Ow 0.9.4 - Passing tests building sibernetic using Intel and AMD drivers

.github/workflows/ci-build-intel.yml

@@ -0,0 +1,77 @@
+name: Build using Intel drivers
+
+on:
+  push:
+    branches: [ master, dev*, ow* ]
+  pull_request:
+    branches: [ master, dev, ow* ]
+
+jobs:
+
+  build:
+
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      fail-fast: false
+      matrix:
+        runs-on: [ ubuntu-latest, ubuntu-20.04 ]
+
+    steps:
+    - name: Set git to use LF
+      run: |
+        git config --global core.autocrlf false
+        git config --global core.eol lf
+
+    - uses: actions/checkout@v3
+
+    - name: Install Intel OpenCL libraries needed for Sibernetic
+      run: |
+
+        lscpu
+
+        echo "Installing OpenCL Drivers"
+
+        # Based on: https://github.com/openworm/OpenWorm/blob/master/Dockerfile
+
+        mkdir intel-opencl-tmp
+        cd intel-opencl-tmp
+        mkdir intel-opencl
+        wget https://github.com/openworm/OpenWorm/raw/dev_inte/SRB5.0_linux64.zip
+        unzip SRB5.0_linux64.zip
+        tar -C intel-opencl -Jxf intel-opencl-r5.0-63503.x86_64.tar.xz
+        tar -C intel-opencl -Jxf intel-opencl-devel-r5.0-63503.x86_64.tar.xz
+        tar -C intel-opencl -Jxf intel-opencl-cpu-r5.0-63503.x86_64.tar.xz
+        sudo cp -R intel-opencl/* /
+        sudo ldconfig
+        cd ..
+        sudo rm -r intel-opencl-tmp
+
+        sudo cp -R /opt/intel/opencl/include/CL /usr/include/
+        sudo apt install -y ocl-icd-opencl-dev vim
+
+        echo "OpenCL Driver Installation Complete"
+
+
+    - name: Build Sibernetic
+      run: |
+
+        sudo apt install -y python3-dev freeglut3-dev libglu1-mesa-dev
+        #sudo apt install -y  --allow-downgrades libc-bin=2.27-3ubuntu1.5 # Fails with 2.27-3ubuntu1.6 for some reason...
+        python -V
+        ls -alt /usr/bin/python*
+        ls -alt
+        make clean
+        make
+
+    - name: Print info on executable
+      run: |
+        ldd ./Release/Sibernetic
+
+        echo "NOTE: not running Sibernetic on GitHub actions test with Intel drivers. Seg faults."
+        ###./Release/Sibernetic -no_g timelimit=0.001
+
+    - name: Final version info
+      run: |
+
+        python -V
+        pip list

.github/workflows/ci-build.yml

@@ -1,4 +1,4 @@
-name: Build Sibernetic
+name: Build using AMD drivers
 
 on:
   push:
@@ -14,36 +14,55 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        runs-on: [ ubuntu-latest ]
+        runs-on: [ ubuntu-latest, ubuntu-20.04 ]
 
     steps:
+    - name: Set git to use LF
+      run: |
+        git config --global core.autocrlf false
+        git config --global core.eol lf
+
     - uses: actions/checkout@v3
 
-    - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version:  ${{ matrix.python-version }}
-
-    - name: Install Intel OpenCL libraries needed for Sibernetic
+    - name: Install AMD OpenCL libraries needed for Sibernetic
       run: |
 
-        # Based on: https://github.com/openworm/OpenWorm/blob/master/Dockerfile
+        lscpu
 
-        mkdir intel-opencl-tmp
-        cd intel-opencl-tmp
-        mkdir intel-opencl
-        wget https://github.com/openworm/OpenWorm/raw/dev_inte/SRB5.0_linux64.zip
-        unzip SRB5.0_linux64.zip
-        tar -C intel-opencl -Jxf intel-opencl-r5.0-63503.x86_64.tar.xz
-        tar -C intel-opencl -Jxf intel-opencl-devel-r5.0-63503.x86_64.tar.xz
-        tar -C intel-opencl -Jxf intel-opencl-cpu-r5.0-63503.x86_64.tar.xz
-        sudo cp -R intel-opencl/* /
-        sudo ldconfig
-        cd ..
-        sudo rm -r intel-opencl-tmp
-
-        sudo cp -R /opt/intel/opencl/include/CL /usr/include/
-        sudo apt install -y ocl-icd-opencl-dev vim
+        echo "Installing OpenCL Drivers"
+
+        # Legacy install of Intel's OpenCL Drivers:
+        # Based on: https://github.com/openworm/OpenWorm/blob/master/Dockerfile
+        # mkdir intel-opencl-tmp
+        # cd intel-opencl-tmp
+        # mkdir intel-opencl
+        # wget https://github.com/openworm/OpenWorm/raw/dev_inte/SRB5.0_linux64.zip
+        # unzip SRB5.0_linux64.zip
+        # tar -C intel-opencl -Jxf intel-opencl-r5.0-63503.x86_64.tar.xz
+        # tar -C intel-opencl -Jxf intel-opencl-devel-r5.0-63503.x86_64.tar.xz
+        # tar -C intel-opencl -Jxf intel-opencl-cpu-r5.0-63503.x86_64.tar.xz
+        # sudo cp -R intel-opencl/* /
+        # sudo ldconfig
+        # cd ..
+        # sudo rm -r intel-opencl-tmp
+
+        # sudo cp -R /opt/intel/opencl/include/CL /usr/include/
+        # sudo apt install -y ocl-icd-opencl-dev vim 
+
+        # Install AMD's OpenCL Drivers (AMD-APP-SDK 3.0):
+        wget https://master.dl.sourceforge.net/project/nicehashsgminerv5viptools/APP%20SDK%20A%20Complete%20Development%20Platform/AMD%20APP%20SDK%203.0%20for%2064-bit%20Linux/AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2
+        tar -xf AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2
+        printf 'Y\n\n' | sudo ./AMD-APP-SDK-v3.0.130.136-GA-linux64.sh
+
+        sudo ln -s /opt/AMDAPPSDK-3.0/lib/x86_64/sdk/libOpenCL.so.1 /usr/lib/libOpenCL.so.1
+        sudo ln -s /opt/AMDAPPSDK-3.0/lib/x86_64/sdk/libamdocl64.so /usr/lib/libamdocl64.so
+
+        sudo apt install -y ocl-icd-opencl-dev
+
+        echo "OpenCL Driver Installation Complete"
+
+        echo "CLINFO:"
+        clinfo
 
     - name: Build Sibernetic
       run: |

sibernetic_c302.py

@@ -9,7 +9,7 @@
 import pprint
 pp = pprint.PrettyPrinter(indent=4)
 
-script_version = '0.1.4' # This will change at different rate to C++ code...
+script_version = '0.1.5' # This will change at different rate to C++ code...
 
 DEFAULTS = {'duration': 2.0,
             'dt': 0.005,

src/main.cpp

@@ -45,7 +45,7 @@ bool load_to = false;
 bool skip_display_particles = false;
 bool skip_display_membranes = false;
 bool skip_display_connections = false;
-std::string version = "0.0.6";
+std::string version = "0.0.7";
 
 int usage() {
   std::cout
@@ -103,13 +103,11 @@ int usage() {
 }
 
 int main(int argc, char **argv) {
-  int exitStatus;
-  std::cout << "S1\n";
+  int exitStatus = -1;
   if (argc == 1) {
     std::cout << "Sibernetic: no arguments specified, run method executing\n";
     exitStatus = run(argc, argv);
   } else {
-  std::cout << "S1e\n";
     bool graph = true;
     bool run_tests = false;
 
@@ -135,7 +133,6 @@ int main(int argc, char **argv) {
           0) { // run load config from file mode
         graph = true;
         load_from_file = true;
-        std::cout << "S1f\n";
       }
       if (std::string("-skip_display_particles").compare(argv[i]) == 0) {
         skip_display_particles = true;
@@ -154,9 +151,7 @@ int main(int argc, char **argv) {
       test_energy_conservation(argc, argv);
     } else
 
-    std::cout << "S1r\n";
       exitStatus = run(argc, argv, graph);
   }
-  std::cout << "S1n\n";
   return exitStatus;
 }

src/owOpenCLSolver.cpp

@@ -63,14 +63,11 @@ owOpenCLSolver::owOpenCLSolver(const float *position_cpp,
                                const int *membraneData_cpp,
                                const int *particleMembranesList_cpp) {
   try {
-      std::cout << "owC1\n";
     initializeOpenCL(config);
-            std::cout << "owC10\n";
     // Create OpenCL buffers
     initializeBuffers(position_cpp, velocity_cpp, config,
                       elasticConnectionsData_cpp, membraneData_cpp,
                       particleMembranesList_cpp);
-                          std::cout << "owC1a\n";
     // Create OpenCL kernels
     create_ocl_kernel("clearBuffers", clearBuffers);
     create_ocl_kernel("findNeighbors", findNeighbors);
@@ -91,14 +88,13 @@ owOpenCLSolver::owOpenCLSolver(const float *position_cpp,
                       pcisph_computeElasticForces);
     // membrane handling kernels
 
-        std::cout << "owC1b\n";
     create_ocl_kernel("clearMembraneBuffers", clearMembraneBuffers);
     create_ocl_kernel("computeInteractionWithMembranes",
                       computeInteractionWithMembranes);
     create_ocl_kernel("computeInteractionWithMembranes_finalize",
                       computeInteractionWithMembranes_finalize);
   } catch (std::runtime_error &ex) {  
-          std::cout << "errrr\n";
+          std::cout << "Error in owOpenCLSolver.cpp!!\n";
     destroy();
     throw;
   }
@@ -239,18 +235,14 @@ void owOpenCLSolver::initializeBuffers(const float *position_cpp,
  *  Contain information about simulating configuration
  */
 void owOpenCLSolver::initializeOpenCL(owConfigProperty *config) {
-  std::cout << "owCi1\n";
   cl_int err;
   std::vector<cl::Platform> platformList;
-    std::cout << "owCi1a\n";
   err = cl::Platform::get(
       &platformList); // TODO make check that returned value isn't error
-        std::cout << "owCi1b\n";
   if (platformList.size() < 1 || err != CL_SUCCESS) {
     std::cout << "No OpenCL platforms found, error code: "<< err<< " \n";
     throw std::runtime_error("No OpenCL platforms found");
   }
-    std::cout << "owCi2\n";
   char cBuffer[1024];
   cl_platform_id cl_pl_id[10];
   cl_uint n_pl;
@@ -262,12 +254,12 @@ void owOpenCLSolver::initializeOpenCL(owConfigProperty *config) {
     ciErrNum = clGetPlatformInfo(cl_pl_id[i], CL_PLATFORM_VERSION,
                                  sz = sizeof(cBuffer), cBuffer, nullptr);
     if (ciErrNum == CL_SUCCESS) {
-      printf(" CL_PLATFORM_VERSION [%d]: \t%s\n", i, cBuffer);
+      printf(" CL_PLATFORM_VERSION [%d]: \t%s", i, cBuffer);
+      std::cout << std::endl;
     } else {
       printf(" Error %i in clGetPlatformInfo Call !!!\n\n", ciErrNum);
     }
   }
-    std::cout << "owCi2\n";
   // 0-CPU, 1-GPU // depends on the time order of system OpenCL drivers
   // installation on your local machine
   // CL_DEVICE_TYPE
@@ -287,6 +279,7 @@ void owOpenCLSolver::initializeOpenCL(owConfigProperty *config) {
   cl_uint device_coumpute_unit_num;
   cl_uint device_coumpute_unit_num_current = 0;
   unsigned int deviceNum = 0;
+
   // Selection of more appropriate device
   while (!findDevice) {
     for (int clSelectedPlatformID = 0; clSelectedPlatformID < (int)n_pl;
@@ -297,8 +290,9 @@ void owOpenCLSolver::initializeOpenCL(owConfigProperty *config) {
                      device_type[config->getDeviceType()], 0, nullptr,
                      &ciDeviceCount);
       if ((devices_t = static_cast<cl_device_id *>(
-               malloc(sizeof(cl_device_id) * ciDeviceCount))) == nullptr)
+               malloc(sizeof(cl_device_id) * ciDeviceCount))) == nullptr) {
         bPassed = false;
+      }
       if (bPassed) {
         result = clGetDeviceIDs(cl_pl_id[clSelectedPlatformID],
                                 device_type[config->getDeviceType()],
@@ -335,12 +329,13 @@ void owOpenCLSolver::initializeOpenCL(owConfigProperty *config) {
       std::cout << "Unfortunately OpenCL couldn't find device "
                 << deviceTypeName << std::endl;
       std::cout << "OpenCL try to init existing device " << std::endl;
-      if (config->getDeviceType() != ALL)
+      if (config->getDeviceType() != ALL) {
         config->setDeviceType(ALL);
-      else
+      } else {
         throw std::runtime_error("Sibernetic can't find any OpenCL devices. "
                                  "Please check you're environment "
                                  "configuration.");
+      }
     }
   }
   cl_context_properties cprops[3] = {
@@ -357,8 +352,7 @@ void owOpenCLSolver::initializeOpenCL(owConfigProperty *config) {
                                       &cBuffer); // CL_INVALID_VALUE = -30;
   if (result == CL_SUCCESS) {
     std::cout << "CL_CONTEXT_PLATFORM [" << plList << "]: CL_DEVICE_NAME ["
-              << deviceNum << "]:\t" << cBuffer << "\n"
-              << std::endl;
+              << deviceNum << "]:\t" << cBuffer << std::endl << std::endl;
   }
   if (strlen(cBuffer) < 1000) {
     config->setDeviceName(cBuffer);

src/owPhysicsFluidSimulator.cpp

@@ -89,11 +89,8 @@ owPhysicsFluidSimulator::owPhysicsFluidSimulator(owHelper *helper, int argc,
         membraneData_cpp, particleMembranesList_cpp,
         config); // Load configuration from file to buffer
 
-    std::cout << "owP1\n";
     this->helper = helper;
-        std::cout << "owP1a\n";
     if (config->numOfElasticP != 0) {
-        std::cout << "owP1b\n";
       ocl_solver = new owOpenCLSolver(
           position_cpp, velocity_cpp, config, elasticConnectionsData_cpp,
           membraneData_cpp,
@@ -114,7 +111,6 @@ owPhysicsFluidSimulator::owPhysicsFluidSimulator(owHelper *helper, int argc,
     throw;
   }
 
-  std::cout << "owP2\n";
 }
 /** Reset simulation
  *

src/owSignalSimulator.cpp

@@ -119,7 +119,6 @@ std::vector<float> SignalSimulator::run() {
   // Call a method of the class
   // pValue = PyObject_CallMethod(pInstance, "rrun
   // un", nullptr);
-  std::cout << "S1s\n";
   pValue = PyObject_CallMethod(pInstance, const_cast<char *>("run"), nullptr);
   if (PyErr_Occurred()) {
       PyErr_Print();