Merge pull request #58 from OpenSEMBA/dev

Bugfix for reading large cellRegions happening in windows intelLLVM

.github/workflows/ubuntu-gnu.yml

@@ -28,6 +28,7 @@ jobs:
 
     - name: Install required packages
       run: |
+        sudo apt update
         sudo apt install libhdf5-dev libopenmpi-dev
       
     - name: Build application

README.md

@@ -44,7 +44,7 @@ Prebuilt binares are available at [releases](https://github.com/OpenSEMBA/fdtd/r
 
 In windows, you need to install [intel oneapi runtime libraries](https://www.intel.com/content/www/us/en/developer/articles/tool/oneapi-standalone-components.html).
 
-## Compilation
+## GNU/Linux Compilation
 
 It is important to point out the repository has dependencies which are available as submodules. It is necessary to run `git submodule init` and `git submodule update` from the root folder before running any `cmake` or `build` commands.
 
@@ -104,7 +104,6 @@ libngspice_la_CFLAGS = -static
 libngspice_la_LDFLAGS = -static -version-info @LIB_VERSION@
 ```
 
-
 #### MPI
 
 If you use intel oneapi, make sure to load the mpi environment variables:
@@ -113,9 +112,65 @@ If you use intel oneapi, make sure to load the mpi environment variables:
   source /opt/intel/oneapi/mpi/latest/env/vars.sh
 ```
 
-## Testing
+## Windows (intelLLVM) Compilation
 
-Tests must be run from the root folder. `python` wrapper test assumes that `semba-fdtd` has been compiled successfully and is located in folder `build/bin/`. For intel compilation it also assumes that the intel runtime libraries are accessible.
+Clone this repository:
+
+```shell
+  git clone https://github.com/OpenSEMBA/fdtd.git
+```
+
+or, if using SSH keys:
+
+```shell
+  git clone git@github.com:OpenSEMBA/fdtd.git
+```
+
+navigate to the `/fdtd/` folder that has been created, this folder will be referred to as `root` for any future purposes.
+
+### Prerequisites
+
+This compilation process will use the already available precompiled libraries included with the project, thus it's not required to build them manually.
+This repository has dependencies that are available as submodules. It is necessary to run `git submodule init` and `git submodule update` from the root folder before running any `cmake` or `build` commands.
+In the .gitmodules file, the submodules use the SSH remote URL by default. If not using a SSH-key in the computer where the following process will be performed, the remote addresses for each submodule must be individually changed to their HTTPS alternative.
+
+This software requires [Windows BaseKit](https://www.intel.com/content/www/us/en/developer/tools/oneapi/base-toolkit.html) and [Windows HPCKit](https://www.intel.com/content/www/us/en/developer/tools/oneapi/hpc-toolkit-download.html). Install these packages with all their features selected.
+
+Additionally, if not done already, install [CMake](https://cmake.org/download/) and [Ninja](https://github.com/ninja-build/ninja), follow their respective installation steps.
+
+### Compilation process
+
+Open a command prompt with OneAPI variables initialised, to do this open a new command prompt and type:
+
+```shell
+"C:\Program Files (x86)\Intel\oneAPI\setvars.bat" intel64
+```
+
+This will load the OneAPI environment for x64.
+
+Navigate to the fdtd root folder, choose between "Debug"/"Release" for `-DCMAKE_BUILD_TYPE`, and "Yes"/"No" for `-DSEMBA_FDTD_ENABLE_MPI`, for example, a Release version with MPI Support would be:
+
+```shell
+cmake -S . -B build -GNinja -DCMAKE_BUILD_TYPE=Release -DSEMBA_FDTD_ENABLE_MPI=Yes
+```
+
+Then,
+
+```shell
+cmake --build build -j
+```
+
+We should now find the compiled executables in `\build\bin\`.
+
+### Usage
+
+In order to use semba-fdtd, the executable must have access to the dynamic libraries it has dependencies on. Either move the libraries to the same folder as the executable, or run the executable through a console with the OneAPI environment loaded:
+
+```shell
+"C:\Program Files (x86)\Intel\oneAPI\setvars.bat" intel64
+```
+
+Once the environment is loaded, follow the steps in the next section.
 
 ## Running cases
 
@@ -126,6 +181,10 @@ These can be run with
   semba-fdtd -i CASE_NAME.fdtd.json
 ```
 
+## Testing
+
+Tests must be run from the root folder. `python` wrapper test assumes that `semba-fdtd` has been compiled successfully and is located in folder `build/bin/`. For intel compilation it also assumes that the intel runtime libraries are accessible.
+
 # License
 
 This code is licensed under the terms of the [MIT License](LICENSE). All rights reserved by the University of Granada (Spain)

src_json_parser/idchildtable.F90

@@ -1,4 +1,6 @@
 module idchildtable_mod
+
+#ifdef CompileWithSMBJSON    
    use json_module
    use fhash, only: fhash_tbl_t, key=>fhash_key
    use labels_mod
@@ -61,5 +63,5 @@ function getId(this, id) result(res)
          res = d
       end select
    end function
-
+#endif
 end module

src_json_parser/labels_mod.F90

@@ -1,4 +1,6 @@
 module labels_mod
+
+#ifdef CompileWithSMBJSON    
    ! LABELS
    ! -- common labels
    character (len=*), parameter :: J_NAME = "name"
@@ -181,5 +183,5 @@ module labels_mod
    character (len=*), parameter :: J_PR_DOMAIN_FREQ_SPACING  = "frequencySpacing"
    character (len=*), parameter :: J_PR_DOMAIN_FREQ_SPACING_LINEAR  = "linear"
    character (len=*), parameter :: J_PR_DOMAIN_FREQ_SPACING_LOGARITHMIC  = "logarithmic"
-
+#endif
 end module

src_json_parser/mesh.F90

@@ -1,5 +1,6 @@
 module mesh_mod
-
+
+#ifdef CompileWithSMBJSON   
    use, intrinsic :: iso_fortran_env , only: error_unit
 
    use fhash, only: fhash_tbl_t, key=>fhash_key
@@ -316,5 +317,5 @@ logical function coordinate_eq(a, b)
       class(coordinate_t), intent(in) :: a, b
       coordinate_eq = all(a%position == b%position)
    end function
-
+#endif
 end module

src_json_parser/nfdetypes_extension.F90

@@ -1,4 +1,5 @@
-module NFDETypes_extension
+module NFDETypes_extension      
+#ifdef CompileWithSMBJSON
    use NFDETypes
 
    implicit none
@@ -951,5 +952,5 @@ elemental logical function volprobes_eq(a, b)
          all(a%collection == b%collection)
    end function volprobes_eq
 
-
+#endif
 end module

src_json_parser/parser_tools.F90

@@ -1,4 +1,6 @@
 module parser_tools_mod
+
+#ifdef CompileWithSMBJSON
    use labels_mod
    use mesh_mod
    use cells_mod
@@ -32,18 +34,35 @@ subroutine addCellRegionsAsCoords(res, cellRegions, cellType)
       type(coords), dimension(:), pointer :: res
       type(cell_region_t), dimension(:), intent(in) :: cellRegions
       integer, intent(in), optional :: cellType
-      type(cell_interval_t), dimension(:), allocatable :: intervals
+      type(cell_interval_t), dimension(:), allocatable :: intervals, intervalsInRegion
       type(coords), dimension(:), allocatable :: cs
-      integer :: i
+      integer :: i, j
+      integer :: numberOfIntervals, copiedIntervals
 
-      allocate(intervals(0))
+
+      numberOfIntervals = 0
       do i = 1, size(cellRegions)
          if (present(cellType)) then
-            intervals = [intervals, cellRegions(i)%getIntervalsOfType(cellType)]
+            numberOfIntervals = numberOfIntervals + count(cellRegions(i)%intervals%getType() == cellType)
+         else 
+            numberOfIntervals = numberOfIntervals + size(cellRegions(i)%intervals)
+         end if
+      end do
+
+      allocate(intervals(numberOfIntervals))
+      copiedIntervals = 0
+      do i = 1, size(cellRegions)
+         if (present(cellType)) then
+            intervalsInRegion = cellRegions(i)%getIntervalsOfType(cellType)
          else
-            intervals = [intervals, cellRegions(i)%intervals]
+            intervalsInRegion = cellRegions(i)%intervals
          end if
+         do j = 1, size(intervalsInRegion)
+            copiedIntervals = copiedIntervals + 1
+            intervals(copiedIntervals) = intervalsInRegion(j) 
+         end do
       end do
+
       cs = cellIntervalsToCoords(intervals)
       allocate(res(size(cs)))
       res = cs
@@ -175,5 +194,5 @@ function scalarToMatrix(scalar) result(res)
       allocate(res(1,1), source = 0.0)
       res(1,1) = scalar
    end function
-
+#endif
 end module

src_json_parser/smbjson.F90

@@ -1,5 +1,6 @@
 module smbjson
 
+#ifdef CompileWithSMBJSON
    use NFDETypes
 
    use NFDETypes_extension
@@ -2879,4 +2880,6 @@ function getSingleVolumeInElementsIds(this, pw) result (res)
       if (size(res) /= 1) &
          write(error_unit, *) "Entity must contain a single cell region defining a volume."
    end function
+
+#endif   
 end module

src_main_pub/anisotropic.F90

@@ -351,7 +351,7 @@ subroutine InitAnisotropic(sgg,sggmiex,sggmiey,sggmiez,sggMiHx ,sggMiHy ,sggMiHz
                   AniMed%info(jmed)%Ex_Shared(i1)%times = sgg%Eshared%elem(j1)%Times
                   if (sgg%Eshared%elem(j1)%Times > 1 ) then
                      allocate (AniMed%info(jmed)%Ex_Shared(i1)%SharedMed(1:sgg%Eshared%elem(j1)%Times)) !OJO, EN EL ORIGINAL LO ALLOCATEABA HASTA -1
-                     !LO CAMBIO EL 26/10 POR ERROR EN LA NACELLE DEL SS5, PERO NO ESTOY SEGURO QUE HAYA UN BUG CON ESTO DE LOS SHARED !Ç
+                     !LO CAMBIO EL 26/10 POR ERROR EN LA NACELLE DEL SS5, PERO NO ESTOY SEGURO QUE HAYA UN BUG CON ESTO DE LOS SHARED !!?
                   endif
                   !PRINT *,'---> eX',sgg%Eshared%elem(j1)%i,sgg%Eshared%elem(j1)%J,sgg%Eshared%elem(j1)%k,sgg%Eshared%elem(j1)%times
                   exit buscaEx

src_main_pub/bordersmur.F90

@@ -526,9 +526,9 @@ subroutine AdvanceMagneticMUR(b, sgg,sggMiHx, sggMiHy, sggMiHz, Hx, Hy, Hz,mur_s
 
 
          call stoponerror(0,0,'ERROR: MUR SECOND not correctly implemented')
-         !!!!!ÇÇÇÇÇ!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-         !!!!!ÇÇÇÇÇ!!!!!!!!!!!!!!!!!!!Edges!!!!!!!!!!!!!!!!!!!!!Mur primer orden
-         !!!!!ÇÇÇÇÇ!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+         !!!!!!?!?!?!?!?!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+         !!!!!!?!?!?!?!?!!!!!!!!!!!!!!!!!!!Edges!!!!!!!!!!!!!!!!!!!!!Mur primer orden
+         !!!!!!?!?!?!?!?!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
          IF (sgg%Border%IsLeftMUR) then
             REGION = left

src_main_pub/farfield.F90

@@ -2657,7 +2657,7 @@ subroutine FlushFarfield(layoutnumber,size, b, dxe, dye, dze, dxh, dyh, dzh,face
                               endif
                               !
                               If( FF%farfieldTr_ClonePEC_LEFT.or.FF%farfieldFr_ClonePEC_LEFT) then
-                                 !!!!!!!!ÇÇÇÇÇÇÇÇÇÇÇÇÇÇÇÇ
+                                 !!!!!!!!!?!?!?!?!?!?!?!?!?!?!?!?!?!?!?!?
                                  new_My = - My
                                  new_Mz = + Mz
                                  new_Jy = + Jy
@@ -3136,7 +3136,7 @@ subroutine FlushFarfield(layoutnumber,size, b, dxe, dye, dze, dxh, dyh, dzh,face
                               call cloneAbAr(comun,new_co,sintheta_cosphi,sintheta_sinphi,costheta,costheta_cosphi,costheta_sinphi,sintheta,sinphi,cosphi,new_Mx,new_My,new_Mz,new_Jx,new_Jy,new_Jz,L_theta,L_phi,N_theta,N_phi,NORMAL)
                               !
                               If( FF%farfieldAb_ClonePEC_LEFT.or.FF%farfieldAr_ClonePEC_LEFT) then
-                                 !ÇÇÇÇÇÇÇÇÇÇÇÇÇÇÇÇÇÇÇÇ
+                                 !!?!?!?!?!?!?!?!?!?!?!?!?!?!?!?!?!?!?!?!?
                                  new_Mx = + Mx
                                  new_My = - My
                                  new_Jx = - Jx