contributors:team_4_page
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contributors:team_4_page [2015/06/01 06:44] 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 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 parallel environment option in the script above: | + | The PE option in the script above: |
| <code> | <code> | ||
| #$ -pe mpi 10 | #$ -pe mpi 10 | ||
| </code> | </code> | ||
| - | The //mpi// designates the choice of a [[parallel environment]] that is installed on the system and the 10 indicates the number of processes over which to run the job. To see which PE's are installed on the system, use the command: | + | The //mpi// designates the choice of a PE that is installed on the system and the 10 indicates the number of processes over which to run the job. To see which PE's are installed on the system, use the command: |
| <code> | <code> | ||
| qconf -spl | qconf -spl | ||
| </code> | </code> | ||
| - | Selecting the proper parallel environment is critical to ensure the success of a parallelized ABySS job. By using the command: | + | Selecting the proper PE is critical to ensure the success of a parallelized ABySS job. By using the command: |
| <code> | <code> | ||
| qconf -sp PE_NAME | qconf -sp PE_NAME | ||
| 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.1433141067.txt.gz · Last modified: 2015/06/01 06:44 by emfeal
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