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**Table of Contents**
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[[_TOC_]]
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# Operating Systems
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Using batch context for local batching should work despite which operating system you are using. Make sure that your [working directory](https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica/wikis/getting-started#preparing-matlab-and-eeglab) is set properly and that you [amica program is set to executable](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/running-scripts#running-scripts-locally).
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Using batch context for local batching should work for any operating system you are using.
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Submitting jobs to SHARCNet requires a **ssh** and it works differently depending on your operating system. You need to make some changes before and during starting the batch.
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Submitting jobs to a remote cluster requires a **ssh** environment and it works differently depending on your operating system.
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# Linux and Mac
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If you are using a linux operating system you can use Octave or Matlab to run batch context.
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You do not have to do anything too special. Make sure that your batch context configs have the *exec_func* field set to *ef_sqsub* or *ef_qsub*d epending on your submission preference. Note that the *qsub_options* help describes sqsub submission.
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At the bottom of the *Run HTB* GUI make sure you have the submission method set to the default *system* command. This will make you system preform the ssh command to connect to SHARCNet.
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Linux and MacOS usually have ssh and scp installed by the default. This means you can use Remote submit communication method "system" for submission.
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![sumissionlinux](/uploads/73bdf424397939178dbfeff40df24c18/sumissionlinux.png)
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Upon submission you will need to type in you password twice for each script. Once to upload the zip file and once to open it.
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# Windows
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If you are using a windows operating system you have to use Matlab to run batch context.
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You will need to make a few samll changes to make sure your instance of matlab can *ssh from matlab*. After you start up Matlab and set the working directory run the following command in the command terminal:
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The system method for submission will prompt you for password if the current environment is not configured for password-less access to the remote cluster. For password-less access to your remote cluster, contact your administrator for details. You may use ssh keys to do so. See [this documentation](https://wiki.archlinux.org/index.php/SSH_keys) which should apply for most Linux and MacOS clients.
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```
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sshfrommatlabinstall(1)
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```
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This will download and set a small java library and add it to the dynamic java path. This will allow this instance of Matlab to run the *ssh* command, since your system can not. It will also clear your workspace to make sure you path is still correct before calling eeglab.
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Additionally you can use the `ssh2` method as well for Linux if you do not have password-less access setup to avoid typing your password as often for the remote cluster.
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Make sure that your batch context configs have the *exec_func* field set to *ef_sqsub* or *ef_qsub* depending on your submission preference. Note that the *qsub_options* help describes sqsub submission.
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# Windows (ssh2)
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At the bottom of the *Run HTB* GUI you will have to manually change the submission method to *ssh from matlab* every time you load the GUI.
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![submissionwindows](/uploads/6746528eaded4bd4f06877a00e02387f/submissionwindows.png)
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For Windows the only method of submission you can use is `ssh2` in the submission window set Remote submit communication method to `ssh2` before clicking Ok . This option is not saved.
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Upon submission the computer will ask from your Password once in a Pop up.
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The `ssh2` driver will ask for your password once for all submissions.
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***
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*Updated/Verified by Brad Kennedy on 2017-08-09*
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[ :house: **Return to Main Page**](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/home) |
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