Merge pull request #4 from LBT-CNRS/feature/enhancement/docker-port-standardization

Feature/enhancement/docker port standardization

Author: lanzac

doc/User_Manual.md

@@ -113,20 +113,22 @@ We advice you to try BioSpring with MDDriver and VMD to understand how this inte
 
 To run BioSpring with VMD and MDDriver, start by launching the BioSpring tools with these MDDriver parameters.
 
-	biospring -c model.nc -s param.msp --wait --port 3000 --log model.log
+	biospring -c model.nc -s param.msp --wait --port 8888 --log model.log
 
 Or run the Docker image:
 
-	docker run --rm -p 3000:3000 --init -v ./:/data ghcr.io/lbt-cnrs/biospring \
-		biospring -s model.nc -c param.msp --wait --port 3000
+	docker run --rm -p 8888:8888 --init -v ./:/data ghcr.io/lbt-cnrs/biospring \
+		biospring -s model.nc -c param.msp --wait --port 8888
 
-Use an alias for convenience:  
+Or use an alias for convenience:  
 You can simplify the command by creating an alias and run the image with a shorter command:
 
-	alias biospring-run='docker run --rm -p 3000:3000 --init -v ./:/data ghcr.io/lbt-cnrs/biospring biospring'
+	alias biospring-run='docker run --rm -p 8888:8888 --init -v ./:/data ghcr.io/lbt-cnrs/biospring biospring'
 
-	biospring-run -s model.nc -c param.msp --wait --port 3000
+	biospring-run -s model.nc -c param.msp --wait --port 8888
 
+Or reuse the Makefile in the example directory:  
+Copy the file `example/base.mk` and some of other Makefile in example subdir as template for your own system (see README in example directory for usage)
 
 #### Lauching VMD
 Start the VMD program (double click on its icon or launch from the command line).

example/README.md

@@ -1,24 +1,52 @@
-# Usage:
+# Usage
 
-## Step 1: Server side
-- `make prep`
-- `make expose_data`
+## Client and server on the same machine
+
+  - ```bash
+	make prep
+	make run
+	```
+  - Check the line in the shell and note the `HOSTNAME` and `PORT`:
+      ```bash
+      MDDriver > Interactive MD bind to /[HOSTNAME]/[PORT]
+      ```
 
-## Step 2: Client side
-- `make get_data`
+  - In VMD: open `model.pdb`
+  - In UnityMol:  open `model.nc` or `model.pdb`
+  - Connect to the server using the `HOSTNAME` and `PORT`
+  - CTRL + C to stop the server running the simulation
+  - ```bash
+	make clean
+	```
+
+## Client and server on different machines
+
+- Step 1: Server side ⚙️
+
+		make prep
+		make expose_data
+
+
+- Step 2: Client side 🖥️
+  	
+		make get_data
 
-## Step 3: Server side
-- CTRL + C to stop the server exposing the data
-- `make run` / `make run_now`
-    - Check the line in the shell and note the `HOSTNAME` and `PORT`:
+- Step 3: Server side ⚙️
+  - CTRL + C to stop the server exposing the data
+  - ```bash 
+	make run
+	```
+  - Check the line in the shell and note the `HOSTNAME` and `PORT`:
       ```bash
       MDDriver > Interactive MD bind to /[HOSTNAME]/[PORT]
       ```
 
-## Step 4: Client side
-- Open `model.nc` or `model.pdb` in VMD or UnityMol
-- Connect to the server using the `HOSTNAME` and `PORT`
+- Step 4: Client side 🖥️
+  - In VMD: open `model.pdb`
+  - In UnityMol:  open `model.nc` or `model.pdb`
+  - Connect to the server using the `HOSTNAME` and `PORT`
 
-## Step 5: Server side
-- CTRL + C to stop the server running the simulation
-- `make clean`
+- Step 5: Server side ⚙️
+  - CTRL + C to stop the server running the simulation
+  - ```bash
+	make clean

example/base.mk

@@ -87,18 +87,46 @@ clean:
 #        and restart biospring or tune certain parameters from UnityMol during 
 #        an interactive simulation (for example IMPALA scale or Input Force, or 
 #        even viscosity).
-run : 
-	@echo "Run BioSpring"
-	docker run --network host --rm --init -v $(PWD):/data $(IMAGE) \
-	$(BIOSPRING) -s $(NC) \
-				 -c $(MSP) \
-				 --wait --port 3000 \
-				 --sasa-classifier biospring
+run:
+	@echo "Starting BioSpring in detached mode..."
+	@CONTAINER_ID=$$(docker run -d --rm -p 8888:8888 --name biospring-container --init -v $(PWD):/data $(IMAGE) $(BIOSPRING) -s $(NC) -c $(MSP) --wait --port 8888 --sasa-classifier biospring); \
+	if [ -z "$$CONTAINER_ID" ]; then \
+		echo "$(RED)❌ Failed to start the container.$(RESET)"; \
+		exit 1; \
+	fi; \
+	HOSTNAME=$$(hostname); \
+	echo "$(GREEN)✅ BioSpring container started successfully!$(RESET)"; \
+	echo ""; \
+	echo "$(YELLOW)⚠️  Before continuing, please note that the BioSpring program is running now in idle mode within the container, waiting for a connection. By proceeding, we will reattach to the container and display BioSpring's logs in real-time. Afterward, you can use the following information to connect:$(RESET)"; \
+	echo ""; \
+	echo "  - On the local machine: $(GREEN)localhost:8888$(RESET) or $(GREEN)127.0.0.1:8888$(RESET)"; \
+	echo "  - On the network: $(GREEN)$$HOSTNAME:8888$(RESET)"; \
+	trap 'docker ps -q --filter "id=$$CONTAINER_ID" | grep -q . && docker stop $$CONTAINER_ID || true; \
+		echo "$(YELLOW)⚠️ Program interrupted manually (SIGINT/SIGTERM).$(RESET)"; exit 130' INT TERM; \
+	while true; do \
+		read -p "🟢 Continue (c) or Kill the container (k)? " choice; \
+		case $$choice in \
+			[cC]) \
+				echo "$(GREEN)Showing logs and attaching to the container...$(RESET)"; \
+				docker logs -f $$CONTAINER_ID & \
+				DOCKER_LOGS_PID=$$!; \
+				docker attach $$CONTAINER_ID; \
+				break;; \
+			[kK]) \
+				echo "$(RED)Killing the container...$(RESET)"; \
+				if docker ps -q --filter "id=$$CONTAINER_ID" | grep -q .; then \
+					docker stop $$CONTAINER_ID; \
+				fi; \
+				exit 0;; \
+			*) \
+				echo "$(YELLOW)Invalid input. Enter 'c' to continue or 'k' to kill.$(RESET)";; \
+		esac; \
+	done
 
 # Run the BioSpring simulation without waiting for the connection
 run_now:
 	@echo "Run BioSpring NOOOW !!!!"
-	docker run --network host --rm --init -v $(PWD):/data $(IMAGE) \
+	docker run -p 8888:8888 --rm --init -v $(PWD):/data $(IMAGE) \
 	$(BIOSPRING) -s $(NC) \
 				 -c $(MSP) \
 				 --sasa-classifier biospring
@@ -111,7 +139,7 @@ expose_data:
 	@echo "Host machine: $(GREEN)$(shell hostname)$(RESET)"
 	@echo "On the client side, you can retrive the data with the following command:"
 	@echo "\n    $(GREEN)make get_data HOSTNAME=$(shell hostname)$(RESET)\n"
-	@docker run --network host --rm --init -v $(PWD):/data $(IMAGE) python -m http.server 4000 --directory /data
+	@docker run -p 4000:4000 --rm --init -v $(PWD):/data $(IMAGE) python -m http.server 4000 --directory /data
 
 # Retrieve the data from the host machine
 get_data :
@@ -156,4 +184,4 @@ usage:
 	@echo "Step 5: Server side"
 	@echo "  CTRL + C to stop the server running the simulation"
 	@echo "  make clean"
-	@echo "------------------------------------------------------------------------------"
+	@echo "------------------------------------------------------------------------------"

src/cli/biospring-cli.cpp

@@ -164,7 +164,7 @@ CommandLineArguments::CommandLineArguments(const std::string & name, const argpa
                                   .name_long("--port")
                                   .description("Listening and outcoming port for MDDriver.")
                                   .argument_type(argparse::ArgumentType::INTEGER)
-                                  .default_value("3000");
+                                  .default_value("8888");
 
     argparse::Argument debug = argparse::Argument()
                                    .name_long("--debug")

src/cli/biospring-cli.h

@@ -17,7 +17,7 @@ const std::string PROGRAM_VERSION = "biospring " + biospring::VERSION_STRING;
 struct MDDriverParameters
 {
     bool wait = true;
-    unsigned port = 3000;
+    unsigned port = 8888;
     unsigned debug = 0;
     std::string logpath = "";
     float forcescale = 1.0;

src/interactor/mddriver/InteractorMDDriver.cpp

@@ -22,7 +22,7 @@ InteractorMDDriver::InteractorMDDriver()
 	strcpy(_IMDlogfilename,"");
 	_IMDlog = NULL;
 	_IMDwait           = 1;
-	_IMDport           = 3000;
+	_IMDport           = 8888;
 	_IMDmode = 1; //server
 	_IMDforcescale =1.0;
 	_IMDenergies.tstep  = 0.0;

src/viewer/biospring-viewer.cpp

@@ -37,7 +37,7 @@ void usage()
 	#ifdef MDDRIVER_SUPPORT
 	cout<<"\tMDDriver support     MDDriver support is enabled : "<<endl;
 	cout<<"\t\tMDDriver is a library which extends the IMD protocol used in VMD for simulation and visualisation coupling."<<endl;
-	cout<<"\t\t[-port portnumber] 			(Listening and outcoming port for MDDriver with default = 3000)"<<endl;
+	cout<<"\t\t[-port portnumber] 			(Listening and outcoming port for MDDriver with default = 8888)"<<endl;
 	cout<<"\t\t[-wait 0 or 1]     			(Wait a connection before starting the simulation with default = 1 means wait)"<<endl;
 	cout<<"\t\t[-debug 0, 1 or 2] 	 		(Debug level of the MDDriver simulation with default = 0 means no debug message)"<<endl;
 	cout<<"\t\t[-log filename]     			(Filename for MDDriver debug messages with default = stdout)"<<endl;
@@ -54,7 +54,7 @@ int main(int argc, char ** argv)
 	{
 	bool openclok=true;
 	#ifdef MDDRIVER_SUPPORT
-   		unsigned port=3000;
+   		unsigned port=8888;
 		unsigned wait=1;
 		unsigned debug=0;
         	char logfilename[FILENAMEMAXSIZE]="";