Save the egs-parallel log inside an *.egsparallel file in the
application directory, and add a verbosity option (-v) to also echo the
log to screen. By default the scripts proceed silently, unless an error
condition arises, which is always echoed to the terminal.

Notably, save log message to a log file, add a verbosity option (-v),
and allow joined single-letter options and argument (without a space
between the option and its argument, as in "-n123").

Apart from format and other minor adjustments, update the standard pbs
script egs-parallel-pbs (whereby EGSnrc jobs are submitted individually)
so that only the second job waits for the .egsjob file and the .lock
file, since the jobs are submitted sequentially anyways.

This egs-parallel-cpu subscript provides the option "--batch cpu" to
egs-parallel, to launch a simulation on multiple cores on the local cpu,
without requiring a job scheduler. Intentionally, this script is simple:
it just launches the jobs sequentially, without waiting around for the
.egsjob or .lock files, as in the pbs scripts. However, the logging is
consistent with the other egs-parallel scripts

The number of threads is always constrained to the number of threads
available on the machine, because it is inefficient to go beyond that,
and launching a large number of threads on a cpu by mistake may well
stall the computer.

Improve the script robustness, in particular by forcing the user to
specify either the -n (--dry-run) option, or the -f (--force) option to
actually remove files, to prevent accidental erasing (to some extent).
This script removes files without warnings (when using -f), so use with
caution: run with the -n option first to see what will be deleted.

Add the concatenation and sorting of egs-parallel log messages into the
.egsparallel file for reference. This is useful, because these log
messages may be scattered in different files, for example the .eo files
from pbs. After cleaning, the .egsparallel contains a time-ordered
sequence of messages from egs-parallel and its subscripts.

Strictly speaking, there can be multiple threads per hardwarde core;
this is typical in modern workstations. Change "ncore" to "nthread"
throughout the egs-parallel scripts, to avoid confusion.

Add a bin directory in HEN_HOUSE/scripts and add it to the PATH in the
shell additions scripts. This allows some EGSnrc scripts to be directly
executable by a user, without using aliases (which are not inherited by
subshells). The immediate motivation is for the top-level egs-parallel
script, and the egs-parallel-clean script, to become visible on the
path, while the egs-parallel sub-scripts remain in scripts and are not
in the path (these should not be invoked directly).

Do not source the shell additions scripts from within the egs-parallel
sub-scripts, as this is not necessary and not secure. Sourcing was only
needed in the dshtask script to get the path to the EGSnrc executables,
because tasks are launched on the pbs nodes without inheriting the
environment. In this case, simply export the PATH variable via the
pbsdsh qsub script.

Use a more portable date command format for the timestamp string, and
tweak the usage message of egs-parallel scripts.

Add -x (--extra) option to clean up egs-parallel log files .egsparallel
and .egsparallel.eo. Although this script always echoes progress to the
terminal, add a -v (--verbose) option to echo the commands that are run
by the script, instead of the more concise messages usually reported.
Internally, add an "action" command to ensure that the log messages
remain up to date with the commands.

For convenience, add a -l (--list) option to the cleaning script to list
all the .egslog file base names in the current directory. This option is
checked first and overrides every other argument: the list is printed to
the terminal and the script terminates. Also, reformat the usage message
and use the extension .egsparallel-eo (with a hyphen) to avoid collision
with the pbs .eo extension. Use executable basename in quit function.

Change the initial value of the --batch option to "cpu" so that the
script invokes the multicore parallel sub-script (egs-parallel-cpu) when
no --batch option is specified on the command line. This allows users to
try egs-parallel out of the box (most computers are multicore nowadays)
without worrying about schedulers.

Don't quit the egs-parallel submit scripts if no lock file is found, and
add a -f (--force) option to override existing .egsjob or .lock files.

The lock file for parallel jobs is managed inside EGSnrc, so the script
should not manage it as well: this creates an obscure correlation
between the code and the script. Moreover, the uniform run control
method does no create a lock file. Previously, the submit script would
quit if there was no lock file. The top-level egs-parallel script now
prevents the run if there is an .egsjob file OR a .lock file, for the
same reason. This can be overridden with the added --force option.

Detect pbs jobs that fail to launch in egs-parallel, by looking at the
echoed job pid: quit immediately if it is not an integer. If the first
job fails, subsequent jobs are not launched. Report the failure in the
log. Also adjust the format of a few log messages.

Fix a crash that occurred when the 14 character truncation of the
filename for an egs-parallel pbsdsh job ended up starting with a '.'.
The first character is now trimmed away if that is the case, so the job
name is only 13 characters.

Ensure that the PBS job name starts with an alphanumeric character
[0-9A-Za-z], following the PBS scheduler requirement. To avoid failed
jobs solely on the account of a bad job name, strip all leading
non-alphanumeric characters from the job name. Note that the egsinp
basename is not affected, this is strictly for the job name passed to
qsub via the -N option.