... | @@ -13,9 +13,7 @@ To synchronize your data/pipeline project directory with the remote cluster, use |
... | @@ -13,9 +13,7 @@ To synchronize your data/pipeline project directory with the remote cluster, use |
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**Setup Script**
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**Setup Script**
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On the remote, through `ssh` run the script `./setup-remote.sh`
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On the remote, do the following:
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*on remote server*
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```bash
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```bash
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cd /path/to/root/of/project
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cd /path/to/root/of/project
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# chmod +x of the setup-remote.sh script is only required if
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# chmod +x of the setup-remote.sh script is only required if
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... | @@ -24,8 +22,10 @@ chmod +x ./setup-remote.sh |
... | @@ -24,8 +22,10 @@ chmod +x ./setup-remote.sh |
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./setup-remote.sh
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./setup-remote.sh
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```
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```
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Note: At this point `./setup-remote.sh` will run various tests and scripts to install the proper octave packages and compile amica. Both Octave and Amica frequently need environment variables to be set in order to properly compile and run. You will receive the message
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Note: At this point `./setup-remote.sh` will run various tests and scripts to install the proper octave packages and compile amica. Both Octave and Amica frequently need environment variables to be set in order to properly compile and run.
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Eventually, you will receive the following message:
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```
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```
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Prompt:We need to load session environment variables for
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Prompt:We need to load session environment variables for
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amica
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amica
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... | @@ -37,10 +37,6 @@ File name: [analysis/support/config/amica.sesinit]: |
... | @@ -37,10 +37,6 @@ File name: [analysis/support/config/amica.sesinit]: |
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* If you are using Sharcnet's orca cluster you will want to leave this as the default. (Just press enter)
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* If you are using Sharcnet's orca cluster you will want to leave this as the default. (Just press enter)
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* If you are using Compute Canada's Graham or Cedar you will want to use "analysis/support/config/amica-sbatch.sesinit". `./setup-remote.sh` has readline enabled so you may use tab completion for the file names.
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* If you are using Compute Canada's Graham or Cedar you will want to use "analysis/support/config/amica-sbatch.sesinit". `./setup-remote.sh` has readline enabled so you may use tab completion for the file names.
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Any problems with setup can be reported in [Issues](https://git.sharcnet.ca/bucanl_pipelines/bids_lossless_eeg/issues)
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**Data**
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**Data**
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Before setting up the remote cluster machine(s) you should consider uploading your
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Before setting up the remote cluster machine(s) you should consider uploading your
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