We recently worked with a user who had a job that exhibited this behavior (it segfaulted when run under HTCondor). It took us a while to figure out what the cause was -- environment variables under HTCondor differed only trivially from the command line (the job was using "getenv = true"), and the command line arguments were exactly the same.
We eventually figured out that the job was crashing because the file descriptor limit when run under HTCondor was higher than when it was run from the command line(!). This was a bit of a surprise, and clearly indicates problems in the code of the program; but it also points up an important, and somewhat non-obvious, way in which running a job under HTCondor differs from running it on the command line.
(HTCondor jobs inherit their limits from the HTCondor daemon that spawns them. In the case of the file descriptor limit, some HTCondor daemons need higher limits that most user jobs typically need. We are considering changing this in the future, but this is the current situation.)
At any rate, system limits are something to keep in mind when debugging this type of problem.
Another thing that is likely to be different between running on the command line and running under HTCondor is the umask setting (controlling the permissions of files created by the job). This is one more thing to check if you are having problems with jobs not working correctly under HTCondor.
Here's an example of a job that prints out the limits, changes the stack size limit, and prints out the limits again.
# File: change_limits.csh
#! /bin/csh limit echo "" echo "Changing stacksize" limit stacksize 4096 echo "" limit
# File: change_limits.sub
universe = vanilla executable = change_limits.csh output = change_limits.out queue
# File: change_limits.out
cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024
Changing stacksize
cputime unlimited filesize unlimited datasize unlimited stacksize 4096 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024
Note that the limits on your process under HTCondor will depend on your HTCondor configuration. Also, the limits may vary according to which universe your job runs under.