[emboss-dev] Profiling and testing water

[Guermonprez, Paul]

hello,

you can find an software optimisation note for water here :
http://www.guermonprez.net/projects/emboss/emboss-EBI_06_06.pdf
http://www.guermonprez.net/projects/emboss/emboss-runsh.tar.gz

the sources are last year emboss release.
11-12x speedup on regular servers (serially).
feel free to send comments.

regards, paul.


-----Original Message-----
From: emboss-dev-bounces at lists.open-bio.org on behalf of Peter Rice
Sent: Fri 4/13/2007 11:09 AM
To: emboss at emboss.open-bio.org
Cc: emboss-dev at emboss.open-bio.org
Subject: [emboss-dev] Profiling and testing water
 
Vivek Menon wrote:
> Hello all, I am having issues compiling the water and needle programs from
> the EMBOSS package.

That makes 3 related requests in the past week! It seems profiling and looking
at the code for water is becoming popular.

For those who want to play with the code, it may be helpful to describe how the
EMBOSS QA testing works. So far this has just been run internally to check that
code changes have not broken anything.

Firstly, edit file test/.embossrc to set the locations of the source test
directory (emboss_qadata) and the installed test directory (emboss_testdata).

The install directory is used for the test databases tsw, tembl (etc.) provided
with the EMBOSS distribution. The source test directory is used so that the
results of one test can be used in another.

cd to the source test directory.

cd to the qa subdirectory.

Run all the QA tests using:
../../scripts/qatest.pl -without=srs

(the command line option turns off tests that require SRS installed locally)

Run one selected QA test:

../../scripts/qatest.pl water-ex

Tests run in a subdirectory with the name of the test (test/qa/water-ex)

If the test succeeds, the directory is removed (the command line option -kk
keeps the directory).

New tests are easy to define - add them to test/qatest.dat Each test has to have
a unique name. Descriptions of the definition line types are in the top of the file.

Tests assume files stderr and stdout are created and empty. All other output
files must be included in the test definition (getting a surprise new file is an
error).

The .embossrc file defines the date to be 15-jul-2006 so do not be surprised if
you see that date in your output - we use it to keep the results constant when
updating the documentation. All the *-ex tests are examples for the manuals.

Have fun!!!

Peter

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