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## Welcome to the FAQ and answers !
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**What is this?**
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. Here we will keep track of the most Frequently Asked Questions and answers.
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## Introduction.
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**How do I start working on Shark the right way?**
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. Read [the intro](HowDoIStart).
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** Why is the Shark cluster called Shark?**
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. Read [the history of Shark](WhyShark).
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## Howto, tips and tricks.
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'''Are there any commands to summarize the cluster's usage/availability ?'''
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. Try to run unique-user-slots.sh or slotsfree.pl script.
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**Can I install any program?**
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. No, not yourself. However, you can request everything with the administrator using the ticket system.
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**Are there reference genomes available?**
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. Yes, you can find them with descriptive readmes in /usr/local/Genomes/.
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**What was that one command for that one thing again?**
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. Read [qsub commands](qsubCommands).
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**Can shark change directory automatically when I log in?**
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. Yes. You can add commands to the bottom of the .bashrc file in your home dir. These will be executed whenever you log into shark.
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**Can shark notify me when my jobs are done?**
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. Yes, either by [email](Examples) or with the [notification](wiki:sshnotification) system on your local machine.
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**Is R installed on the new Shark?**
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. Yes, You need to load the module first before you can use R.
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List all available module
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module avail
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The load the R module version you want to use.
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module load R/3.1.1
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'''Can I restrict java to a fixed number of cpu's?'''
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. Yes, java -XX:ParallelGCThreads=1 (set 1 to the number of cpu you want)
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. To restrict the memory java uses : java -Xmx2048m -Xms2048m
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## When stuff doesn't work.
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'''Why won't my job run?'''
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. Read [error queues](Errorqueue).
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'''Why can't my qlogin be scheduled?'''
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. Whenever this happens it's most likely that there are no slots available in your queue(s). Run **qstat -u "*"** or **unique-user-slots.sh** and view the usage of the shark cluster. You can still submit your job with **qsub**, the fair-share policy will take care that your jobs gets scheduled according to your rights.
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**Why is my job killed when I my script uses more then 4G of memory**
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. Shark has a default h_vmem=4G value set. If your job exceeds the memory threshold of 4G Open Grid Scheduler will auto kill that job. You should specify a higher h_vmem limit if your jobs needs more then 4G of memory like this
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qsub -l h_vmem=xxG
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The G means Gigabyte.
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**What does this exit code means?**
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. Read the manual for accounting go to exit_status.
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man accounting
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exit_status
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Exit status of the job script (or xxQS_NAMExx specific status in case of certain error conditions). The exit status is determined by following the normal shell conventions. If the command terminates normally the value of the command is its exit status. However, in the case that the command exits abnormally, a value of 0200 (octal), 128 (decimal) is added
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to the value of the command to make up the exit status.
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For example: If a job dies through signal 9 (SIGKILL) then the exit status becomes 128 + 9 = 137. |