Commit b3c44f9f authored by Alex Waite's avatar Alex Waite

update READMEs

parent ae4630c4
# HTCondor Examples
This is a collection of working examples to demonstrate best practices and to
speed bootstrapping of new projects on Juseless.
A collection of working examples to speed bootstrapping of new projects on
Juseless and demonstrate best practices.
If you see something that is missing or should be improved, please contribute!
| name | description |
| ---- | ----------- |
| [fMRIPrep](fmriprep/) | |
| [matlab](matlab/) | |
| [ncal](ncal/) | |
| [python](python/) | |
| [fMRIPrep](fmriprep/) | A full-featured template that uses a script to generate the submit file. |
| [matlab](matlab/) | A very simple submit file that passes an argument to a Matlab script. |
| [ncal](ncal/) | The [calendar printing example](https://docs.inm7.de/tools/htcondor/#generating-a-submit) used in the docs. A script is used to generate the submit file. |
| [python](python/) | A very simple submit file that passes an argument to a Python script. |
# fMRIPrep
This template serves only as an example. It will need to be adapted in order to
run for your project. Most importantly the
This template uses a script (`gen_submit.sh`) to generate the submit file.
This template will need to be adapted in order to run for your project. Most
importantly the
1) `bids_dir`
2) `output_dir`
3) [command-line arguments](https://fmriprep.readthedocs.io/en/stable/usage.html#command-line-arguments)
to control which workflows are run
to control which workflows are run. If you're unsure about which options to
use, talk with your group leader.
4) subject for-loop
## Prerequisites
* a BIDS dataset
## Things to Note
* a library of fMRIPrep images are stored on Juseless in `/data/project/singularity`.
* a collection of fMRIPrep images are stored in `/data/project/singularity` on
Juseless.
* **CPU:**: 1 CPU was chosen as (with the option used in this example) there was
no appreciable speed difference between 1 CPU and multi-CPU jobs.
* **RAM:** 8GB is [recommended by upstream](https://brainscan.uwo.ca/research/cores/computational_core/img/Nov26-Fmriprep.pdf)
......@@ -26,7 +31,11 @@ Adjust the variables in the script, most especially the `BIDS_DIR`,
`OUTPUT_DIR`, and `FMRIPREP`. Also adjust the subjects for-loop to meet your
needs.
When you've made your changes, run it like so:
Once you've made your changes, verify that it's working:
```
./gen_submit.sh
```
If the output looks correct, then submit the jobs like so:
```
./gen_submit.sh | condor_submit
```
# Matlab
The `matlab.submit` file submits one job that calls `analyze_subject.m` ---
which simply prints out the subject ID that is passed to it.
......@@ -29,7 +28,6 @@ should read the INM-7 Docs section on
To restrict your jobs to two machines, add the following to your submit file
(adjust the machine names to your needs):
```
requirements = Machine == "cpu7.htc.inm7.de" || Machine == "cpu8.htc.inm7.de"
```
......
......@@ -4,8 +4,9 @@ The `ncal_submit_gen.sh` generates a submit file with a series of jobs. Each job
calls `ncal` --- which prints the calendar for that year.
To run:
```./ncal_submit_gen.sh | condor_submit```
```
./ncal_submit_gen.sh | condor_submit
```
## Prerequisites
This example assumes that it is located in `~/htcondor-templates/ncal`. If you
......
# Python
The `python.submit` file submits one job that calls `analyze_subject.py` ---
which simply prints out the subject ID that is passed to it.
......
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