[GenABEL-dev] Benchmarks: Speed of ProbABEL

[L.C. Karssen]

Dear list,

I've started doing some benchmarks for ProbABEL. In the attached figures
you can see how much time (s) an analysis took for a given version of
ProbABEL. The only difference in the figures are the limits of the
vertical axis.

Notes:
- Each analysis was run 3 times, and the average is shown (as well as
the error bars for the std.dev., but these are not/hardly visible)
- v0.4.3 means SVN trunk
- v0.5.0 means SVN branch probabel-0.50, checked out last Satureday,
after Maarten's 10x speedup of reading text files.
- The reduction in mmscore run time at v0.3.0 is because of the use of
the EIGEN lib.
- The fact that Cox regression has zero run time before v0.4.0 is
because only since that version does that module work without manual
intervention.
- The increase in run time for filevector data at v0.4.0 is attributable
to the fact that since then the fv data is no longer simply cast from
float to double, but converted via a string, followed by strtod(). This
is very time consuming, especially in v0.4.0/0.4.1 when C++ streams were
used.

Description of the benchmarks:
- CPU Core i7
- RAM: 12 GB (was never a limiting factor)
- Disk: SSD
- All benchmarks were run 3 times, consecutively (i.e. only a single
core was used)
- The EIGEN lib was used when compiling each version.



So, two conclusions:
- We must always benchmark our code before release, it would have caught
the use increase in run time at v0.4.0
- ProbABEL v0.5.0 will be a great release!



Best,

Lennart.

-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

l.c.karssen at gmail.com
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
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