Compiling via mcc command, updates in readme

Author: chyumin

ironclust-compiled/README.md

@@ -21,31 +21,46 @@ There are three main steps for generating a functional ironclust docker image:
 
 Licenses for Matlab and toolboxes are needed only for compiling ironclust as Standalone Application and to generate the base Docker image. After this process, no license will be required, either to extend the base image or to run the sorter.
 
-
 ## Compiling Ironclust as Matlab's Standalone Application
 - Git clone or Download ironclust [source code](https://github.com/flatironinstitute/ironclust.git)
 - Open Matlab
-- Set Matlab's workspace folder to: `<local-path-to-project>/ironclust/matlab`
-- Open Matlab's `Application Compiler` (located in `APPS` Tab)
-- Click on `+` sign in Add Main File, Select `p_ironclust.m` and Click Open
-- In the section `Files required for your application to run`, click on `+` sign button and Select all files (some might not be needed, but we haven't tested removing them), also select the following folders:  `prb` and `prb_json`. Click Open
-- On Application Compiler window, Click on `Package`, Save the `p_ironclust.prj` file and wait for Matlab to Compile the project. A folder (named `p_ironclust` by default) with compiled files will be generated.
-
+- Set Matlab's workspace folder to: `<git-cloned-path>/ironclust/matlab`
+- In Matlab console run:
+```
+>> mcc -m p_ironclust.m -a <git-cloned-path>/ironclust/matlab/*.* -a <git-cloned-path>/ironclust/matlab/prb -a <git-cloned-path>/ironclust/matlab/prb_json
+```
 
 ## Generating Base Docker Image
-- Close `Package` and `Application Compiler` windows
-- In Matlab console run:
+- To generate the base docker image (called `ironclust-matlab-base`) with the compiled application, run the following command in Matlab console:
 ```
-compiler.package.docker('p_ironclust/for_testing/p_ironclust', 'p_ironclust/for_testing/requiredMCRProducts.txt', 'ImageName', 'ironclust-matlab-base')
+>> compiler.package.docker('p_ironclust', 'requiredMCRProducts.txt', 'ImageName', 'ironclust-matlab-base')
 ```
-This command will create an image called `ironclust-matlab-base` to be used in the next step
+
+- [Optional] Files generated by Matlab Compiler can be deleted:
+  - In your terminal, go to the folder for this project:
+  ```
+  $ cd <git-cloned-path>/ironclust/
+  ```
+  - Run `rm` command:
+  ```
+  $ rm -r \
+    matlab/includedSupportPackages.txt \
+	matlab/ironclust-matlab-basedocker \
+	matlab/mccExcludedFiles.log \
+	matlab/p_ironclust \
+	matlab/readme.txt \
+	matlab/requiredMCRProducts.txt \
+	matlab/run_p_ironclust.sh \
+	matlab/unresolvedSymbols.txt
+  ```
+
 
 ## Extending Base Image/Creating final image
 The Dockerfile in this folder applies some fixes and updates to the base image generated automatically by Matlab in order to properly run ironclust:
 
-- In your terminal, go to the current folder:
+- In your terminal, go to the  folder for this project:
 ```
-$ cd <local-path-to-project>/spikeinterface-dockerfiles/ironclust-compiled
+$ cd /path/to/spikeinterface-dockerfiles/ironclust-compiled
 ```
 
 - Run build script:
@@ -56,6 +71,8 @@ $ source build.sh
 
 ## Running a container
 
+- [nvidia-container-toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#setting-up-nvidia-container-toolkit) is required to run a docker with GPU capabilities
+
 The base syntax to run dockerized ironclust is:
 
 ```
@@ -68,4 +85,3 @@ Sample run:
 ```
 docker run -v /home/user/data:/opt/data -it spikeinterface/ironclust p_ironclust /opt/data/tmp /opt/data/raw.mda /opt/data/geom.csv '' '' /opt/data/tmp/firing.mda /opt/data/argfile.txt
 ```
-