contributors:team_4_page
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| Both sides previous revision Previous revision Next revision | Previous revision | ||
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contributors:team_4_page [2015/06/01 06:46] emfeal |
contributors:team_4_page [2015/07/18 20:52] (current) 92.247.181.31 ↷ Links adapted because of a move operation |
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| % --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 98: | Line 103: | ||
| </code> | </code> | ||
| Note that the parallel version of ABySS requires two things in particular: | Note that the parallel version of ABySS requires two things in particular: | ||
| - | * The use of a [[parallel environment]] (PE) which can be selected using a qsub option. | + | * The use of a [[archive:parallel_environment]] (PE) which can be selected using a qsub option. |
| * The //np// option of abyss-pe. The number of processes here must reflect the number included in the parallel environment option. | * The //np// option of abyss-pe. The number of processes here must reflect the number included in the parallel environment option. | ||
| The PE option in the script above: | The PE option in the script above: | ||
| 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.1433141219.txt.gz · Last modified: 2015/06/01 06:46 by emfeal
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