diff --git a/Golden_Repo/a/AMBER/Fix_FFTW_find_error_due_to_MPI_components.patch b/Golden_Repo/a/AMBER/Fix_FFTW_find_error_due_to_MPI_components.patch new file mode 100644 index 0000000000000000000000000000000000000000..7a0851792102771354c98ed172ae8d03d4734964 --- /dev/null +++ b/Golden_Repo/a/AMBER/Fix_FFTW_find_error_due_to_MPI_components.patch @@ -0,0 +1,40 @@ +diff -ruN A20_src/AmberTools/src/quick/cmake/jedbrown/FindFFTW.cmake A20_src1/AmberTools/src/quick/cmake/jedbrown/FindFFTW.cmake +Fix MPI related errors in CMake FindFFTW modules +author: Sandipan Mohanty (Juelich Supercomputing Centre) +--- A20_src/AmberTools/src/quick/cmake/jedbrown/FindFFTW.cmake 2023-01-28 14:19:26.575506981 +0100 ++++ A20_src1/AmberTools/src/quick/cmake/jedbrown/FindFFTW.cmake 2023-01-28 14:05:09.172659586 +0100 +@@ -242,7 +242,7 @@ + + set(CMAKE_REQUIRED_LIBRARIES ${FFTW_LIBRARY_MPI}) + if(EXISTS "${FFTW_LIBRARY_MPI}") +- fftw_check_c_function(fftw_mpi_init FFTW_MPI_WORKS) ++ fftw_check_c_function(fftw_mpi_init FFTW_MPI_WORKS ${FFTW_LIBRARY_MPI} ${FFTW_LIBRARY_SERIAL} ${MPI_C_LIBRARIES}) + else() + set(FFTW_MPI_WORKS FALSE) + endif() +@@ -365,4 +365,4 @@ + endif() + + # don't leak required libraries +-set(CMAKE_REQUIRED_LIBRARIES "") +\ No newline at end of file ++set(CMAKE_REQUIRED_LIBRARIES "") +diff -ruN A20_src/cmake/jedbrown/FindFFTW.cmake A20_src1/cmake/jedbrown/FindFFTW.cmake +--- A20_src/cmake/jedbrown/FindFFTW.cmake 2023-01-28 14:18:50.145392374 +0100 ++++ A20_src1/cmake/jedbrown/FindFFTW.cmake 2023-01-28 14:03:56.662393042 +0100 +@@ -242,7 +242,7 @@ + + set(CMAKE_REQUIRED_LIBRARIES ${FFTW_LIBRARY_MPI}) + if(EXISTS "${FFTW_LIBRARY_MPI}") +- fftw_check_c_function(fftw_mpi_init FFTW_MPI_WORKS) ++ fftw_check_c_function(fftw_mpi_init FFTW_MPI_WORKS ${FFTW_LIBRARY_MPI} ${FFTW_LIBRARY_SERIAL} ${MPI_C_LIBRARIES}) + else() + set(FFTW_MPI_WORKS FALSE) + endif() +@@ -365,4 +365,4 @@ + endif() + + # don't leak required libraries +-set(CMAKE_REQUIRED_LIBRARIES "") +\ No newline at end of file ++set(CMAKE_REQUIRED_LIBRARIES "") diff --git a/Golden_Repo/a/AMBER/Fix_netcdf_find_error_due_to_missed_F77_F90_interfaces.patch b/Golden_Repo/a/AMBER/Fix_netcdf_find_error_due_to_missed_F77_F90_interfaces.patch new file mode 100644 index 0000000000000000000000000000000000000000..7850e149d00dc1e31667c71147b7f6e2e24b37ee --- /dev/null +++ b/Golden_Repo/a/AMBER/Fix_netcdf_find_error_due_to_missed_F77_F90_interfaces.patch @@ -0,0 +1,14 @@ +diff -ruN A20_src/cmake/jedbrown/FindNetCDF.cmake A20_src1/cmake/jedbrown/FindNetCDF.cmake +Fix NetCDF find errors in CMake modules due to F77 and F90 interface detection errors +author: Sandipan Mohanty (Juelich Supercomputing Centre) +--- A20_src/cmake/jedbrown/FindNetCDF.cmake 2023-01-28 14:29:38.347400350 +0100 ++++ A20_src1/cmake/jedbrown/FindNetCDF.cmake 2023-01-28 14:02:28.892122573 +0100 +@@ -51,7 +51,7 @@ + get_filename_component(NetCDF_lib_dirs "${NetCDF_LIBRARIES_C}" PATH) + + macro (NetCDF_check_interface lang header libs) +- find_path (NetCDF_INCLUDES_${lang} NAMES ${header} HINTS "${NetCDF_INCLUDES}" NO_DEFAULT_PATH) ++ find_path (NetCDF_INCLUDES_${lang} NAMES ${header}) + + find_library (NetCDF_LIBRARIES_${lang} NAMES ${libs} HINTS "${NetCDF_lib_dirs}") + diff --git a/Golden_Repo/a/AMBER/fix_nmrat_error.patch b/Golden_Repo/a/AMBER/fix_nmrat_error.patch new file mode 100644 index 0000000000000000000000000000000000000000..5bdaf088b19f893cd1142b25b9393ced1016423e --- /dev/null +++ b/Golden_Repo/a/AMBER/fix_nmrat_error.patch @@ -0,0 +1,14 @@ +diff -ruN amber20_src/src/pmemd/src/cuda/gpu.cpp amber20_src1/src/pmemd/src/cuda/gpu.cpp +Fix error about the 2D array nmrat being given 1 index before a comparison with 0 +author: Sandipan Mohanty (Juelich Supercomputing Centre) +--- amber20_src/src/pmemd/src/cuda/gpu.cpp 2022-02-28 12:02:56.035534480 +0100 ++++ amber20_src1/src/pmemd/src/cuda/gpu.cpp 2022-02-28 12:26:15.265104588 +0100 +@@ -2849,7 +2849,7 @@ + } + // torsions, resttype = 3 + else if (resttype[i] == 3) { +- if (nmrat[i][0] >= 0 && nmrat[i][1] >= 0 && nmrat[i][2] >= 0 && nmrat[3] >= 0) { ++ if (nmrat[i][0] >= 0 && nmrat[i][1] >= 0 && nmrat[i][2] >= 0 && nmrat[i][3] >= 0) { + torsions++; + } + else {