archive:bioinformatic_tools:abyss
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archive:bioinformatic_tools:abyss [2010/05/15 20:09] jstjohn |
archive:bioinformatic_tools:abyss [2010/05/16 01:47] jstjohn |
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| Note that I originally started this process on campusrocks-1-0.local with two cores allocated per available compute node on campusrocks. The process was eventually killed either by a cluster admin, or something else. I then decided to re run the program from campusrocks-0-6.local due to its larger amount of available ram. The assembly picked up where it left off and the process that previously was killed finished within a fairly short period of time. | Note that I originally started this process on campusrocks-1-0.local with two cores allocated per available compute node on campusrocks. The process was eventually killed either by a cluster admin, or something else. I then decided to re run the program from campusrocks-0-6.local due to its larger amount of available ram. The assembly picked up where it left off and the process that previously was killed finished within a fairly short period of time. | ||
| + | |||
| + | After completely crashing campusrocks-0-6.local with my process I realized that the makefile was taking the -j j=2 command, probably ignoring the -j=2 part, and parallelizing as much as possible at each step (on each core). On my head node I was running 8 huge processes simultaniously, which probably lead to node 6 going down. I almost did the same to node 1-20 before I realized what was going on and stopped the script. I have reissued the makefile with the following command which doesn't try to pump more parallelization out of the head node: | ||
| + | |||
| + | <code> | ||
| + | /campus/BME235/programs/abyss_tmp/bin/abyss-pe mpirun="/opt/openmpi/bin/mpirun -machinefile machines -x PATH=/campus/BME235/bin/programs/abyss_tmp/bin:$PATH" np=23 n=8 k=28 name=slugAbyss lib='lane1 lane2 lane3 lane5 lane6 lane7 lane8' lane1='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_1_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_1_2_all_qseq.fastq' lane2='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_2_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_2_2_all_qseq.fastq' lane3='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_3_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_3_2_all_qseq.fastq' lane5='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_5_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_5_2_all_qseq.fastq' lane6='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_6_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_6_2_all_qseq.fastq' lane7='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_7_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_7_2_all_qseq.fastq' lane8='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_8_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_8_2_all_qseq.fastq' | ||
| + | </code> | ||
| ===== References ===== | ===== References ===== | ||
| <refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
| ~~REFNOTES cite~~ | ~~REFNOTES cite~~ | ||
archive/bioinformatic_tools/abyss.txt · Last modified: 2015/07/28 06:23 by ceisenhart
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