contributors:team_4_page
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
|
contributors:team_4_page [2015/06/01 06:46] emfeal |
contributors:team_4_page [2015/07/18 20:31] ceisenhart ↷ Page moved from team_4_page to contributors:team_4_page |
||
|---|---|---|---|
| Line 39: | Line 39: | ||
| % --enable-dependency-tracking\ | % --enable-dependency-tracking\ | ||
| % --with-boost=/campusdata/BME235/include/boost\ | % --with-boost=/campusdata/BME235/include/boost\ | ||
| - | % --with-mpi=/campusdata/BME235/include\ | + | % --with-mpi=/opt/openmpi\ |
| - | % CC=gcc-4.9.2 CXX=g++-4.9.2\ | + | % CC=gcc CXX=g++\ |
| - | % CPPFLAGS=-I/campusdata/BME235/include/sparsehash | + | % CPPFLAGS=-I/campusdata/BME235/include/ |
| </code> | </code> | ||
| Then ABySS can be installed via the makefile | Then ABySS can be installed via the makefile | ||
| Line 48: | Line 48: | ||
| % make install | % make install | ||
| </code> | </code> | ||
| + | ==== Notes on Installation ==== | ||
| + | * the //-enable-maxk// is by default set to 64. Always ensure the max kmer is set to the smallest possible value that accommodates your target kmers so as to minimize ABySS's memory footprint. | ||
| + | * ensure that the CPPFLAGS specified directory holds the google sparsehash includes. Look for a warning in the ABySS compilation to be sure. | ||
| + | * the boost libraries do not need to be compiled before installing. | ||
| + | * ensure openmpi is installed with the --with-sge option (for SGE) to ensure tight integration. | ||
| =====ABySS parameters===== | =====ABySS parameters===== | ||
| Line 126: | Line 131: | ||
| accounting_summary TRUE | accounting_summary TRUE | ||
| </code> | </code> | ||
| - | For using ABySS with openmpi, there are two settings in particular which should be noted: | + | For using ABySS with openmpi, there are three settings in particular which should be noted: |
| * slots: indicates maximum number of slots that can be designated with the PE | * slots: indicates maximum number of slots that can be designated with the PE | ||
| * allocation_rule: indicates the form of scheduling to be used to allocate slots to nodes | * allocation_rule: indicates the form of scheduling to be used to allocate slots to nodes | ||
contributors/team_4_page.txt · Last modified: 2015/07/18 20:52 by 92.247.181.31
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
