Parallel CLUSTAL X 1.8 available on SGI/IRIX

Haruna Cofer haruna at columbus.sgi.com
Wed Dec 1 16:42:56 EST 1999


Hello!

This is just a quick message to let you know that SGI has implemented
the parallel features of Parallel CLUSTAL W 1.8 into CLUSTAL X 1.8.  So
if any of you are interested in Parallel CLUSTAL X on SGI/IRIX, then
simply go to the following page:

  http://www.sgi.com/chembio/resources/clustalw/parallel_clustalw.html

And when you click the "I accept" button at the bottom of the page (the
software is of course free), then both Parallel CLUSTAL W
("clustalw_mp") and Parallel CLUSTAL X ("clustalx_mp") will be
downloaded in the same file together.

Thank you very much for your support, and please do let me know if you
have any questions or problems!  Just FYI, I have attached the README
file for Parallel CLUSTAL W and Parallel CLUSTAL X, which are available
for IRIX 6.2 and IRIX 6.5.

With regards,

Haruna Cofer  :)

=====

12 November 1999

This distribution contains a parallelized version of CLUSTAL W 1.8
and CLUSTAL X 1.8 for SGI systems running IRIX 6.5.  Specifically, 
the Pairwise Alignments and Guide Tree computations are parallelized.

It should be noted that these releases use a modification of the
original 
pairalign.c file, which was modified to fix a memory access bug in the 
original code.  Specifically, the original CLUSTAL W and CLUSTAL X codes
read beyond the bounds of an allocated array, resulting in either a 
numerical error or a core dump of the program.  The change made in 
pairalign.c (in both CLUSTAL W and CLUSTAL X) is as follows:

 Replace line 214 of pairalign.c:

   maxscore = diff(sb1, sb2, se1-sb1+1, se2-sb2+1, (sint)0, (sint)0);

 with the following line:

   maxscore = diff(sb1-1, sb2-1, se1-sb1+1, se2-sb2+1, (sint)0,
(sint)0);


To use the parallelized versions of CLUSTAL W and CLUSTAL X, simply set 
the MP_SET_NUMTHREADS environment variable to the number of processors 
you want to use.  For example, to use 4 processors:

 setenv MP_SET_NUMTHREADS 4

If this environment variable is not set, then the default is to use
the maximum number of processors on your machine.  Then use the
"clustalw_mp" executable to run the parallelized version of CLUSTAL W,
and the "clustalx_mp" executable to run the parallelized version of
CLUSTAL X, in the same way you would use the original "clustalw" and
"clustalx" programs.  

With CLUSTAL X, however, there is an additional option available 
(-noinfo) that will suppress the status messages that are by default
generated at the bottom of the CLUSTAL X window during the Pairwise 
Alignment calculation.  Using the -noinfo option can significantly 
improve the performance of the Pairwise Alignments, since it eliminates 
the communication and synchronization required to write the status 
messages to the X window.  To use the -noinfo option, simply call 
clustalx_mp with the -noinfo option: 
 
 clustalx_mp -noinfo

The clustalx_help file, included in this distribution, has been amended 
to include the additional -noinfo option.

Please send questions or problems to Haruna Cofer (haruna at sgi.com).

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