I have an extraordinary problem with a csh script.....(feel free to berate the use of this but I'm modifying an existing bunch of them)
Anyway, I have a master csh script which in turn calls a second csh script. This second csh script is below. Within this second script are two compiled C++ programs that are called to perform two different tasks.
#!/bin/csh
# This script is set up to execute in the directory it is called from
# (ie. The ${PAT_ID} variable is actually = DIAP_xCM_LES_yyMM/wi/ANG)
if ( ${#argv} == 0 ) then
echo " Please input gantry angle (format = 000) "
exit 1
endif
set ANG=${1}
foreach t ( 0 2 4 6 8 ) # so t1 will be set to values of 1,2,3,4,5
set t1=`echo " scale=0; ( $t + 2 ) / 2" | bc -l`
echo " Mapping dose cube ${t1}... "
# Perform the defomation of the dose cubes for each phase using the NCAT deformation vectors and function NCAT_2_MCdose
/scratch5/jseco/bin/NCAT_2_MCdose /scratch5/jseco/DPM/NCAT/DEFORMATION_VECTORS/ncat_diap_1cm_ph${t1}to1_vec.dat ${ANG}_ph${t1}_w1_H2O.3ddose 256 256 256 1 0
mv dose_out.3ddose ${ANG}_ph${t1}to1_mapped.3ddose
rm ${ANG}_ph${t1}_w1_H2O.3ddose
end
# add the mapped dose cubes together to get a total dose cube for this beam
echo " Adding mapped dose cubes for angle ${ANG}... "
/scratch5/jseco/..../add_dose_joao_weighted ${ANG}_total_mapped.3ddose ${ANG}_ph?to1_mapped.3ddose 0.2 0.2 0.2 0.2 0.2
# get rid of mapped dose cubes so only dose cube left for this run is the total for this beam and move it into the run directory to sum
#rm ${ANG}_ph*to1_mapped.3ddose
The problem is that only part of the script is being executed. The 'foreach' loop is completed without fail and does exactly what it is supposed too - calls the NCAT_2_MCdose C++ function (which is an image deformation type program). This tells me that the parent script is calling the second script correctly. However, when it attempts to execute the next line of
/scratch5/jseco/...../add_dose_joao_weighted ${ANG}_total_mapped.3ddose ....
it fails. This function has execution permission and the path is correct. Now for the truly strange part. When I run the second script with these two C++ functions in it from the command line it executes perfectly. However, executing it from the parent (first script) only performs the foreach loop and the second program isn't even called (I can't even get any stout or sterr output to be written using the 1> and 2> redirection options.
Is there any suggestions to resolve this? I've spent 2 straight days on this and have finally conceded that I don't know enough and would really appreciate a fresh outlook on this.
Edit: I should add, this second function takes 5 files (with naming convention ${ANG}_ph1to1_mapped.3ddose) and adds them together, each with a weighting of 0.2 with the result being output in the ${ANG}_total_mapped.3ddose. Again, this command works flawlessly when used separately on the command line, or by running this script independently from the parent program.