Merge pull request #178 from OpenSEMBA/dev

Merge pull request #166 from OpenSEMBA/feature/mtl_mpi

Feature/mtl mpi

Author: Alberto-o

.github/workflows/ubuntu.yml

@@ -21,7 +21,7 @@ jobs:
       matrix: 
         os: [ubuntu-latest]
         compiler: [
-          {name: 'intel', version: '2025.0'},
+          {name: 'intel', version: '2025.1'},
           {name: 'gcc', version: 11}
         ]
         build-type: ["Release"]
@@ -56,7 +56,7 @@ jobs:
             double-precision: "No"
 
           - os: ubuntu-latest # This is the only test with double precision.
-            compiler: {name: 'intel', version: '2025.0'}
+            compiler: {name: 'intel', version: '2025.1'}
             build-type: "Release"
             mpi: "Yes"
             mtln: "No"

.gitmodules

@@ -20,4 +20,4 @@
 
 [submodule "external/googletest"]
 	path = external/googletest
-	url = https://github.com/google/googletest.git
+	url = https://github.com/google/googletest.git

CMakeLists.txt

@@ -78,7 +78,17 @@ if (CMAKE_SYSTEM_NAME MATCHES "Linux")
 			set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -fp-model fast=2w")
 
 			if(SEMBA_FDTD_ENABLE_INTEL_IPO)
+				include(CheckIPOSupported)
+				check_ipo_supported(RESULT iporesult)
+				if(iporesult)
+				  message (STATUS "IPO is supported and being enabled")
+				else()
+				  message(FATAL_ERROR "IPO is not supported")
+				endif()
 				set(CMAKE_INTERPROCEDURAL_OPTIMIZATION ON)
+				set(CMAKE_C_FLAGS_RELEASE "-ipo")
+				set(CMAKE_CXX_FLAGS_RELEASE "-ipo")
+				set(CMAKE_Fortran_FLAGS_RELEASE "-ipo")
 			else()
 				set(CMAKE_INTERPROCEDURAL_OPTIMIZATION OFF)
 			endif()
@@ -248,6 +258,7 @@ if (SEMBA_FDTD_EXECUTABLE)
 	target_link_libraries(semba-fdtd ${MPI_Fortran_LIBRARIES})
 endif()
 
+
 include_directories(${CMAKE_BINARY_DIR}/mod)
 include_directories(${HDF5_INCLUDE_DIRS})
-include_directories(${FHASH_INCLUDES})
+include_directories(${FHASH_INCLUDES})

doc/development.md

@@ -301,7 +301,7 @@ To run the tests:
 
 ## Debugging the project
 
-For a correct debugging experience is needed to configure a launch.json file. This file usually is created by vscode automatically. In case it does not exist. You can create your own on .vscode folder.
+For a correct debugging experience configuring a launch.json file is needed. This file usually is created by vscode automatically. In case it does not exist. You can create your own on .vscode folder.
 
 An example of launch.json filke is given. This will use a file as argument when calling to semba-fdtd.
 ```json
@@ -323,3 +323,56 @@ An example of launch.json filke is given. This will use a file as argument when
 ```
 
 Now you are ready to work with the project.
+
+### Debugging with MPI 
+
+gdb is a serial debugger, but can be attached to one of the parallel processes after they have started running. 
+
+
+1. Modify the file launch.json to attach to a running process after launching the debugger:
+
+```json
+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+        "name": "(gdb) Attach",
+        "type": "cppdbg",
+        "request": "attach",
+        "processId": "${command:pickProcess}",
+        "program": "${workspaceFolder}/build/bin/semba-fdtd",
+        "MIMode": "gdb",
+        "miDebuggerPath": "/usr/bin/gdb",
+        "setupCommands": [
+            {
+                "description": "Enable pretty-printing for gdb",
+                "text": "-enable-pretty-printing",
+                "ignoreFailures": true
+            },
+            {
+                "description": "Set Disassembly Flavor to Intel",
+                "text": "-gdb-set disassembly-flavor intel",
+                "ignoreFailures": true
+            }
+        ]
+    }
+  ]
+}
+```
+
+2. Use *mpirun* to execute semba-fdtd paralellized in 'np' processes:
+``` 
+mpirun -np 2 build/bin/semba-fdtd -i input_file.fdtd.json -args
+```
+
+3. Once mpirun is running, launch the debuuger. A selection box will ask which process to attach to. Type *semba-fdtd* and all mpirun processes running semba will display. Selecto which process the debugger should attach to
+
+#### Troubleshooting
+
+1. After selecting the process the debugger should attach to, a new terminal opens with the message "Superuser access is required to attach to a process"
+
+Run the following command as super user: 
+```
+echo 0| sudo tee /proc/sys/kernel/yama/ptrace_scope 
+```
+([source](https://github.com/Microsoft/MIEngine/wiki/Troubleshoot-attaching-to-processes-using-GDB))