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Use our summer school reservation (CoreNGS-Tue) when submitting batch jobs to get higher priority on the ls6 normal queue today:
Note that the reservation name (CoreNGS-Tue) is different from the TACC allocation/project for this class, which is OTH21164. |
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Command 1 of 16 (4 per node) ran on node c302c303-005.ls6.tacc.utexas.edu core 0 Command 10 of 16 (4 per node) ran on node c305c304-005.ls6.tacc.utexas.edu core 9 Command 11 of 16 (4 per node) ran on node c305c304-005.ls6.tacc.utexas.edu core 10 Command 12 of 16 (4 per node) ran on node c305c304-005.ls6.tacc.utexas.edu core 11 Command 13 of 16 (4 per node) ran on node c305c304-006.ls6.tacc.utexas.edu core 12 Command 14 of 16 (4 per node) ran on node c305c304-006.ls6.tacc.utexas.edu core 13 Command 15 of 16 (4 per node) ran on node c305c304-006.ls6.tacc.utexas.edu core 14 Command 16 of 16 (4 per node) ran on node c305c304-006.ls6.tacc.utexas.edu core 15 Command 2 of 16 (4 per node) ran on node c302c303-005.ls6.tacc.utexas.edu core 1 Command 3 of 16 (4 per node) ran on node c302c303-005.ls6.tacc.utexas.edu core 2 Command 4 of 16 (4 per node) ran on node c302c303-005.ls6.tacc.utexas.edu core 3 Command 5 of 16 (4 per node) ran on node c302c303-006.ls6.tacc.utexas.edu core 4 Command 6 of 16 (4 per node) ran on node c302c303-006.ls6.tacc.utexas.edu core 5 Command 7 of 16 (4 per node) ran on node c302c303-006.ls6.tacc.utexas.edu core 6 Command 8 of 16 (4 per node) ran on node c302c303-006.ls6.tacc.utexas.edu core 7 Command 9 of 16 (4 per node) ran on node c305c304-005.ls6.tacc.utexas.edu core 8 |
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We've already touched on the need to redirect standard output and standard error for each task. Just remember that funny redirection syntax:
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my_program input_file1 output_file1 > file1.log 2>&1 |
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For example, you might have a script called align_bwa.sh (a bash script) or align_bowtie2.py (written in python Python) that performs multiple steps needed during the alignment process:
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The BioITeam maintains a set of such scripts in the /work/projects/BioITeam/common/script directory. Take a look at some of them after you feel more comfortable with initial NGS processing steps. They can be executed by anyone with a TACC account.
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# navigate through the symbolic link in your Home directory cd ~scratch/core_ngs/slurm/simple ls ../wayness ls ../.. ls -l ~/.bashrc |
And read more about Absolute and relative pathname syntax
Interactive sessions (idev)
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idev -m 3060 -N 1 -A OTH21164 -p normal -r CoreNGSday2CoreNGS-Tue |
Notes:
- -p normal requests nodes on the normal queue
- this is the default for our reservation, while the development queue is the normal default
- -m 60 asks for a 60 minute session
- -A OTH21164 specifies the TACC allocation/project to use
- -N 1 asks for 1 node
- --reservation=CoreNGSday2CoreNGS-Tue gives us priority access to TACC nodes for the class. You normally won't use this argumentoption.
When you ask for an idev session, you'll see output as shown below. Note that the process may repeat the "job status: PD" (pending) step while it waits for an available node.
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