Fix some of lisa's barchart changes

util/stats/barchart.py:
- there is no self.inner_axes
- don't append an empty value to self.xsubticks, otherwise
subsequent calls will get extra empty ticks
- rotate labels 30 degrees instead of 90 so it looks better

code cleanup

util/stats/barchart.py:
clean up some of lisa's messy code
remove trailing whitespace while I'm at it.

add error bars and more options for legend placement

util/stats/barchart.py:
Add support for error bars
util/stats/barchart.py:
add support to choose between a legend inside or
outside the figure.

better colors for barcharts

util/stats/barchart.py:
If there are fewer than 5 colors, pick from a subset of
5 so there is more consistency in colors between graphs

1) make it pretty for large clusters
2) make subticks vertical so they can be longer
3) make inner and outer axes farther apart to make room for subtick's vertical labels

few changes for nate:
1) cosmetic - removing visibility of meta axes except for the tick labels.
2) unless subticklabels defined, don't do meta axes. (instead of assuming if you have 3D graph, do meta axes)

remove print statements

more changes for subtick labels.

util/stats/barchart.py:
oop forgot this for 1D graph cases.
util/stats/chart.py:
need to add default param to chart.

Now you can have sublabels for every bar using the self.xsubticklabels parameter.

Major improvements in the graph output code. Mostly adding more
options, making existing options more visible and dealing with
holes in data better.

util/stats/barchart.py:
- move the options for BarChart to a base class ChartOptions so
they can be more easily set and copied.
- add an option to set the chart size (so you can adjust the aspect ratio)
- don't do the add_subplot thing, use add_axes directly so we can
affect the size of the figure itself to make room for the legend
- make the initial array bottom floating point so we don't lose precision
- add an option to set the limits on the y axis
- use a figure legend instead of an axes legend so we can put the legend
outside of the actual chart. Also add an option to set the fontsize of
the legend.
- initial hack at outputting csv files
util/stats/db.py:
don't print out an error when the run is missing from the database
just return None, the error will be print elsewhere.
util/stats/output.py:
- make StatOutput derive from ChartOptions so that it's easier to
set default chart options.
- make the various output functions (graph, display, etc.) take the
name of the data as a parameter instead of making it a parameter to
__init__. This allows me to create the StatOutput object with
generic parameters while still being able to specialize the name
after the fact
- add support for graph_group and graph_bars to be applied to multiple
configuration groups. This results in a cross product of the groups
to be generated and used.
- flush the html file output as we go so that we can load the file
while graphs are still being generated.
- make the proxy a parameter to the graph function so the proper system's
data can be graphed
- for any groups or bars that are completely missing, remove them from
the graph. This way, if we decide not to do a set of runs, there won't
be holes in the data.
- output eps and ps by default in addition to the png.
util/stats/profile.py:
- clean up the data structures that are used to store the function
profile information and try our best to avoid keeping extra data
around that isn't used.
- make get() return None if a job is missing so we know it was
missing rather than the all zeroes thing.
- make the function profile categorization stuff total up to 100%
- Fixup the x-axis and y-axis labels.
- fix the dot file output stuff.
util/stats/stats.py:
support the new options stuff for StatOutput

Totally re-work the way that jobfiles are done so there is more
information that can be used for other aspects of sending jobs.
New graphing output stuff with matplotlib.

util/pbs/job.py:
Shuffle code around and create the JobDir class which encapsulates
all of the functionality needed for making, organizing, and cleaning
a job directory.
Better status output
util/pbs/jobfile.py:
Majory re-working of the jobfile code.
A job file now consists of several objects that describe how
jobs should be run, it includes information about checkpoints,
and graphing.
util/pbs/send.py:
use the new jobfile code.
deal with the 15 character limit of pbs by truncating the name and
using the raj hack.
util/stats/db.py:
fix the __str__ function for nodes
provide __getitem__ for the Database class
util/stats/stats.py:
use the jobfile stuff to figure out what the proper naming
and organziation of the graphs should be.
move all output code to output.py, get rid of ploticus and use
matplotlib