Updated the Fedora setup guide to version 40/Minor fixes in the 'ecg.c'

bergolho · Jan 15, 2025 · bbc0215 · bbc0215
1 parent 1c6761b
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diff --git a/bsbash/find_functions.sh b/bsbash/find_functions.sh
@@ -22,7 +22,7 @@ FIND_CUDA () {
 
 		if [ "$OS" == "Manjaro Linux" ]; then
 			CUDA_INCLUDE_PATH="/opt/cuda/include"
-		elif [ "$OS" == "Fedora" ]; then
+		elif [ "$OS" == "Fedora Linux" ]; then
 			CUDA_INCLUDE_PATH="/usr/local/cuda/include"
 			CUDA_LIBRARY_PATH="/usr/local/cuda/lib64"
 		elif [ "$OS" == "openSUSE Tumbleweed" ]; then
@@ -120,9 +120,9 @@ FIND_CRITERION() {
 }
 
 FIND_MPI () {
-	FIND_LIB "ompi"
-	MPI_FOUND=$OMPI_FOUND
-	MPI_LIBRARIES=$OMPI_LIBRARIES
+	#FIND_LIB "ompi"
+	MPI_FOUND="y"
+	MPI_LIBRARIES="mpi"
 	MPI_LIBRARY_PATH=$OMPI_LIBRARY_PATH
 	MPI_INCLUDE_PATH=$OMPI_INCLUDE_PATH
 }

diff --git a/guide-monoalg3d-fedora.md b/guide-monoalg3d-fedora.md
@@ -1,18 +1,18 @@
-## GUIDE TO CONFIGURE THE MONOALG_3D ON A FEDORA 33 MACHINE
+## GUIDE TO CONFIGURE MONOALG_3D ON A FEDORA 40 MACHINE
 
 ----------------------------------------------------------
 
-This guide provides instructions to configure the MonoAlg3D solver in a fresh instalation of Fedora 33 with all its features working.
+This guide provides instructions to configure the MonoAlg3D solver in a fresh instalation of Fedora 40 with all its features working.
 
 ## 1) Download and build a USB boot drive
 
-### Download the Fedora 33 ISO image:
+### Download the Fedora 40 ISO image for your system:
 
-- https://getfedora.org/pt_BR/
+- https://dl.fedoraproject.org/pub/fedora/linux/releases/40/Workstation/
 
-### Burn the ISO image in a USB device using the Rufus program (Windows) or any other program.
+- Burn the ISO image in a USB device using the Rufus program (Windows) or any other similar program.
 
-### Install Fedora 33 in the target machine
+- Install Fedora 40 on the target machine
 
 ### Perform a system update:
 
@@ -24,7 +24,7 @@ $ sudo dnf update
 
 - Close your current session
 - Click on your user
-- Click on the gear symbol and select the "GNOME over Xorg"
+- Click on the gear symbol and select the _"GNOME over Xorg"_
 - Begin your session again
 
 ### Reboot your system
@@ -39,27 +39,32 @@ $ reboot
 $ sudo dnf install gnome-tweak-tool
 ```
 
-### Open the Gnome-Tweak-Tool
+### Open Configurations
 
-- Disable animations to save memory
+- Disable energy saving options
 - Disable the suspend screen when notebook is closed
 
-## 2) Install RPMFusion
-
-### Add the packages to your system:
-
+### Install gedit
 ```sh
-$ sudo dnf install https://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-$(rpm -E %fedora).noarch.rpm https://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-$(rpm -E %fedora).noarch.rpm
-$ sudo dnf update
+$ sudo dnf gedit
 ```
 
-### Open the Gnome-Programs
+### Install the Resources program to replace the System Monitor
 
-- Go to Program Repositories
-- Enable the RPMFusion repositories for NVIDIA
-- Update the repositories again
+- Search for the 'Programs' software
+- Open 'Programs' and search for the Resources program
+- Install using the Flathub package
+
+### Install the Engrampa package manager
+
+- Get the 'Engrampa' software from Programs
+
+## 2) Install RPMFusion
+
+### Add the packages to your system:
 
 ```sh
+$ sudo dnf install https://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-$(rpm -E %fedora).noarch.rpm https://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-$(rpm -E %fedora).noarch.rpm
 $ sudo dnf update
 ```
 
@@ -69,14 +74,12 @@ $ sudo dnf update
 $ reboot
 ```
 
-## 3) Install the NVIDIA driver
-
-### Reboot your system
-
 - Enter your BIOS by pressing F12 (check your computer key)
 - Disable the Secure Boot
 - Save your changes and exit
 
+## 3) Install the NVIDIA driver
+
 ### Run the following commands
 
 ```sh
@@ -103,36 +106,39 @@ $ reboot
 
 ### Check if the NVIDIA driver is correctly installed 
 
-- Go to Settings > About
-- Your NVIDIA Graphics Card should appear below the Processor field.
+- Go to Settings > System > About > System Details
+- Your NVIDIA Graphics Card should appear in Graphics field.
 
 ## 4) Install CUDA libraries
 
 ### Download the CUDA runfile for your operating system
 
 ```sh
 $ cd ~; mkdir CUDA-Install; cd CUDA-Install
-$ wget -nc https://developer.download.nvidia.com/compute/cuda/11.3.0/local_installers/cuda_11.3.0_465.19.01_linux.run
+$ wget -nc https://developer.download.nvidia.com/compute/cuda/12.6.3/local_installers/cuda_12.6.3_560.35.05_linux.run
 ```
 
+- Here, I am using the CUDA version 12.6.3.
+
 ### Install dependencies
 
 ```sh
-$ sudo dnf install gcc-c++ mesa-libGLU-devel libX11-devel libXi-devel libXmu-devel libXcursor-devel libXrandr-devel
+$ sudo dnf install gcc-c++ mesa-libGLU-devel libX11-devel libXi-devel libXmu-devel 
 $ sudo dnf install freeglut freeglut-devel
+$ sudo dnf install gcc13-c++-13.3.1-2.fc40.x86_64
 ```
 
 ### Run the CUDA runfile
 
 ```sh
-$ chmod +x cuda_11.3.0_465.19.01_linux.run
-$ sudo ./cuda_11.3.0_465.19.01_linux.run
+$ chmod +x cuda_12.6.3_560.35.05_linux.run
+$ sudo ./cuda_12.6.3_560.35.05_linux.run
 ```
 
 ### Configure the installation
 
 - Accept the terms
-- Disable the NVIDIA Driver installation
+- **IMPORTANT!** Disable the NVIDIA Driver installation
 - Enable the installation: CUDA Toolkit, CUDA Samples, CUDA Demo, CUDA Documentation
 - Install the package
 
@@ -144,7 +150,7 @@ $ sudo ./cuda_11.3.0_465.19.01_linux.run
 $ su -
 ```
 
-- If is the first time logging as root, you can set a password to the "root" user with:
+- If is the first time logging as root, you can set a password to the _"root"_ user with:
 
 ```sh
 $ sudo passwd root
@@ -166,21 +172,25 @@ export PATH LD_LIBRARY_PATH
 EOF
 ```
 
-#### Logout and login again and check the variables
+#### Logout and login again. Check the variables
 
 ```sh
 $ echo $PATH
 $ echo $LD_LIBRARY_PATH
 ```
 
+- The new paths must appear.
+
 #### Test the CUDA library
 
 ```sh
-$ cd /home/<username>/NVIDIA_CUDA-11.1_Samples/1_Utilities/deviceQuery
+$ cd /home/<username>/NVIDIA_CUDA-12.6_Samples/1_Utilities/deviceQuery
 $ make
 $ ./deviceQuery
 ```
 
+- This should print some information about your GPU hardware.
+
 ## 5) Configure MonoAlg3D_C
 
 ### Download remaining dependencies
@@ -189,15 +199,30 @@ $ ./deviceQuery
 $ sudo dnf install libXcursor-devel libXrandr-devel libXinerama-devel
 ```
 
+### Make a symbolic link for GCC version 13
+
+```sh
+$ sudo ln -s /usr/bin/gcc-13 /usr/local/cuda/bin/gcc
+$ sudo ln -s /usr/bin/g++-13 /usr/local/cuda/bin/g++
+```
+
+### Build and compile MonoAlg3D
+
+```sh
+$ ./build.sh -f
+```
+
+**IMPORTANT!** If you stop here you already have a working MonoAlg3D binary executable in the _/bin_ folder
+
 #### If you stop here you already have a working MonoAlg3D binary executable in the /bin folder
 
 ### [OPTIONAL] Install and configure MPI for batch simulations
 
 #### Download OpenMPI
 
 ```sh
-$ cd ~; make OpenMPI-Install; cd OpenMPI-Install
-$ wget -nc https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.gz
+$ cd ~; mkdir OpenMPI-build; cd OpenMPI-build
+$ wget -nc https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.6.tar.gz
 ```
 
 #### Build OpenMPI
@@ -208,3 +233,24 @@ $ cd openmpi-4.1.1
 $ ./configure --prefix=/usr/local
 $ sudo make all install
 ```
+
+#### Configure OpenMPI for MonoAlg3D
+
+- Change the following function in the _'bsbash/find_functions.sh'_ file:
+
+```sh
+FIND_MPI () {
+	MPI_FOUND="y"
+	MPI_LIBRARIES="mpi"
+	MPI_LIBRARY_PATH=$OMPI_LIBRARY_PATH
+	MPI_INCLUDE_PATH=$OMPI_INCLUDE_PATH
+}
+```
+
+- Rebuild MonoAlg3D
+
+```sh
+./build.sh -f
+```
+
+- Check if you have the _"MonoAlg3D_batch"_ executable inside the _"/bin"_ folder.
diff --git a/src/ecg_library/ecg.c b/src/ecg_library/ecg.c
@@ -587,7 +587,7 @@ CALC_ECG(pseudo_bidomain_with_diffusive_current_cpu) {
 
     // DIFFUSIVE CURRENT PLOT
     if (time_info->iteration % PSEUDO_BIDOMAIN_DATA->diff_curr_rate == 0 && time_info->current_t <= PSEUDO_BIDOMAIN_DATA->diff_curr_max_time) {
-        char *filename_diffusive_current[200];
+        char filename_diffusive_current[200];
         sprintf(filename_diffusive_current, "%s/diffusive_current_t_%g_ms.txt", output_dir, time_info->current_t);
         FILE *output_diffusive_current = fopen(filename_diffusive_current, "w");
         for(uint32_t i = 0; i < n_active; i++) {
@@ -749,7 +749,7 @@ CALC_ECG(pseudo_bidomain_with_diffusive_current_gpu) {
 
     // DIFFUSIVE CURRENT
     if (time_info->iteration % PSEUDO_BIDOMAIN_DATA->diff_curr_rate == 0 && time_info->current_t <= PSEUDO_BIDOMAIN_DATA->diff_curr_max_time) {
-        char *filename_diffusive_current[200];
+        char filename_diffusive_current[200];
         sprintf(filename_diffusive_current, "%s/diffusive_current_t_%g_ms.txt", output_dir, time_info->current_t);
         FILE *output_diffusive_current = fopen(filename_diffusive_current, "w");
         check_cuda_error(cudaMemcpy(PSEUDO_BIDOMAIN_DATA->beta_im_cpu, PSEUDO_BIDOMAIN_DATA->beta_im, n_active * sizeof(real), cudaMemcpyDeviceToHost));