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Full Discussion: redirect time command output to file (cygwin bash)
Top Forums Shell Programming and Scripting redirect time command output to file (cygwin bash) Post 302671633 by LMHmedchem on Friday 13th of July 2012 09:13:55 PM
Old 07-13-2012
This is the ugly triple loop that I set up to run this long batch,
Code:
#!/usr/bin/bash

echo "testing output" > test_times.txt
echo "" >> test_times.txt

# list directory names here
SIZE=( 100K 500K 1M )

for SIZE in ${SIZE[@]}
do

   echo "Runtimes for servlet 4," $SIZE "structures" >> test_times.txt
   echo "" >> test_times.txt

   CPDS=( 10 100 500 1000 2500 5000 10000 25000 50000 )

   for CPDS in ${CPDS[@]}
   do

      echo "Runs where N="$CPDS >> test_times.txt 

      REP=( 1 2 3 4 5 )

      for REP in ${REP[@]}
      do

         echo 'run' $REP 'test_ActiMol_'$SIZE'.sdf -n 4 -t 1000 -l 100 -d t -N' $CPDS >> test_times.txt 
         time ./servert.exe -n 4 -t 1000 -l 100 -d t -N $CPDS \
         -i  'test_ActiMol_'$SIZE'.sdf' \
         -o  'test_ActiMol_100K_'$CPDS'N_'$REP'.s'  >> test_times.txt
         
         echo "   TIMEOUTS=" $(grep -c "TIMEOUT" 'test_ActiMol_100K_'$CPDS'N_'$REP'.s') >> test_times.txt
         echo "   SEGFAULTS=" $(grep -c "SEGFAULT" 'test_ActiMol_100K_'$CPDS'N_'$REP'.s') >> test_times.txt
         echo "   NUMBER PROCESSED=" $(wc -l 'test_ActiMol_100K_'$CPDS'N_'$REP'.s') >> test_times.txt

      done

      echo " " >> test_times.txt 

   done

      echo " " >> test_times.txt
      echo " " >> test_times.txt 

done

This works in every respect other than printing the output of time to the file. I am very unclear as to how to utilize the here-document in this context.

This is giving me the output I need,
Code:
Runtimes for servlet 4, 100K structures

Runs where N=10
run 1 test_ActiMol_100K.sdf -n 4 -t 1000 -l 100 -d t -N 10
   TIMEOUTS= 0
   SEGFAULTS= 0
   NUMBER PROCESSED= 100002 test_ActiMol_100K_10N_1.s
run 2 test_ActiMol_100K.sdf -n 4 -t 1000 -l 100 -d t -N 10
   TIMEOUTS= 0
   SEGFAULTS= 0
   NUMBER PROCESSED= 100002 test_ActiMol_100K_10N_2.s
run 3 test_ActiMol_100K.sdf -n 4 -t 1000 -l 100 -d t -N 10
   TIMEOUTS= 0
   SEGFAULTS= 0
   NUMBER PROCESSED= 100002 test_ActiMol_100K_10N_3.s
run 4 test_ActiMol_100K.sdf -n 4 -t 1000 -l 100 -d t -N 10
   TIMEOUTS= 0
   SEGFAULTS= 0
   NUMBER PROCESSED= 100002 test_ActiMol_100K_10N_4.s
run 5 test_ActiMol_100K.sdf -n 4 -t 1000 -l 100 -d t -N 10
   TIMEOUTS= 0
   SEGFAULTS= 0
   NUMBER PROCESSED= 100002 test_ActiMol_100K_10N_5.s

minus the times.

LMHmedchem

---------- Post updated at 08:44 PM ---------- Previous update was at 08:27 PM ----------

Quote:
Originally Posted by alister
time output is printed on the standard error, which hasn't been redirected.

Regards,
Alister
I have tried the following to get stderr appended to my output file,
Code:
   time ./servert.exe -n 4 -t 1000 -l 100 -d t -N $CPDS \
   -i  'test_ActiMol_'$SIZE'.sdf' \
   -o  'test_ActiMol_100K_'$CPDS'N_'$REP'.s' >>test_times.txt 2>&1

Code:
   time ./servert.exe -n 4 -t 1000 -l 100 -d t -N $CPDS \
   -i  'test_ActiMol_'$SIZE'.sdf' \
   -o  'test_ActiMol_100K_'$CPDS'N_'$REP'.s' 2>>test_times.txt

Code:
   time ./servert.exe -n 4 -t 1000 -l 100 -d t -N $CPDS \
   -i  'test_ActiMol_'$SIZE'.sdf' \
   -o  'test_ActiMol_100K_'$CPDS'N_'$REP'.s' &>>test_times.txt

the third one being a shot in the dark. None of these make any difference and I am still getting the time data printed to the terminal.

There always seems to be a hangup somewhere.

LMHmedchem

---------- Post updated at 09:13 PM ---------- Previous update was at 08:44 PM ----------

Apparently, but using the following command,
Code:
   time ./servert.exe -n 4 -t 1000 -l 100 -d t -N $CPDS \
   -i  'test_ActiMol_'$SIZE'.sdf' \
   -o  'test_ActiMol_100K_'$CPDS'N_'$REP'.s' >> test_times.txt 2>&1

I am redirecting the stderr and stdout of servert.exe to test_times.txt and not the stderr/stdout of time. This was fixed by grouping the time and servert.exe commands,
Code:
   ( time ./servert.exe -n 4 -t 1000 -l 100 -d t -N $CPDS \
     -i  'test_ActiMol_'$SIZE'.sdf' \
     -o  'test_ActiMol_100K_'$CPDS'N_'$REP'.s' ) >> test_times.txt 2>&1

with this revision, the output is as expected,
Code:
Runtimes for servlet 4, 100K structures

Runs where N=10
run 1 test_ActiMol_100K.sdf -n 4 -t 1000 -l 100 -d t -N 10

real	0m43.656s
user	0m0.015s
sys	0m0.015s
TIMEOUTS= 0
SEGFAULTS= 0
NUMBER PROCESSED= 100002 test_ActiMol_100K_10N_1.s

run 2 test_ActiMol_100K.sdf -n 4 -t 1000 -l 100 -d t -N 10

real	0m43.203s
user	0m0.031s
sys	0m0.015s
TIMEOUTS= 0
SEGFAULTS= 0
NUMBER PROCESSED= 100002 test_ActiMol_100K_10N_2.s

run 3 test_ActiMol_100K.sdf -n 4 -t 1000 -l 100 -d t -N 10

now I think I need to try to incorporate the here-document suggested by Corona688 to minimize the number of echo commands.

LMHmedchem
 

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