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| doku:smrtanalysis [2017/01/31 11:29] – markus | doku:smrtanalysis [2017/01/31 12:14] (current) – markus |
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| </code> | </code> |
| - Reset MYSQL password: <code> | - Reset MYSQL password: <code> |
| | cd $SMRTAnalysis_HOME |
| ./smrtanalysis/admin/bin/smrtportald-initd start | ./smrtanalysis/admin/bin/smrtportald-initd start |
| export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${start_dir}/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/mysql-5.1.73/lib/mysql/ | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${SMRTAnalysis_HOME}/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/mysql-5.1.73/lib/mysql/ |
| ${start_dir}/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/mysql/bin/mysqladmin -u root -S /tmp/mysql_53306.sock password 'asdf' | ${SMRTAnalysis_HOME}/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/mysql/bin/mysqladmin -u root -S /tmp/mysql_53306.sock password 'asdf' |
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| </code> | </code> |
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| - allocate a node: <code>salloc -p mem_0128 --qos=normal_0128</code> | - allocate a node: <code>salloc -p mem_0128 --qos=normal_0128</code> |
| - after allocation the environment variable 'SLURM_NODELIST' contains the node to run SMRTAnalysis on: | - start server on allocated: <code>srun $SMRTAnalysis_HOME/smrtanalysis/admin/bin/smrtportald-initd start</code> |
| | - create SSH tunnel |
| | * on the login node: <code>echo "ssh -L8090:$SLURM_JOB_NODELIST:8090 `whoami`@vsc3.vsc.ac.at"</code> |
| | * on your local machine: paste the command from the previous step and create the SSH tunnel |
| | - navigate to http://localhost:8090/ in your local browser |
| | - when finished stop the server on the compute node: <code>srun $SMRTAnalysis_HOME/smrtanalysis/admin/bin/smrtportald-initd stop</code> |
| | - follow the instructions on [[http://www.pacb.com/wp-content/uploads/2015/09/SMRT-Analysis-Software-Installation-v2.3.0.pdf]] |
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