Compiles and runs, but ends up in segmentation fault; static linking …

…for mkl has to be fixed

Makefile

@@ -8,47 +8,78 @@ CPP = icx
 USE_CUDA = 1
 USE_CVODE = 0
 USE_MATLAB = 1
-COMPILE_MICROMAG = 1
+USE_MICROMAG = 1
 
-CVODE_ROOT= /usr/local/sundials-4.1.0/instdir
+CVODE_ROOT = /usr/local/sundials-4.1.0/instdir
 # MATLAB_INCLUDE = /usr/local/MATLAB/R2023b/extern/include			# Linux
 MATLAB_INCLUDE = "C:\Program Files\MATLAB\R2023b\extern\include"	# Win
 MKL_ROOT = ${CONDA_PREFIX} 											# Linux - mkl
 # MKL_ROOT = "C:\Program Files (x86)\Intel\oneAPI\mkl\latest" 		# Win - mkl (oneapi)
 # MKL_ROOT = ${CONDA_PREFIX}/Library 								# Win - mkl (conda)
 
-ifeq (${FC}, ifort)
+ifeq (${FC}, ifx)
 	ifeq ($(OS),Windows_NT)
-		FFLAGS = /O3 /fpp /real-size:64 /assume:nocc_omp /Qopenmp \
-		/fpe:0 /fp:source /libs:static /DUSE_CVODE=${USE_CVODE} \
-		/DUSE_CUDA=${USE_CUDA} /DUSE_MATLAB=${USE_MATLAB}
+		FFLAGS = /O3 /fpp /real-size:64 /Qopenmp /assume:nocc_omp \
+		/fpe:0 /fp:source /nologo /libs:static /DUSE_CVODE=${USE_CVODE} \
+		/DUSE_MATLAB=${USE_MATLAB} /DUSE_MICROMAG=${USE_MICROMAG}
+
+		LIB_SUFFIX = .lib
 	else
 		FFLAGS = -O3 -fpp -real-size 64 -assume nocc_omp -qopenmp \
-		-fpe0 -fp-model=source -fpic -DUSE_CVODE=${USE_CVODE} \
-		-DUSE_CUDA=${USE_CUDA} -DUSE_MATLAB=${USE_MATLAB}
+		-fpe0 -fp-model=source -fpic -nologo -DUSE_CVODE=${USE_CVODE} \
+		-DUSE_MATLAB=${USE_MATLAB} -DUSE_MICROMAG=${USE_MICROMAG}
+
+		LIB_SUFFIX = .a
 	endif
 else ifeq (${FC}, gfortran)
-FFLAGS = -O3 -fdefault-real-8 -fopenmp -ffree-line-length-512 -cpp -fPIC -DUSE_CVODE=${USE_CVODE}
-USE_CUDA = 0
-COMPILE_MICROMAG= 0
+	FFLAGS = -O3 -fdefault-real-8 -fopenmp -ffree-line-length-512 -cpp -fPIC \
+		-DUSE_CVODE=${USE_CVODE} -DUSE_MICROMAG=0 -DUSE_CVODE=${USE_CVODE}
 endif
 
-ifeq ($(USE_CUDA),0)
-	COMPILE_CUDA =
+NUM_INT_PATH = source/NumericalIntegration/NumericalIntegration
+TILE_DEMAG_TENSOR_PATH = source/TileDemagTensor/TileDemagTensor
+DEMAG_FIELD_PATH = source/DemagField/DemagField
+MICROMAG_PATH = source/MagTenseMicroMag
+FORTRAN_CUDA_PATH = source/MagTenseFortranCuda/cuda
+STANDALONE_PATH = source/MagTense_StandAlone/MagTense_StandAlone
+FORCEINTEGRATOR_PATH = source/MagneticForceIntegrator/MagneticForceIntegrator
+
+ifeq ($(USE_MICROMAG),0)
+	MICROMAG =
+	ifeq ($(OS),Windows_NT)
+		CP_LIB = cp ${DEMAG_FIELD_PATH}/libDemagField${LIB_SUFFIX} .
+	else
+		CP_LIB = cp ${NUM_INT_PATH}/libNumericalIntegration${LIB_SUFFIX} .
+		CP_LIB += && cp ${TILE_DEMAG_TENSOR_PATH}/libTileDemagTensor${LIB_SUFFIX} .
+		CP_LIB += && cp ${DEMAG_FIELD_PATH}/libDemagField${LIB_SUFFIX} .
+	endif
 else
-	COMPILE_CUDA = cuda
+	MICROMAG = micromagnetism
+	ifeq ($(OS),Windows_NT)
+		LIB_OPT = -llibMagTenseMicroMag
+		CP_LIB = cp ${MICROMAG_PATH}/libMagTenseMicroMag${LIB_SUFFIX} .
+
+	else
+		LIB_OPT += -lMagTenseMicroMag
+		CP_LIB = cp ${NUM_INT_PATH}/libNumericalIntegration${LIB_SUFFIX} .
+		CP_LIB += && cp ${TILE_DEMAG_TENSOR_PATH}/libTileDemagTensor${LIB_SUFFIX} .
+		CP_LIB += && cp ${DEMAG_FIELD_PATH}/libDemagField${LIB_SUFFIX} .
+		CP_LIB += && cp ${MICROMAG_PATH}/libMagTenseMicroMag${LIB_SUFFIX} .
+	endif
 endif
 
 ifeq ($(USE_MATLAB),0)
 	FORCEINTEGRATOR =
 else
 	FORCEINTEGRATOR = forceintegrator
+	CP_LIB += && cp ${FORCEINTEGRATOR_PATH}/libMagneticForceIntegrator${LIB_SUFFIX} .
 endif
 
-ifeq ($(COMPILE_MICROMAG),0)
-	MICROMAG =
+ifeq ($(USE_CUDA),0)
+	COMPILE_CUDA =
 else
-	MICROMAG = micromagnetism
+	COMPILE_CUDA = cuda
+	CP_LIB += && cp ${FORTRAN_CUDA_PATH}/libCuda${LIB_SUFFIX} .
 endif
 #=======================================================================
 #							Targets
@@ -58,30 +89,30 @@ endif
 all: magnetostatic ${MICROMAG} ${COMPILE_CUDA} ${FORCEINTEGRATOR} # standalone
 
 magnetostatic:
-	cd source/NumericalIntegration/NumericalIntegration && $(MAKE) FC=$(FC) FFLAGS="$(FFLAGS)" USE_CVODE=$(USE_CVODE) CVODE_ROOT=$(CVODE_ROOT) USE_MATLAB=$(USE_MATLAB) MATLAB_INCLUDE=$(MATLAB_INCLUDE)
-	cd source/TileDemagTensor/TileDemagTensor && $(MAKE) FC=$(FC) FFLAGS="$(FFLAGS)" USE_CVODE=$(USE_CVODE) CVODE_ROOT=$(CVODE_ROOT) USE_MATLAB=$(USE_MATLAB) MATLAB_INCLUDE=$(MATLAB_INCLUDE)
-	cd source/DemagField/DemagField && $(MAKE) FC=$(FC) FFLAGS="$(FFLAGS)" USE_CVODE=$(USE_CVODE) CVODE_ROOT=$(CVODE_ROOT) USE_MATLAB=$(USE_MATLAB) MATLAB_INCLUDE=$(MATLAB_INCLUDE)
+	cd ${NUM_INT_PATH} && $(MAKE) FC=$(FC) FFLAGS="$(FFLAGS)" USE_CVODE=$(USE_CVODE) CVODE_ROOT=$(CVODE_ROOT) USE_MATLAB=$(USE_MATLAB) MATLAB_INCLUDE=$(MATLAB_INCLUDE)
+	cd ${TILE_DEMAG_TENSOR_PATH} && $(MAKE) FC=$(FC) FFLAGS="$(FFLAGS)" USE_CVODE=$(USE_CVODE) CVODE_ROOT=$(CVODE_ROOT) USE_MATLAB=$(USE_MATLAB) MATLAB_INCLUDE=$(MATLAB_INCLUDE)
+	cd ${DEMAG_FIELD_PATH}  && $(MAKE) FC=$(FC) FFLAGS="$(FFLAGS)" USE_CVODE=$(USE_CVODE) CVODE_ROOT=$(CVODE_ROOT) USE_MATLAB=$(USE_MATLAB) MATLAB_INCLUDE=$(MATLAB_INCLUDE)
 
 micromagnetism:
-	cd source/MagTenseMicroMag && $(MAKE) FFLAGS="$(FFLAGS)" USE_CVODE=$(USE_CVODE) CVODE_ROOT=$(CVODE_ROOT) USE_MATLAB=$(USE_MATLAB) MATLAB_INCLUDE=$(MATLAB_INCLUDE) MKL_ROOT=$(MKL_ROOT)
+	cd ${MICROMAG_PATH} && $(MAKE) FFLAGS="$(FFLAGS)" USE_CVODE=$(USE_CVODE) CVODE_ROOT=$(CVODE_ROOT) USE_MATLAB=$(USE_MATLAB) MATLAB_INCLUDE=$(MATLAB_INCLUDE)
 
 cuda:
-	cd source/MagTenseFortranCuda/cuda && $(MAKE) CPP=$(CPP)
+	cd ${FORTRAN_CUDA_PATH} && $(MAKE) CPP=$(CPP)
 
 forceintegrator:
-	cd source/MagneticForceIntegrator/MagneticForceIntegrator && $(MAKE) FC=$(FC) FFLAGS="$(FFLAGS)" MATLAB_INCLUDE=$(MATLAB_INCLUDE)
+	cd $(FORCEINTEGRATOR_PATH) && $(MAKE) FC=$(FC) FFLAGS="$(FFLAGS)" MATLAB_INCLUDE=$(MATLAB_INCLUDE)
 
 standalone:
-	cd source/MagTense_StandAlone/MagTense_StandAlone && $(MAKE) FC=$(FC) FFLAGS="$(FFLAGS)"
+	cd $(STANDALONE_PATH) && $(MAKE) FC=$(FC) FFLAGS="$(FFLAGS)"
 	mkdir build
-	cp source/MagTense_StandAlone/MagTense_StandAlone/MagTense.x build/MagTense.x
+	cp $(STANDALONE_PATH)/MagTense.x build/MagTense.x
 
 clean:
-	cd source/NumericalIntegration/NumericalIntegration && make clean
-	cd source/TileDemagTensor/TileDemagTensor && make clean
-	cd source/DemagField/DemagField && make clean
-	cd source/MagTenseMicroMag && make clean
-	cd source/MagTenseFortranCuda/cuda && make clean
-	cd source/MagTense_StandAlone/MagTense_StandAlone && make clean
-	cd source/MagneticForceIntegrator/MagneticForceIntegrator && make clean
-	rm -r build/
+	cd ${NUM_INT_PATH} && make clean
+	cd ${TILE_DEMAG_TENSOR_PATH} && make clean
+	cd ${DEMAG_FIELD_PATH}  && make clean
+	cd ${MICROMAG_PATH} && make clean
+	cd ${FORTRAN_CUDA_PATH} && make clean
+	cd $(STANDALONE_PATH) && make clean
+	cd $(FORCEINTEGRATOR_PATH) && make clean
+	rm *${LIB_SUFFIX}

matlab/README.md

@@ -36,13 +36,13 @@ If you want to compile MagTense with a Visual Studio project file for Windows, [
 
   [ Linux ] `/usr/local/sundials-4.1.0/instdir`
 
-  A guide for custom installation of sundials-4.1.0 from this repository can be found [here].(#install-cvode-from-sundials-4.1.0) 
+  A guide for custom installation of sundials-4.1.0 from this repository can be found [here](#install-cvode-from-sundials-4.1.0).
 
   **Note:** Shared libraries for Fortran modules are not distributed in conda package of [sundials](https://anaconda.org/conda-forge/sundials). CVODE has to be built beforehand locally when linked dynamically. During runtime, path has to be added to LD_LIBRARY_PATH on Linux.
 
 ### Compilation
 
-Prepare your terminal, so that ifort compiler can be found:
+Prepare your terminal, so that ifx compiler can be found:
 
 - [ Windows]
 
@@ -60,12 +60,12 @@ Set flags and paths in [Makefile](https://github.com/cmt-dtu-energy/MagTense/blo
 
 ```bash
 cd path/to/MagTense/
-make USE_CUDA=1 USE_CVODE=1 USE_MATLAB=1 CVODE_ROOT=/usr/local/sundials-4.1.0/instdir MATLAB_INCLUDE=/usr/local/MATLAB/R2021b/extern/include MKL_ROOT=/opt/intel/oneapi/mkl/latest
+make USE_CUDA=1 USE_CVODE=1 USE_MATLAB=1 CVODE_ROOT=/usr/local/sundials-4.1.0/instdir MATLAB_INCLUDE=/usr/local/MATLAB/R2023b/extern/include MKL_ROOT=/opt/intel/oneapi/mkl/latest
 ```
 
 ## Building MEX-files
 
-Prepare your terminal, so that ifort compiler can be found:
+Prepare your terminal, so that `ifx` compiler can be found:
 
 - [ Windows]
 
@@ -81,27 +81,16 @@ Prepare your terminal, so that ifort compiler can be found:
   . /opt/intel/oneapi/setvars.sh
   ```
 
-  For static linking of MKL, the file `mex_FORTRAN_glnxa64.xml` located in `/home/<user>/.matlab/R2021b/` has to be adjusted as follows:
-
-  ```bash
-  LINKLIBS="[...] -Wl,--start-group"
-  CMDLINE2="$LDF $LDFLAGS $LDTYPE $LINKOPTIM $LINKEXPORTVER $OBJS $FLIBS $LINKLIBS -Wl,--end-group -o $EXE"
-  ```
-
-  The reason for that is that Matlab recognizes `-Wl,--end-group` as `Error: Illegal use of reserved keyword "end".`, when running the build script.
-
-
 Start Matlab via command line and run build script:
 
 ```bash
-cd path/to/MagTense/matlab
-/usr/local/MATLAB/R2021b/bin/matlab -nodisplay -nosplash -nodesktop
-run('buildMagTenseMEX.m')
+/usr/local/MATLAB/R2023b/bin/matlab -nodisplay -nosplash -nodesktop
+run('matlab/buildMagTenseMEX.m')
 ```
 
 ## Runtime
 
-Prepare your terminal, so that ifort compiler and required libraries can be found:
+Prepare your terminal, so that `ifx` compiler and required libraries can be found:
 
 - [ Linux ]
 
@@ -110,14 +99,13 @@ Prepare your terminal, so that ifort compiler and required libraries can be foun
   export LD_LIBRARY_PATH=<path_to_CVODE_libs>:<path_to_CUDA_libs>:$LD_LIBRARY_PATH
   ```
 
-  When MKL is statically linked, having [Runtime for Intel® Fortran Compiler](https://anaconda.org/intel/intel-fortran-rt) is sufficient and no installation of `ifort` or `mkl` is required.
+  When MKL is statically linked, having [Runtime for Intel® Fortran Compiler](https://anaconda.org/intel/intel-fortran-rt) is sufficient and no installation of `ifx` or `mkl` is required.
 
 - Test with standard problem #3
 
   ```bash
-  cd path/to/MagTense/matlab/
-  /usr/local/MATLAB/R2021b/bin/matlab -nodisplay -nosplash -nodesktop
-  run('examples/Micromagnetism/mumag_micromag_Std_problem_3/Standard_problem_3.m')
+  /usr/local/MATLAB/R2023b/bin/matlab -nodisplay -nosplash -nodesktop
+  run('matlab/examples/Micromagnetism/mumag_micromag_Std_problem_3/Standard_problem_3.m')
   ```
 
 ## Install CVODE from sundials-4.1.0

matlab/buildMagTenseMEX.m

@@ -3,7 +3,7 @@ function buildMagTenseMEX(USE_RELEASE, USE_CUDA, USE_CVODE)
 
 arguments
     USE_RELEASE {mustBeNumericOrLogical} = true;
-    USE_CUDA {mustBeNumericOrLogical} = true;
+    USE_CUDA {mustBeNumericOrLogical} = false;
     USE_CVODE {mustBeNumericOrLogical} = true;
 end
 
@@ -29,10 +29,10 @@ function buildMagTenseMEX(USE_RELEASE, USE_CUDA, USE_CVODE)
 else
     VS_STUDIO = false;
     MKL_STATIC = false;
-    compiler_root = '/opt/intel/oneapi/compiler/latest';
-    mkl_root = '/opt/intel/oneapi/mkl/latest';
-    mkl_lib = '/opt/intel/oneapi/mkl/latest/lib/intel64';
-    cuda_root = '/usr/local/cuda-12.3/lib64/';
+    compiler_root = '/home/spol/miniconda3/envs/magtense-env-py12';
+    mkl_root = '/home/spol/miniconda3/envs/magtense-env-py12';
+    mkl_lib = '/home/spol/miniconda3/envs/magtense-env-py12/lib';
+    cuda_root = '/home/spol/miniconda3/envs/magtense-env-py12/lib';
     cvode_include = '/usr/local/sundials-4.1.0/instdir/fortran';
     cvode_lib = '/usr/local/sundials-4.1.0/instdir/lib';
     mex_suffix = 'a';
@@ -62,8 +62,9 @@ function buildMagTenseMEX(USE_RELEASE, USE_CUDA, USE_CVODE)
 
 if (USE_CVODE)
     CVODE_include = join(['-I' cvode_include], '');
-    CVODE = ['-L' cvode_lib ' -lsundials_nvecserial -lsundials_sunmatrixdense -lsundials_sunlinsoldense' ...
-    ' -lsundials_fnvecserial_mod -lsundials_cvode -lsundials_fsunnonlinsolfixedpoint_mod'];
+    CVODE = ['LINKLIBS="$LINKLIBS ' cvode_lib '/libsundials_nvecserial.a ' cvode_lib '/libsundials_sunmatrixdense.a ' ...
+        cvode_lib '/libsundials_sunlinsoldense.a ' cvode_lib '/libsundials_fnvecserial_mod.a ' ...
+        cvode_lib '/libsundials_cvode.a ' cvode_lib '/libsundials_fsunnonlinsolfixedpoint_mod.a"'];
 else
     CVODE_include = '';
     CVODE = '';
@@ -82,7 +83,7 @@ function buildMagTenseMEX(USE_RELEASE, USE_CUDA, USE_CVODE)
 
 if (ispc)
     DEFINES = '-R2018a';
-    FFLAGS = 'COMPFLAGS="$COMPFLAGS /free /O3 /fpp /real-size:64 /Qopenmp /assume:nocc_omp /fpe:0 /fp:source"';
+    FFLAGS = 'COMPFLAGS="$COMPFLAGS /free /O3 /fpp /real-size:64 /Qopenmp /assume:nocc_omp /fpe:0 /fp:source /nologo"';
     if (USE_CUDA)
         FFLAGS = [FFLAGS(1:(end-1)) ' /libs:static"'];
     end
@@ -98,7 +99,7 @@ function buildMagTenseMEX(USE_RELEASE, USE_CUDA, USE_CVODE)
         MKL = ['-L' mkl_lib ' -lmkl_rt -lmkl_blas95_lp64'];
     end
 else
-    DEFINES = ['FC="' compiler_root '/bin/ifort" DEFINES="-DMATLAB_DEFAULT_RELEASE=R2018a"'];
+    DEFINES = ['FC="' compiler_root '/bin/ifx" DEFINES="-DMATLAB_DEFAULT_RELEASE=R2018a"'];
     INCLUDE = ['INCLUDE="$INCLUDE -I' mkl_root '/include -I' NumericalIntegration_path ' -I' DemagField_path ...
         ' -I' TileDemagTensor_path ' -I' MagTenseMicroMag_path ' -I' ForceIntegrator_path ' -I' mkl_root];
     LIBS = ['-L' MagTenseMicroMag_path ' -lMagTenseMicroMag -L' DemagField_path ' -lDemagField -L' ...
@@ -110,7 +111,7 @@ function buildMagTenseMEX(USE_RELEASE, USE_CUDA, USE_CVODE)
             '/libmkl_core.a ' mkl_lib '/libmkl_blas95_lp64.a ' mkl_lib '/libmkl_intel_lp64.a"'];
         INCLUDE = [INCLUDE '/include/intel64/lp64 '];
     else
-        MKL = ['-L' mkl_root '/lib/intel64 -lmkl_rt -lpthread -lm -ldl '];
+        MKL = ['-L' mkl_lib ' -lmkl_rt -lpthread -lm -ldl '];
         if (USE_CUDA)
             INCLUDE = [INCLUDE '/include/intel64/lp64 '];
             MKL = [MKL '-lmkl_blas95_lp64'];
@@ -121,7 +122,7 @@ function buildMagTenseMEX(USE_RELEASE, USE_CUDA, USE_CVODE)
         end
     end
     INCLUDE = [INCLUDE CVODE_include '"'];
-    FFLAGS = [FFLAGS '-O3 -fpp -real-size 64 -qopenmp -assume nocc_omp -fpe0 -fp-model=source -fpic -diag-disable 10006"'];
+    FFLAGS = [FFLAGS '-O3 -fpp -real-size 64 -qopenmp -assume nocc_omp -fpe0 -fp-model=source -fpic -nologo -diag-disable 10006"'];
 end
 
 %%------------------------------------------------------------------

python/README.md

@@ -16,9 +16,9 @@ For MacOS ARM architectures, currently only magnetostatics with the `gfortran` c
   conda create -y -n magtense-env 
   conda activate magtense-env
   conda config --env --add channels conda-forge
+  conda install -y python
   conda config --env --add channels nvidia/label/cuda-12.6.3
   conda config --env --add channels https://software.repos.intel.com/python/conda/
-  conda install -y python
   conda install -y numpy matplotlib meson charset-normalizer ncurses git notebook h5py tqdm
   ```
 

python/src/magtense/lib/Makefile

@@ -85,15 +85,6 @@ ifeq ($(USE_MKL),0)
 	MKL =
 endif
 
-ifeq (${USE_CVODE},0)
-	CVODE =
-	CVODE_OPT =
-else
-	CVODE = -L${CVODE_ROOT}/lib -lsundials_nvecserial -lsundials_sunmatrixdense \
-		-lsundials_sunlinsoldense -lsundials_fnvecserial_mod -lsundials_cvode \
-		-lsundials_fsunnonlinsolfixedpoint_mod
-	CVODE_OPT = -I${CVODE_ROOT}/fortran
-endif
 
 ifeq ($(USE_MICROMAG),0)
 	MICROMAG =
@@ -191,7 +182,7 @@ clean_build:
 	${CLEAN_FOLDER}
 
 magnetostatic:
-	cd ${NUM_INT_PATH} && ${MAKE} FC=${FC} FFLAGS='${FFLAGS}' CVODE_OPT=${CVODE_OPT} USE_MATLAB=0
+	cd ${NUM_INT_PATH} && ${MAKE} FC=${FC} FFLAGS='${FFLAGS}' USE_CVODE=${USE_CVODE} CVODE_ROOT=${CVODE_ROOT} USE_MATLAB=0
 	cd ${TILE_DEMAG_TENSOR_PATH} && ${MAKE} FC=${FC} FFLAGS='${FFLAGS}'
 	cd ${DEMAG_FIELD_PATH} && ${MAKE} FC=${FC} FFLAGS='${FFLAGS}' USE_MATLAB=0