyGALEVwNGC1856A.exe
awk '{gsub(/FileHere/,"GALEVwNGC1903A.dat");print}' Step2.dat > ApplyGALEVwNGC1903A.exe

# 7  
Old 12-11-2011
cut -d ' ' -c 1 ResultOfChiNGC1856A.dat --> you're using a delimiter which will cut input into fields, so you cannot use -c switch which will cut out characters.

To delimit input (with ' ' as FS) and print field 1, try cut-d' ' -f1 or if you want the first character alone from input, try cut -c1
 
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