This is an old revision of the document!
ALLPATHS is the most recent (as of this writing) tool developed by the broad institute to assemble shotgun sequences[(cite:broad>http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development)]. The broad institute claims that version 3 of the program can assemble up to mammalian sized genomes if the reads are at least 100+ base pairs[(cite:broad)]. Version 3 (currently 3.1) of the program may be downloaded from [ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/] and that folder also contains some documentation on how to use the program. Also the program ships with test data that you can assemble. ===== References ===== <refnotes>notes-separator: none</refnotes> ~~REFNOTES cite~~
Discussion
30 of the boxes have 4 cores with 16GB each 32 boxes have 2 cores with 16GB each The CPUs are in the 2Ghz range.
So if the cores are sharing 64Gb, we're in luck, but if they really are 16GB separately for each core (or worse, 16Gbytes/box) we may be in trouble.
Would I send the IT request to SOE? Who manages campusrocks?
It looks like the experimental parallel extension to libstdc++ started with gcc 4.3 You'll have to do an IT request to get a newer gcc installed (and even that might not work). Remember to explain why you need a newer gcc.