merge dev

CMakeLists.txt

@@ -95,6 +95,7 @@ if (CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANGXX OR ${CMAKE_CXX_COMPILE
 
     set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -ansi -pedantic -fno-omit-frame-pointer -Wall")
     #set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -std=c++11 -ansi -pedantic -fno-omit-frame-pointer -Wall")
+    set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fopenmp")
 
     ### debug settings
     # run with -DCMAKE_BUILD_TYPE=Debug
@@ -652,31 +653,55 @@ find_package(Sphinx 3.1)
 
 if (SPHINX_FOUND AND NOT SKIP_SPHINX)
     add_subdirectory(doc EXCLUDE_FROM_ALL)
-    message(STATUS "Search recursive for *.rst from here: " ${CMAKE_SOURCE_DIR})
-    file(GLOB_RECURSE DOCFILES RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "*.rst")
-    message(STATUS "DOCFILES: " ${DOCFILES})
-
-    file(GLOB_RECURSE PNGFILES RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "*.png")
-    list(APPEND DOCFILES ${PNGFILES})
-
-    message(STATUS "PNGFILES: " ${PNGFILES})
-
-    file(GLOB_RECURSE BIBFILES RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "*.bib")
-    list(APPEND DOCFILES ${BIBFILES})
+    message(STATUS "Search recursive for related doc files from here: " ${CMAKE_SOURCE_DIR})
 
-    message(STATUS "BIBFILES: " ${BIBFILES})
-
-    file(GLOB_RECURSE PYFILES RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "doc/paper/*.py")
-    message(STATUS "PYFILES: " ${PYFILES})
+    file(GLOB DOCFILES LIST_DIRECTORIES false
+            RELATIVE "${CMAKE_SOURCE_DIR}"
+        "*.rst")
+    message(STATUS "DOCFILES: " ${DOCFILES})
 
-    list(APPEND DOCFILES ${PYFILES})
+    file(GLOB DFILES LIST_DIRECTORIES false
+            RELATIVE "${CMAKE_SOURCE_DIR}"
+        "*.md")
+    message(STATUS "MDFILES: " ${DFILES})
+    list(APPEND DOCFILES ${DFILES})
+
+    set (RECDOCTYPES "*.rst" "*.md" "*.png" "*.svg" "*.bib" "paper/*.py")
+
+    foreach (DTYPE ${RECDOCTYPES})
+        file(GLOB_RECURSE DFILES
+                LIST_DIRECTORIES false
+                RELATIVE "${CMAKE_SOURCE_DIR}"
+            "./doc/${DTYPE}")
+        message(STATUS "Append DOC files: (${DTYPE}) " ${DFILES})
+        list(APPEND DOCFILES ${DFILES})
+    endforeach()
+    # message(STATUS "RSTFILES: " ${DFILES})
+
+    # file(GLOB_RECURSE DFILES LIST_DIRECTORIES false
+    # RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "./doc/*.md")
+    # message(STATUS "MDFILES: " ${DFILES})
+    # list(APPEND DOCFILES ${DFILES})
+
+    # file(GLOB_RECURSE DFILES LIST_DIRECTORIES false
+    # RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "./doc/*.png")
+    # message(STATUS "PNGFILES: " ${DFILES})
+    # list(APPEND DOCFILES ${DFILES})
+
+    # file(GLOB_RECURSE DFILES LIST_DIRECTORIES false
+    # RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "./doc/*.bib")
+    # message(STATUS "BIBFILES: " ${DFILES})
+    # list(APPEND DOCFILES ${DFILES})
+
+    # file(GLOB_RECURSE PYFILES LIST_DIRECTORIES false
+    #     RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "doc/paper/*.py")
+    # message(STATUS "PYFILES: " ${PYFILES})
+    # list(APPEND DOCFILES ${PYFILES})
 
     set(RSTFILES ${DOCFILES} CACHE INTERNAL "RST source file that we need to copy")
 
-    set(RSTFILES ${DOCFILES} CACHE INTERNAL "RST source file that we need to copy")
-    execute_process(
-        COMMAND ${SPHINX_EXECUTABLE} --version
-        OUTPUT_VARIABLE SPHINX_VERSION
+    execute_process(COMMAND ${SPHINX_EXECUTABLE} --version
+                    OUTPUT_VARIABLE SPHINX_VERSION
     )
 
     add_custom_target(removedoc

INSTALLATION.rst

@@ -126,12 +126,18 @@ retrieve the source code by git
     git clone https://github.com/gimli-org/gimli
     cd gimli
 
-and install pygimli as a development package
+and install pygimli as a development package using conda
 
 .. code-block:: bash
 
     conda develop .
 
+or using pip
+
+.. code-block:: bash
+
+    pip install --no-build-isolation --no-deps -e .
+
 Alternatively you could set the PYTHONPATH variable but you would have to care
 for dependencies by yourself.
 

core/scripts/buildThirdParty.sh

@@ -24,12 +24,7 @@ CASTXML_URL=https://github.com/CastXML/CastXML.git
 #CASTXML_REV=9d7a46d639ce921b8ddd36ecaa23c567d003294a #last functional
 
 # Check for updates https://data.kitware.com/#search/results?query=castxml&mode=text
-#CASTXML_BIN_LINUX=https://data.kitware.com/api/v1/file/5b6c5b4d8d777f06857c323b/download # 0.1
-#CASTXML_BIN_MAC=https://data.kitware.com/api/v1/file/57b5de9f8d777f10f2696378/download # 0.1.0
-#CASTXML_BIN_WIN=https://data.kitware.com/api/v1/file/5b68bfc28d777f06857c1f44/download # 0.1.0
-
 CASTXML_BIN_LINUX=https://data.kitware.com/api/v1/item/63bed74d6d3fc641a02d7e98/download # 0.5.0
-CASTXML_BIN_MAC=https://data.kitware.com/api/v1/item/63bed7726d3fc641a02d7e9e/download # 0.5.0
 CASTXML_BIN_WIN=https://data.kitware.com/api/v1/file/63bed83a6d3fc641a02d7ea3/download # 0.5.0
 
 if [[ $(uname -m) == 'arm64' ]]; then
@@ -39,6 +34,10 @@ else
     CASTXML_BIN_MAC=https://data.kitware.com/api/v1/item/63bed7726d3fc641a02d7e9e/download # Intel chips
 fi
 
+#.. needs testing
+# Check for updates https://github.com/CastXML/CastXMLSuperbuild/releases/tag/v0.6.5
+#CASTXML_BIN_LINUX=https://github.com/CastXML/CastXMLSuperbuild/releases/download/v0.6.5/
+
 PYGCCXML_URL=https://github.com/CastXML/pygccxml
 PYGCCXML_REV=v2.2.1
 

core/src/bert/bertJacobian.cpp

@@ -299,7 +299,7 @@ MEMINFO
     std::sort(cells.begin(), cells.end(), lessCellMarker);
 
     double maxMemSize = max(0.0, getEnvironment("SENSMATMAXMEM", 0.0, verbose));
-    double maxSizeNeeded = mByte((double)nData * nModel * sizeof(double));
+    double maxSizeNeeded = MByte(nData * nModel * sizeof(double));
 
     if (maxMemSize > 0 && verbose){
         std::cout << "Size of S: " << maxSizeNeeded << " MB" << std::endl;
@@ -329,7 +329,7 @@ MEMINFO
             throwError(WHERE_AM_I + " sorry, size of single sensitivity-row exceeds memory limitations.");
         }
 
-        std::cout << "Size of S cluster: " << mByte((double)nData * modelCluster * sizeof(ValueType)) << " MB" << std::endl;
+        std::cout << "Size of S cluster: " << MByte(nData * modelCluster * sizeof(ValueType)) << " MB" << std::endl;
         std::cout << "Using model cluster " << nModel << " x " << modelCluster << std::endl;
 
         S.resize(nData, modelCluster);

core/src/bert/dcfemmodelling.cpp

@@ -567,7 +567,7 @@ void DCMultiElectrodeModelling::init_(){
     Index nThreads = getEnvironment("BERTTHREADS", 0, verbose_);
     nThreads = getEnvironment("BERT_NUM_THREADS", 0, verbose_);
     if (nThreads > 0) setThreadCount(nThreads);
-
+    //log(Info, "DCMultiElectrodeModelling init with thread count:", nThreads);
 }
 
 void DCMultiElectrodeModelling::setComplex(bool c) {
@@ -1847,9 +1847,9 @@ void DCMultiElectrodeModelling::calculateK_(const std::vector < ElectrodeShape *
         solver = new LinSolver(debug);
         solverNeedsDelete = true;
         dynamic_cast< LinSolver * >(solver)->setMatrix(S_, 1);
-        if (debug) std::cout << "Factorize (" << solver->name() << ") matrix ... " << swatch.duration() << std::endl;        
+        if (debug) std::cout << "Factorize (" << solver->name() << ") matrix ... " << swatch.duration() << std::endl;
     }
-    
+
 // MEMINFO
 
     Vector < ValueType > sol(S_.cols());
@@ -2208,7 +2208,7 @@ void DCSRMultiElectrodeModelling::calculateK(const std::vector < ElectrodeShape
         dynamic_cast< LinSolver * >(solver)->setMatrix(S_, 1);
         if (debug) std::cout << "Factorize (" << solver->name() << ") matrix ... " << swatch.duration() << std::endl;
     }
-    
+
 
 // MEMINFO
 
@@ -2288,11 +2288,11 @@ void DCSRMultiElectrodeModelling::calculateK(const std::vector < ElectrodeShape
 
         if (singleVerbose) singleVerbose = false;
     }
-    
+
     if (solverNeedsDelete == true){
         delete solver;
     }
-    
+
 }
 
 } // namespace GIMLI{

core/src/gimli.cpp

@@ -39,6 +39,7 @@
     std::mutex __GIMLILogWriteMutex__;
 #endif
 
+#include <omp.h>
 
 namespace GIMLI{
 
@@ -48,6 +49,11 @@ static int __GIMLI_DEEP_DEBUG__ = 0;
 
 Index __setTC__(){
     // to close to number of cpu can bring significent shedular overhead
+    int omp = getEnvironment("OMP_NUM_THREADS", -1, false);
+    if (omp == -1){
+        omp_set_num_threads(min(8, numberOfCPU()-2));
+    }
+
     int tc = getEnvironment("OPENBLAS_NUM_THREADS", -1, false);
 
     if (tc == -1){
@@ -85,6 +91,7 @@ void setThreadCount(Index nThreads){
     log(Debug, "Set amount of threads to " + str(nThreads));
     //log(Debug, "omp_get_max_threads: " + str(omp_get_max_threads()));
     //omp_set_num_threads
+
 #if OPENBLAS_CBLAS_FOUND
     openblas_set_num_threads(nThreads);
     //omp_set_num_threads

core/src/memwatch.cpp

@@ -30,13 +30,13 @@
     #define USE_PROC_READPROC 0
 #endif
 
-#if USE_BOOST_THREAD
-    #include <boost/thread.hpp>
-    /*! Lock proc reading to be thread safe */
-    static boost::mutex __readproc__mutex__;
+#include <mutex>
+static std::mutex __readproc__mutex__;
+
+#ifdef WIN32_LEAN_AND_MEAN
+    #include <windows.h>
 #else
-    #include <mutex>
-    static std::mutex __readproc__mutex__;
+    #include <unistd.h>
 #endif
 
 namespace GIMLI {
@@ -73,7 +73,7 @@ double MemWatch::inUse() {
 
     PROCESS_MEMORY_COUNTERS pmc;
     if (GetProcessMemoryInfo(GetCurrentProcess(), &pmc, sizeof(pmc))){
-        double ret = mByte(pmc.WorkingSetSize);
+        double ret = MByte(pmc.WorkingSetSize);
         return ret;
     } else { return 0; }
 #else // no WINDOWS
@@ -87,7 +87,7 @@ double MemWatch::inUse() {
 //      __MS("resident: " << usage.resident/1024)//         number of resident set (non-swapped) pages (4k)
 //      __MS("share: " << usage.share/1024)
 //      __MS("rss: " << usage.rss/1024)
-    double ret = mByte(usage.vsize);
+    double ret = MByte(usage.vsize);
     return ret;
 #else 
     // no windows and no libproc
@@ -116,4 +116,17 @@ void MemWatch::info(const std::string & str){
     }
 }
 
+long maxMem(){
+#if defined(WIN32_LEAN_AND_MEAN)
+    MEMORYSTATUSEX status;
+    status.dwLength = sizeof(status);
+    GlobalMemoryStatusEx(&status);
+    return status.ullTotalPhys;
+#else
+    long pages = sysconf(_SC_PHYS_PAGES);
+    long page_size = sysconf(_SC_PAGE_SIZE);
+    return pages * page_size;
+#endif
+}
+
 } // namespace GIMLI

core/src/memwatch.h

@@ -26,10 +26,13 @@
 namespace GIMLI{
 
 /*! Convert byte into KByte. */
-inline double kByte(long byte){ return double(byte / 1024.0); }
+inline double KByte(long byte){ return double(byte / 1024.0); }
 
 /*! Convert byte into MByte */
-inline double mByte(long byte){ return double(byte / (1024.0 * 1024.0)); }
+inline double MByte(long byte){ return double(byte / (1024.0 * 1024.0)); }
+
+/*! Convert byte into GByte */
+inline double GByte(long byte){ return double(byte / (1024.0 * 1024.0 * 1024)); }
 
 //! Memory watch.
 /*! Class that might help debugging memory usage.
@@ -72,6 +75,7 @@ inline double memoryInUse(){
     return GIMLI::MemWatch::instance().inUse();
 }
 
+DLLEXPORT long maxMem();
 
 } // namespace GIMLI
 

core/src/modellingbase.cpp

@@ -74,7 +74,7 @@ void ModellingBase::init_() {
     constraints_        = 0;
     dataContainer_      = 0;
 
-    nThreads_           = numberOfCPU();
+    nThreads_           = min(16, numberOfCPU()-2);
     nThreadsJacobian_   = 1;
 
     ownJacobian_        = false;
@@ -401,13 +401,13 @@ RSparseMapMatrix & ModellingBase::constraintsRef() {
     return *dynamic_cast < RSparseMapMatrix *>(constraints_);
 }
 
-RVector ModellingBase::createMappedModel(const RVector & model, 
+RVector ModellingBase::createMappedModel(const RVector & model,
                                          double background) const {
     if (mesh_ == 0) throwError("ModellingBase has no mesh for ModellingBase::createMappedModel");
 
     // __MS("ModellingBase::createMappedModel: " << this << " rm: " << regionManager_
     //             << " " << model.size() << " " <<  mesh_->cellCount())
-    
+
     if (model.size() == mesh_->cellCount()) {
         IVector cM(mesh_->cellMarkers());
 
@@ -467,10 +467,10 @@ RVector ModellingBase::createMappedModel(const RVector & model,
         // if (abs(cellAtts[i]) < TOLERANCE){ // this will never work since the prior prolongation
         if (mesh_->cell(i).marker() <= MARKER_FIXEDVALUE_REGION){
                 // setting fixed values
-            SIndex regionMarker = -(mesh_->cell(i).marker() -           
+            SIndex regionMarker = -(mesh_->cell(i).marker() -
                                     MARKER_FIXEDVALUE_REGION);
 
-            // __MS(regionManagerInUse_ << " " << this <<  " " << 
+            // __MS(regionManagerInUse_ << " " << this <<  " " <<
             //         regionManager_->region(regionMarker)->fixValue())
 
             if (regionManagerInUse_){
@@ -527,7 +527,7 @@ void ModellingBase::setRegionManager(RegionManager * reg){
     } else {
         regionManagerInUse_ = false;
         regionManager_      = new RegionManager(verbose_);
-        ownRegionManager_   = true; 
+        ownRegionManager_   = true;
         // __MS("ModellingBase::setRegionManager new " << this << " rm: " << regionManager_)
     }
     // __MS("MB:setRegionManager: " << this << " rm: " << regionManager_)

dev_requirements.txt

@@ -1,12 +1,15 @@
 # recommand to create a suitable virtual environment first:
-# python -m venv $ENVNAME
-# source $ENVNAME/bin/activate
+# python -m venv .venv --prompt=gimli
+# source .venv/bin/activate
 # python -m pip install -r dev_requirements.txt
 # python -m pip list
 # python -m pip install package==version
 
-# needed to build
+# needed
+setuptools
 numpy>=1.25
+matplotlib
+pyqt5 #pyqtagg backend
 pyplusplus==1.8.4
 pygccxml==2.0.0
 
@@ -18,7 +21,7 @@ ipython
 jupytext
 
 # optional, but strongly recommended
-scipy>=1.11 
+scipy>=1.11
 scooby
 pyvista[all]>=0.42
 pyqt5