[Next-Generation Sequencing Book]
  • [Photo] J.W. Bizzaro • September 21, 2000
    ``The real problem arises in lab use where a scientist has to compare a new gene sequence to an existing database of hundreds of thousands of sequences. There are already a lot of web sites to do this but this particular piece of software was supposed to be `ours' (sigh). At first I didnt know much about the whole subject so I decided to conduct an experiment using a dynamic programming algorithm. To be fast, C was the programming language choice. The sequential version of the algorithm worked smoothly, however wasnt nearly as fast for what we wanted to do. So I decided to try and parallelize the algorithm. Writing threaded applications that work under different platforms can be a pain, no matter how much standardization people have thrown in it. Soon, my parallelized version worked on a two-cpu Alpha machine and I was pleased (it was faster too). However, when compiled under Linux or Solaris or FreeBSD it trashed the memory and then the painful task of debugging a multi-threaded application started. Due to lack of time and proper tools (my finals were coming) I abandoned the code.''

    Full story:
    http://www.kuro5hin.org/?op=displaystory;sid=2000/9/20/125616/415

    Reference by Snowdeal.org.

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