Update

[Daniel Gates]

Greetings TreEvo group!

I finished a TreEvo run on the mac computers in our lab (hooray!) and
added the run file, profile output and workspace printout to the
folder CompletedProf.

I was comparing the two profile outputs (the summaryRprof output vs.
Derrick's python script) and noticed some big differences that I was
hoping someone could give me a bit more background on. Mostly I was
curious about the self# and total# output in the python script. I was
under the impression that we couldn't get info about the number of
times a function is called given the Rprof output but the self# seems
to be quite different in the python profile than the R profile (for
example ConvertTaxonFrameToGeiger has a self% of nearly 25% in the
python script and a self# of +1000 but has a 0 self time and 0 self %
in the summaryRprof output...). I was wondering what could be causing
this difference and how I should interpret this going forth.

Before I realized that the convertTaxonFrameToGeiger didn't really
register in the summaryRprof timing I went ahead and vectorized the
one little for loop in it. It seems like it could make a difference if
the function was called frequently but would be totally negligible if
the summaryRprof output is correct. The file set up to run the
modified function is in the ConvertTaxtoGeiger folder

Thanks!
-Dan

[Derrick Zwickl]

Hi Dan,

Well, I'm back home from DC, after getting trapped in Dallas last night
due to bad weather. Annoying.

This is embarrassing, but the oddities that you are seeing there are due
to a bug in my parsing script. I was getting overly fancy with negative
slicing and strides. I committed the fix. Sorry about that. See if it
make more sense now.

Cheers,
Derrick

[Daniel Gates]

Hi Derrick,

I'm not sure this code is working on my end. For example
when I run

>python parseRprof.py ./CompletedProf/doRun_labMac.out

I get:

Traceback (most recent call last):
File "parseRprof.py", line 54, in <module>
toplevel.add_children(reversed(samp))
File "parseRprof.py", line 22, in add_children
if len(child_list) == 0:
TypeError: object of type 'listreverseiterator' has no len()


It seems like I have things set up correctly but I could be running it
wrong


-Dan

[Derrick Zwickl]

D'oh, update again. Sorry.

Derrick