diff --git a/.github/workflows/docker-image-intel.yml b/.github/workflows/docker-image-intel.yml index a9d5a0a..ff0975f 100644 --- a/.github/workflows/docker-image-intel.yml +++ b/.github/workflows/docker-image-intel.yml @@ -1,4 +1,4 @@ -name: Docker Image Test Build - Intel drivers +name: Docker Image Build - Intel drivers on: push: @@ -18,7 +18,7 @@ jobs: - name: Build the Docker image run: | chmod a+w output/ - ls -alt + ls -alth ./build_intel.sh - name: Info on Docker images diff --git a/.github/workflows/docker-image-quickrun.yml b/.github/workflows/docker-image-quickrun.yml index 31f1cfc..4c07b99 100644 --- a/.github/workflows/docker-image-quickrun.yml +++ b/.github/workflows/docker-image-quickrun.yml @@ -1,4 +1,4 @@ -name: Docker Image Test - quick +name: Docker Image Quick Run on: push: @@ -17,7 +17,7 @@ jobs: - name: Build the Docker image run: | chmod a+w output/ - ls -alt + ls -alth ./build.sh - name: Info on Docker images run: | diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml index 3bd3c08..f5ea7d3 100644 --- a/.github/workflows/docker-image.yml +++ b/.github/workflows/docker-image.yml @@ -1,4 +1,4 @@ -name: Docker Image Test Build +name: Docker Image Build & Run on: push: @@ -17,7 +17,7 @@ jobs: - name: Build the Docker image run: | chmod a+w output/ - ls -alt + ls -alth ./build.sh - name: Info on Docker images run: | diff --git a/Dockerfile b/Dockerfile index 1a4bf89..bad9d2b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -20,6 +20,7 @@ RUN mkdir -p /etc/sudoers.d && \ ENV DEBIAN_FRONTEND noninteractive # TODO: change + ################################################################################ ######## Update/install essential libraries @@ -52,7 +53,7 @@ RUN sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10 ################################################################################ ######## Install NEURON simulator -RUN pip3 install neuron==8.0.1 +RUN sudo pip3 install neuron==8.1.0 ################################################################################ @@ -60,7 +61,7 @@ RUN pip3 install neuron==8.0.1 RUN git clone https://github.com/openworm/c302.git && \ cd c302 && \ - git checkout ow-0.9.4 && \ + git checkout ow-0.9.5 && \ sudo pip install . # Note: pyNeuroML installed with the above library @@ -74,7 +75,7 @@ RUN owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/ RUN git clone https://github.com/openworm/sibernetic.git && \ cd sibernetic && \ - git checkout ow-0.9.4 # fixed to a specific branch + git checkout ow-0.9.5 # fixed to a specific branch ################################################################################ diff --git a/Dockerfile_intel b/Dockerfile_intel index 3ffc2b7..a9b027d 100644 --- a/Dockerfile_intel +++ b/Dockerfile_intel @@ -61,7 +61,7 @@ RUN pip3 install neuron==8.0.1 RUN git clone https://github.com/openworm/c302.git && \ cd c302 && \ - git checkout ow-0.9.4 && \ + git checkout ow-0.9.5 && \ sudo pip install . # Note: pyNeuroML installed with the above library @@ -75,7 +75,7 @@ RUN owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/ RUN git clone https://github.com/openworm/sibernetic.git && \ cd sibernetic && \ - git checkout ow-0.9.4 # fixed to a specific branch + git checkout ow-0.9.5 # fixed to a specific branch ################################################################################ diff --git a/README.md b/README.md index 6a6df24..ac7d595 100644 --- a/README.md +++ b/README.md @@ -2,21 +2,20 @@ [![Docker Image CI](https://github.com/openworm/OpenWorm/actions/workflows/docker-image.yml/badge.svg)](https://github.com/openworm/OpenWorm/actions/workflows/docker-image.yml) [![Docker Image Test - quick](https://github.com/openworm/OpenWorm/actions/workflows/docker-image-quickrun.yml/badge.svg)](https://github.com/openworm/OpenWorm/actions/workflows/docker-image-quickrun.yml) [![Docker Image Test Build - Intel drivers](https://github.com/openworm/OpenWorm/actions/workflows/docker-image-intel.yml/badge.svg)](https://github.com/openworm/OpenWorm/actions/workflows/docker-image-intel.yml) -About **OpenWorm** ------------------- +## About **OpenWorm** [OpenWorm](http://openworm.org) aims to build the first comprehensive computational model of *Caenorhabditis elegans* (*C. elegans*), a microscopic roundworm. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance. Despite being extremely well-studied in biology, a deep, principled understanding of the biology of this organism remains elusive. -We are using a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so, we are incorporating the data available from the scientific community into software models. We are also forging new collaborations with universities and research institutes to collect data that fill in the gaps. +We are using a bottom-up approach, aimed at observing the worm behavior emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so, we are incorporating the data available from the scientific community into software models. We are also forging new collaborations with universities and research institutes to collect data that fill in the gaps. You can earn a badge with us simply by trying out this package! Click on the image below to get started. [![OpenWorm Docker Badge](https://raw.githubusercontent.com/openworm/OpenWorm/master/img/ow-docker-badge.png)](https://www.badgelist.com/OpenWorm/OpenWorm-Docker-Apprentice) -Quickstart ----------- -We have put together a [Docker container](https://hub.docker.com/r/openworm/openworm) that pulls together the major components of our simulation and runs it on your machine. When you get it all running it does the following: +## Quickstart -1. Run our nervous system model, known as [c302](https://github.com/openworm/c302), on your computer. +We have put together a [Docker container](https://hub.docker.com/r/openworm/openworm) that pulls together the major components of our simulation and runs it on your machine. When you get it all running, it does the following: + +1. Run our nervous system model, known as [c302](https://github.com/openworm/c302), on your computer. 2. In parallel, run our 3D worm body model, known as [Sibernetic](https://github.com/openworm/sibernetic), on your computer, using the output of the nervous system model. 3. Produce graphs from the nervous system and body model that demonstrate its behavior on your computer for you to inspect. 4. Produce a movie showing the output of the body model. @@ -27,89 +26,90 @@ We have put together a [Docker container](https://hub.docker.com/r/openworm/open -**NOTE**: Running the simulation for the full amount of time would produce content like the above. However, in order to run in a reasonable amount of time, **the default run time for the simulation is limited**. As such, you will see only a partial output, equivalent to about 5% of run time, compared to the examples above. To extend the run time, use the `-d` argument as described below. +**NOTE**: Running the simulation for the full amount of time would produce content like the above. However, in order to run in a reasonable amount of time, **the default run time for the simulation is limited**. As such, you will see only a partial output, equivalent to about 5% of run time, compared to the examples above. To extend the run time, use the `-d` argument as described below. -**Installation** +## Installation -Pre-requisites: +### Pre-requisites -1) You should have at least 60 GB of free space on your machine and at least 2GB of RAM -2) You should be able to clone git repositories on your machine. [Install git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git), or [this GUI](https://desktop.github.com/) may be useful. +1. At least 60 GB of free space on your machine and at least 2GB of RAM. +2. Ability to clone git repositories on your machine. [Install git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git), or use [this GUI](https://desktop.github.com/). -To Install: +### To Install -1. Install [Docker](http://docker.com) on your system. -2. If your system does not have enough free space, you can use -an external hard disk. On MacOS X, the location for image storage -can be specified in the [Advanced Tab](https://forums.docker.com/t/change-docker-image-directory-for-mac/18891/15) in Preferences. See [this thread](https://forums.docker.com/t/how-do-i-change-the-docker-image-installation-directory/1169/18) -in addition for Linux instructions. +1. Install [Docker](http://docker.com) on your system. +2. If your system does not have enough free space, you can use an external hard disk. On MacOS X, the location for image storage can be specified in the [Advanced Tab](https://forums.docker.com/t/change-docker-image-directory-for-mac/18891/15) in Preferences. See [this thread](https://forums.docker.com/t/how-do-i-change-the-docker-image-installation-directory/1169/18) for Linux instructions. -**Running** +## Running -1. Ensure the Docker daemon is running in the background (on MacOS/Windows there should be an icon with the Docker whale logo showing in the menu bar/system tray). -2. Open a terminal and run: `git clone http://github.com/openworm/openworm`; `cd openworm` -3. Optional: Run `./build.sh` (or `build.cmd` on Windows). If you skip this step, it will download the latest released Docker image from the [OpenWorm Docker hub](https://hub.docker.com/r/openworm/openworm). -4. Run `./run.sh` (or `run.cmd` on Windows). +1. Ensure the Docker daemon is running in the background (on MacOS/Windows there should be an icon with the Docker whale logo showing in the menu bar/system tray). +2. Open a terminal and run: + ```bash + git clone http://github.com/openworm/openworm + cd openworm + ``` +3. Optional: Run `./build.sh` (`build.cmd` on Windows or `.\build.cmd` on [PowerShell](https://learn.microsoft.com/en-us/powershell/dsc/overview?view=dsc-2.0)). If you skip this step, it will download the latest released Docker image from the [OpenWorm Docker hub](https://hub.docker.com/r/openworm/openworm). +4. Run `./run.sh` (`run.cmd` on Windows or `.\run.cmd` in PowerShell). 5. About 5-10 minutes of output will display on the screen as the steps run. -6. The simulation will end. Run `stop.sh` (`stop.cmd` on Windows) on your system to clean up the running container. +6. The simulation will end. Run `stop.sh` (`stop.cmd` on Windows or `.\stop.cmd` in PowerShell) on your system to clean up the running container. 7. Inspect the output in the `output` directory on your local machine. -**Advanced** +## Advanced -***Arguments*** +### Arguments -* -d [num] : Use to modify the duration of the simulation in milliseconds. Default is 15. Use 5000 to run for time to make the full movie above (i.e. 5 seconds). +- `-d [num]`: Use to modify the duration of the simulation in milliseconds. Default is 15. Use 5000 to run for time to make the full movie above (i.e. 5 seconds). -***Other things to try*** +### Other Things to Try -* Open a terminal and run `./run-shell-only.sh` (or `run-shell-only.cmd` on Windows). This will let you log into the container before it has run `master_openworm.py`. From here you can inspect the internals of the various checked out code bases and installed systems and modify things. Afterwards you'll still need to run `./stop.sh` to clean up. -* If you wish to modify what gets installed, you should modify `Dockerfile`. If you want to modify what runs, you should modify `master_openworm.py`. Either way you will need to run `build.sh` in order to rebuild the image locally. Afterwards you can run normally. +- Open a terminal and run `./run-shell-only.sh` (`run-shell-only.cmd` on Windows or `.\run-shell-only.cmd` in PowerShell). This will let you log into the container before it has run `master_openworm.py`. From here you can inspect the internals of the various checked out code bases and installed systems and modify things. Afterwards, you'll still need to run `./stop.sh` to clean up. +- If you wish to modify what gets installed, you should modify `Dockerfile`. If you want to modify what runs, you should modify `master_openworm.py`. Either way you will need to run `build.sh` in order to rebuild the image locally. Afterwards, you can run normally. -### FAQ +## FAQ -#### **What is the Docker container?** +### What is the Docker container? -The Docker container is a self-contained environment in which you can run OpenWorm simulations. It's fully set up to get you started by following the steps above. At the moment, -it runs simulations and produces visualizations for you, but these visualizations must be viewed outside of the Docker container. While you do not need to know -much about Docker to use OpenWorm, if you are planning on working extensively with the platform, you may benefit -from understanding some basics. [Docker Curriculum](https://docker-curriculum.com) -is an excellent tutorial for beginners that is straightforward to work through (Sections 1 - 2.5 are plenty sufficient). +The Docker container is a self-contained environment in which you can run OpenWorm simulations. It's fully set up to get you started by following the steps above. At the moment, it runs simulations and produces visualizations for you, but these visualizations must be viewed outside of the Docker container. While you do not need to know much about Docker to use OpenWorm, if you are planning on working extensively with the platform, you may benefit from understanding some basics. [Docker Curriculum](https://docker-curriculum.com) is an excellent tutorial for beginners that is straightforward to work through (Sections 1 - 2.5 are plenty sufficient). -#### **Is it possible to modify the simulation without having to run `build.sh`?** +### Is it possible to modify the simulation without having to run `build.sh`? -Yes, but it is marginally more complex. The easiest way is to modify anything in the Docker container once you are inside of it - it will work just like a bash shell. If you want to modify any code in the container, you'll need to use an editor that runs in the terminal, like nano. Once you've modified something in the container, you don't need to re-build. However, if you run `stop.sh` once you exit, those changes will be gone. +Yes, but it is marginally more complex. The easiest way is to modify anything in the Docker container once you are inside of it - it will work just like a bash shell. If you want to modify any code in the container, you'll need to use an editor that runs in the terminal, like nano. Once you've modified something in the container, you don't need to re-build. However, if you run `stop.sh` once you exit, those changes will be gone. -#### **How do I access more data than what is already output?** +### How do I access more data than what is already output? -The simulation by default outputs only a few figures and movies to your home system (that is, outside of the Docker container). If you want to access the entire output of the simulation, you will need to copy it from the Docker container. +The simulation by default outputs only a few figures and movies to your home system (that is, outside of the Docker container). If you want to access the entire output of the simulation, you will need to copy it from the Docker container. -For example, say you want to extract the worm motion data. This is contained in the file `worm_motion_log.txt`, which is found in the `/home/ow/sibernetic/simulations/[SPECIFIC_TIMESTAMPED_DIRECTORY]/worm_motion_log.txt`. The directory `[SPECIFIC_TIMESTAMPED_DIRECTORY]` will have a name like `C2_FW_2018_02-12_18-36-32`, and its name can be found by checking the `output` directory. This is actually the main output directory for the simulation, and contains all output, including cell modelling and worm movement. +For example, say you want to extract the worm motion data. This is contained in the file `worm_motion_log.txt`, which is found in the `/home/ow/sibernetic/simulations/[SPECIFIC_TIMESTAMPED_DIRECTORY]/worm_motion_log.txt`. The directory `[SPECIFIC_TIMESTAMPED_DIRECTORY]` will have a name like `C2_FW_2018_02-12_18-36-32`, and its name can be found by checking the `output` directory. This is actually the main output directory for the simulation, and contains all output, including cell modelling and worm movement. Once the simulation ends and you exit the container with `exit`, but before you run `stop.sh`, run the following command from the openworm-docker-master folder: -`docker cp openworm:/home/ow/sibernetic/simulations/[SPECIFIC_TIMESTAMPED_DIRECTORY]/worm_motion_log.txt ./worm_motion_log.txt` +```bash +docker cp openworm:/home/ow/sibernetic/simulations/[SPECIFIC_TIMESTAMPED_DIRECTORY]/worm_motion_log.txt ./worm_motion_log.txt +``` -This will copy the file from the Docker container, whose default name is `openworm`. **It is crucial that you do not run `stop.sh` before trying to get your data out (see below)** +This will copy the file from the Docker container, whose default name is `openworm`. **It is crucial that you do not run `stop.sh` before trying to get your data out (see below)** -#### **What is the difference between `exit` and `stop.sh`?** +### What is the difference between `exit` and `stop.sh`? -When you are in the Docker Container `openworm`, and are done interacting with it, you type `exit` to return to your system's shell. This stops execution of anything in the container, and that container's status is now `Exited`. If you try to re-start the process using `run-shell-only.sh`, you will get an error saying that the container already exists. You can choose, at this point, to run `stop.sh`. Doing so will remove the container and any files associated with it, allowing you to run a new simulation. However, if you don't want to remove that container, you will instead want to re-enter it. +When you are in the Docker Container `openworm`, and are done interacting with it, you type `exit` to return to your system's shell. This stops execution of anything in the container, and that container's status is now `Exited`. If you try to re-start the process using `run-shell-only.sh`, you will get an error saying that the container already exists. You can choose, at this point, to run `stop.sh`. Doing so will remove the container and any files associated with it, allowing you to run a new simulation. However, if you don't want -#### **How do I enter a container I just exited?** + to remove that container, you will instead want to re-enter it. -If you run `stop.sh` you'll delete your data and reset the container for a new run. If, however, you don't want to do that, you can re-enter the Docker container like this: +### How do I enter a container I just exited? - docker start openworm # Restarts the container - docker exec -it openworm /bin/bash # Runs bash inside the container +If you run `stop.sh` you'll delete your data and reset the container for a new run. If, however, you don't want to do that, you can re-enter the Docker container like this: -This tells Docker to start the container, to *execute* commands (`exec`) with an *interactive, tty* (`-it`) bash (`bash`) shell in the container `openworm`. +```bash +docker start openworm # Restarts the container +docker exec -it openworm /bin/bash # Runs bash inside the container +``` -You'll be able to interact with the container as before. +This tells Docker to start the container, to *execute* commands (`exec`) with an *interactive, tty* (`-it`) bash (`bash`) shell in the container `openworm`. -Documentation -------------- -to find out more about OpenWorm, please see the documentation at [http://docs.openworm.org](http://docs.openworm.org) or [join us on Slack](http://bit.ly/OpenWormVolunteer). +You'll be able to interact with the container as before. -This repository also contains project-wide tracking via high-level [issues](https://github.com/openworm/OpenWorm/issues) and [milestones](https://github.com/openworm/OpenWorm/milestones). +## Documentation +To find out more about OpenWorm, please see the documentation at [http://docs.openworm.org](http://docs.openworm.org) or [join us on Slack](http://bit.ly/OpenWormVolunteer). +This repository also contains project-wide tracking via high-level [issues](https://github.com/openworm/OpenWorm/issues) and [milestones](https://github.com/openworm/OpenWorm/milestones). \ No newline at end of file diff --git a/VERSION b/VERSION index a602fc9..b0bb878 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.9.4 +0.9.5 diff --git a/build.sh b/build.sh index 4ab0e61..1481427 100755 --- a/build.sh +++ b/build.sh @@ -1,4 +1,14 @@ #!/bin/bash version=$(