My professor wrote this shell script to time my program, and display the results. For some reason it just outputs 0s with my program. He provided the following files:
timeit.csh
sequence
ecoli2500.txt
ecoli3000.txt
ecoli5000.txt
ecoli7000.txt
ecoli8000.txt
ecoli9000.txt
ecoli10000.txt
Here are the contents of sequence
java EditDistance
The contents of timeit.csh are further below.
java EditDistance < ecoli2500.txt works as expected
In fact the program executes flawlessly with each of the above files other than sequence.
What I don't understand is why
./timeit.csh sequence
produces all zeros
Here is timeit.csh... (further below is EditDistance.java):
#!/bin/csh
#
# A Unix script to time programs.
#
# Command line: timeit sequence
# the array of programs from the commandline
set program = $argv[1]
# adjust as needed
set CPULIMIT = 120
limit cpu $CPULIMIT seconds
limit core 0
# input files
set input = ( stx1230.txt \
ecoli2500.txt \
ecoli3000.txt \
ecoli5000.txt \
ecoli7000.txt \
ecoli8000.txt \
ecoli9000.txt \
ecoli10000.txt)
# adjust as needed
set inputpath = `pwd`
# print header
printf "CPU limit = %d seconds\n\n" $CPULIMIT
printf "%-25s" "Data File"
foreach program ($argv)
printf "%16s" $program
end
printf "\n"
# print right number of = for table
@ i = 25 + 16 * $#argv
while ($i > 0)
printf "="
@ i = $i - 1
end
printf "\n"
# time it and print out row for each data file and column for each program
foreach datafile ($input)
printf "%-25s" $datafile
if (-f $inputpath/$datafile) then
foreach program ($argv)
# printing running time of program on datafile
# -p flag with time to ensure its output is measured in seconds and not minutes
nice /usr/bin/time -p $program < \
$inputpath/$datafile |& \
egrep '^user[ ]*[0-9]' | \
awk '{ if ($2 >= '$CPULIMIT') printf " CPU limit"; else printf("%16.2f", $2) }'
# egrep, awk commands extract second column of row corresponding to user time
end
else printf "could not open" $datafile
endif
printf "\n"
end
Here is EditDistance.java
import java.util.*;
class EditDistance {
public static int min(int a, int b, int c) {
return Math.min(a,Math.min(b,c));
}
public static int distance(String one, String two) {
if (one.length()>two.length()) {
String temp1 = one;
String temp2 = two;
one = temp2;
two = temp1;
}
int[][] d = new int[one.length()+1][two.length()+1];
d[0][0] = 0;
int top, left, topleft, cost;
for (int i = 1; i <= one.length(); i++) {
d[0][i] = 2*i;
d[i][0] = 2*i;
}
for (int i = 1; i <= one.length(); i++) {
for (int j = 1; j <= two.length(); j++) {
if (one.charAt(i-1) == two.charAt(j-1))
cost = 0;
else
cost = 1;
top = d[i][j-1];
left = d[i-1][j];
topleft = d[i-1][j-1];
d[i][j] = min(top+2,left+2,topleft+cost);
}
}
return d[one.length()][two.length()];
}
public static void main(String[] args) {
Scanner scanner = new Scanner(System.in);
String one = scanner.next();
String two = scanner.next();
System.out.println(distance(one,two));
}
}
Any Ideas why things aren't working? I don't know much about shell scripts, but this section of the shell script:
nice /usr/bin/time -p $program < \
$inputpath/$datafile |& \
egrep '^user[ ]*[0-9]' | \
awk '{ if ($2 >= '$CPULIMIT') printf " CPU limit"; else printf("%16.2f", $2) }'
confirms in my mind that my program should be expecting this command:
java EditDistance < ecoli2500.txt
java EditDistance...etc. etc.
but the program works with those commands. I need to set up my program to respond correctly to the shell script. Maybe some of you can help.
