Drop GSL and finalize fortnum wiring (8/8)

.github/workflows/ci.yml

@@ -37,7 +37,6 @@ jobs:
             libopenblas-dev \
             liblapack-dev \
             doxygen \
-            libgsl-dev \
             libsuitesparse-dev \
             libsuperlu-dev \
             python3-dev \

AGENTS.md

@@ -58,7 +58,7 @@ make clean
 - **LAPACK/BLAS** - Linear algebra
 - **SuiteSparse** - Sparse matrix operations
 - **HDF5** - Data storage
-- **GSL** - GNU Scientific Library
+- **fortnum** - Numerical core (special functions, quadrature, ODE, root finding)
 - **SUNDIALS** - Numerical solvers
 
 ### Python Dependencies

CMakeLists.txt

@@ -53,12 +53,14 @@ project(KAMEL LANGUAGES C CXX Fortran)
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
+# OpenMP is a project-wide dependency: -fopenmp is on the global compile flags
+# below, and libneo objects in the KiLCA link closure use OMP critical sections
+# (GOMP_critical_*). Resolve the imported target once at top scope so it is
+# visible to every subdirectory and can ride on targets' PUBLIC link interfaces.
+find_package(OpenMP REQUIRED COMPONENTS C Fortran)
+
 # Set architecture flags based on platform
 if(APPLE)
-    # On macOS, use libomp from Homebrew for OpenMP support
-    # find_package(OpenMP REQUIRED)
-    find_package(OpenMP REQUIRED C Fortran)
-
     # Locate libomp from Homebrew
     find_program(BREW_EXECUTABLE brew HINTS /opt/homebrew/bin /usr/local/bin)
     if(BREW_EXECUTABLE)

KIM/README.md

@@ -5,7 +5,7 @@ This is the integral plasma response model based on the code and model Kinetic L
 
 ### Required Libraries
 - **LAPACK/BLAS** - Linear algebra
-- **GSL** - GNU Scientific Library
+- **fortnum** - Special functions (Bessel) and error function
 - **HDF5** - Data storage (with Fortran bindings)
 - **SuiteSparse** - Sparse matrix operations (UMFPACK)
 - **SuperLU** - Sparse direct solver

KIM/src/CMakeLists.txt

@@ -31,11 +31,6 @@ target_include_directories(KIM_lib PUBLIC "${CMAKE_BINARY_DIR}/OBJS/sparse/")
 # fortnum provides the special functions (bessel_in) used by FLR2_asymptotics.
 target_link_libraries(KIM_lib PUBLIC fortnum)
 
-# TODO: unify this: either use the system library everywhere, or use the cloned version
-# KiLCA uses the cloned libraries for now, QL-Balance the system libraries
-find_package(GSL REQUIRED)
-target_include_directories(KIM_lib PUBLIC "${GSL_INCLUDE_DIRS}")
-
 find_package(LAPACK REQUIRED)
 if("${LAPACK_FOUND}")
     message(" ====== LAPACK was found! ======")
@@ -111,13 +106,11 @@ if("${SUPERLU_FOUND}")
 endif()
 
 set(KILCA_PATH ${CMAKE_SOURCE_DIR}/KiLCA)
-set(KiLCA_lib_path ${CMAKE_SOURCE_DIR}/build/install/lib/libKiLCA_Lib_V_2.4.2_MDNO_FPGEN_POLYNOMIAL_Release_64bit.a)
 # KiLCA is NOT linked to KIM_lib: KIM does not use any KiLCA symbols.
 # Previously PUBLIC, this caused duplicate library linking when QL-Balance
 # linked both KIM_lib and kilca_lib, corrupting symbol resolution order
 # and breaking KiLCA's wave solver (besselj failures, vacuum stitching errors).
 # KIM_exe links KiLCA directly via slatec (which provides the math routines).
-target_link_libraries(KIM_lib PUBLIC GSL::gsl GSL::gslcblas)
 target_include_directories(KIM_lib PUBLIC ${KILCA_PATH}/math/)
 
 find_package(HDF5 COMPONENTS C Fortran HL REQUIRED)
@@ -141,7 +134,7 @@ set_target_properties(KIM_exe PROPERTIES
                         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/install/bin/")
 target_link_libraries(KIM_exe
                         KIM_lib
-                        "${KiLCA_lib_path}"
+                        kilca_lib
                         lapack
                         slatec
 )

KIM/src/math/ddeabm/CMakeLists.txt

@@ -13,7 +13,8 @@ set(ddeabm_files
     dsteps.f
 )
 add_library(ddeabm "${ddeabm_files}")
-# ddeabm.f/ddes.f reference xermsg (and i1mach/d1mach via that path); those
-# live in libslatec.  Declare the dependency so the linker orders libslatec
-# after libddeabm and resolves xermsg_ instead of dropping it.
+
+# ddeabm calls the slatec error machinery (xermsg and friends); declare the
+# dependency explicitly so the static-archive link order resolves xermsg_
+# regardless of how the consuming executable orders its libraries.
 target_link_libraries(ddeabm PUBLIC slatec)

KIM/tests/CMakeLists.txt

@@ -1,12 +1,13 @@
-# KiLCA library path (needed for tests that use KIM_lib symbols depending on KiLCA math)
-set(KiLCA_lib_path ${CMAKE_SOURCE_DIR}/build/install/lib/libKiLCA_Lib_V_2.4.2_MDNO_FPGEN_POLYNOMIAL_Release_64bit.a)
+# OpenMP runtime (GOMP_critical_* from libneo's OMP critical sections) is
+# carried transitively by kilca_lib's PUBLIC link interface, so no per-target
+# OpenMP linkage is needed here.
 
 # Optional: build QUADPACK/RKF45 integration comparison test
 add_executable(test_integration_methods ${CMAKE_SOURCE_DIR}/KIM/tests/test_integration_methods.f90)
 set_target_properties(test_integration_methods PROPERTIES
                         OUTPUT_NAME test_integration_methods.x
                         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests/")
-target_link_libraries(test_integration_methods KIM_lib "${KiLCA_lib_path}" lapack cerf ddeabm slatec)
+target_link_libraries(test_integration_methods KIM_lib kilca_lib lapack cerf ddeabm slatec)
 add_test(NAME test_integration_methods
          COMMAND ${CMAKE_BINARY_DIR}/tests/test_integration_methods.x)
 
@@ -34,31 +35,31 @@ set_target_properties(test_profile_input PROPERTIES
                         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests/")
 # Links the full math set: using profile_input_m pulls KIM objects whose
 # transitive deps (W2_arr) need the hypergeometric routines from KiLCA/slatec.
-target_link_libraries(test_profile_input KIM_lib "${KiLCA_lib_path}" lapack cerf ddeabm slatec)
+target_link_libraries(test_profile_input KIM_lib kilca_lib lapack cerf ddeabm slatec)
 add_test(NAME test_profile_input
          COMMAND ${CMAKE_BINARY_DIR}/tests/test_profile_input.x)
 
 add_executable(test_profile_input_integration ${CMAKE_SOURCE_DIR}/KIM/tests/test_profile_input_integration.f90)
 set_target_properties(test_profile_input_integration PROPERTIES
                         OUTPUT_NAME test_profile_input_integration.x
                         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests/")
-target_link_libraries(test_profile_input_integration KIM_lib "${KiLCA_lib_path}" lapack cerf ddeabm slatec)
+target_link_libraries(test_profile_input_integration KIM_lib kilca_lib lapack cerf ddeabm slatec)
 add_test(NAME test_profile_input_integration
          COMMAND ${CMAKE_BINARY_DIR}/tests/test_profile_input_integration.x)
 
 add_executable(test_kim_diagnostics ${CMAKE_SOURCE_DIR}/KIM/tests/test_kim_diagnostics.f90)
 set_target_properties(test_kim_diagnostics PROPERTIES
                         OUTPUT_NAME test_kim_diagnostics.x
                         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests/")
-target_link_libraries(test_kim_diagnostics KIM_lib "${KiLCA_lib_path}" lapack cerf ddeabm slatec)
+target_link_libraries(test_kim_diagnostics KIM_lib kilca_lib lapack cerf ddeabm slatec)
 add_test(NAME test_kim_diagnostics
          COMMAND ${CMAKE_BINARY_DIR}/tests/test_kim_diagnostics.x)
 
 add_executable(test_ampere_matrices ${CMAKE_SOURCE_DIR}/KIM/tests/test_ampere_matrices.f90)
 set_target_properties(test_ampere_matrices PROPERTIES
                         OUTPUT_NAME test_ampere_matrices.x
                         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests/")
-target_link_libraries(test_ampere_matrices KIM_lib "${KiLCA_lib_path}" lapack cerf ddeabm slatec)
+target_link_libraries(test_ampere_matrices KIM_lib kilca_lib lapack cerf ddeabm slatec)
 add_test(NAME test_ampere_matrices
          COMMAND ${CMAKE_BINARY_DIR}/tests/test_ampere_matrices.x)
 
@@ -69,23 +70,23 @@ add_executable(test_plag_coeff ${CMAKE_SOURCE_DIR}/KIM/tests/test_plag_coeff.f90
 set_target_properties(test_plag_coeff PROPERTIES
                         OUTPUT_NAME test_plag_coeff.x
                         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests/")
-target_link_libraries(test_plag_coeff KIM_lib "${KiLCA_lib_path}" lapack cerf ddeabm slatec)
+target_link_libraries(test_plag_coeff KIM_lib kilca_lib lapack cerf ddeabm slatec)
 add_test(NAME test_plag_coeff
          COMMAND ${CMAKE_BINARY_DIR}/tests/test_plag_coeff.x)
 
 add_executable(test_findIndex ${CMAKE_SOURCE_DIR}/KIM/tests/test_findIndex.f90)
 set_target_properties(test_findIndex PROPERTIES
                         OUTPUT_NAME test_findIndex.x
                         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests/")
-target_link_libraries(test_findIndex KIM_lib "${KiLCA_lib_path}" lapack cerf ddeabm slatec)
+target_link_libraries(test_findIndex KIM_lib kilca_lib lapack cerf ddeabm slatec)
 add_test(NAME test_findIndex
          COMMAND ${CMAKE_BINARY_DIR}/tests/test_findIndex.x)
 
 add_executable(test_grid_equidistant ${CMAKE_SOURCE_DIR}/KIM/tests/test_grid_equidistant.f90)
 set_target_properties(test_grid_equidistant PROPERTIES
                         OUTPUT_NAME test_grid_equidistant.x
                         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests/")
-target_link_libraries(test_grid_equidistant KIM_lib "${KiLCA_lib_path}" lapack cerf ddeabm slatec)
+target_link_libraries(test_grid_equidistant KIM_lib kilca_lib lapack cerf ddeabm slatec)
 add_test(NAME test_grid_equidistant
          COMMAND ${CMAKE_BINARY_DIR}/tests/test_grid_equidistant.x)
 
@@ -94,7 +95,7 @@ add_executable(test_kim_solver ${CMAKE_SOURCE_DIR}/KIM/tests/test_kim_solver.f90
 set_target_properties(test_kim_solver PROPERTIES
                         OUTPUT_NAME test_kim_solver.x
                         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests/")
-target_link_libraries(test_kim_solver KIM_lib "${KiLCA_lib_path}" lapack cerf ddeabm slatec)
+target_link_libraries(test_kim_solver KIM_lib kilca_lib lapack cerf ddeabm slatec)
 add_test(NAME test_kim_solver
          COMMAND ${CMAKE_BINARY_DIR}/tests/test_kim_solver.x)
 
@@ -103,7 +104,7 @@ add_executable(test_kim_solver_em ${CMAKE_SOURCE_DIR}/KIM/tests/test_kim_solver_
 set_target_properties(test_kim_solver_em PROPERTIES
                         OUTPUT_NAME test_kim_solver_em.x
                         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests/")
-target_link_libraries(test_kim_solver_em KIM_lib "${KiLCA_lib_path}" lapack cerf ddeabm slatec)
+target_link_libraries(test_kim_solver_em KIM_lib kilca_lib lapack cerf ddeabm slatec)
 configure_file(${CMAKE_SOURCE_DIR}/KIM/tests/test_data/KIM_config_em_small.nml
                ${CMAKE_BINARY_DIR}/tests/KIM_config_em_small.nml COPYONLY)
 add_test(NAME test_kim_solver_em

KiLCA/CMakeLists.txt

@@ -109,9 +109,8 @@ set (kilca_eigparam_main progs/main_eig_param.cpp)
 
 # include paths:
 set (libs_root_path ${CMAKE_BINARY_DIR}/external-install)
-set (gsl_include_path ${libs_root_path}/gsl/include)
 
-set(EXTERNAL_LIBS slatec lapack blas SUNDIALS::cvode SUNDIALS::nvecserial fortnum gsl gslcblas)
+set(EXTERNAL_LIBS slatec lapack blas SUNDIALS::cvode SUNDIALS::nvecserial fortnum)
 
 # configure a header file to pass some of the CMake settings to the source code
 configure_file(
@@ -121,7 +120,6 @@ configure_file(
 # Make generated header available
 include_directories("${CMAKE_CURRENT_BINARY_DIR}")
 
-include_directories ("${gsl_include_path}")
 # fortnum C ABI header (fortnum.h); the Fortran fortnum target is linked above.
 include_directories ("${fortnum_SOURCE_DIR}/include")
 include_directories ("${PROJECT_BINARY_DIR}")
@@ -251,7 +249,11 @@ set_target_properties(kilca_lib PROPERTIES
     ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/install/lib/
     Fortran_MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/OBJS/kilca/)
 add_dependencies(kilca_lib ${EXTERNAL_LIBS})
-target_link_libraries(kilca_lib PUBLIC ${EXTERNAL_LIBS})
+# libneo objects pulled into the KiLCA link closure use OMP critical sections
+# (GOMP_critical_*). Carry the OpenMP runtime on kilca_lib's PUBLIC interface so
+# every consumer (KIM_exe, ql-balance_lib, and all KIM tests) inherits it and no
+# downstream target has to re-declare OpenMP to link.
+target_link_libraries(kilca_lib PUBLIC ${EXTERNAL_LIBS} OpenMP::OpenMP_Fortran)
 
 # Add include directories on `kilca_lib` target for all source and module paths
 target_include_directories(kilca_lib PUBLIC
@@ -284,7 +286,6 @@ target_include_directories(kilca_lib PUBLIC
     ${CMAKE_CURRENT_SOURCE_DIR}/spline
     # External dependencies
     ${sundials_include_path}
-    ${gsl_include_path}
     ${fortnum_SOURCE_DIR}/include
 )
 

KiLCA/interface/make_it

@@ -18,4 +18,4 @@ kilca_64bit="KiLCA_Lib_V_2.4_MDNO_FPGEN_USUAL_Debug_64bit"
 #kilca_64bit="KiLCA_Lib_V_2.4_MDYES_FPGEN_POLYNOMIAL_Debug_64bit"
 #kilca_64bit="libkilca_64bit"
 
-gfortran ql-balance_mod.f90 wave_code_data_64bit.f90 bessel.f90 amn_of_r.f90 test_interface.f90 -L$kilca_lib_path -l$kilca_64bit -L$cvode_lib_path -lsundials_cvode -lsundials_nvecserial -L$slatec_lib_path -lslatec -lgsl -lgslcblas -lblas -llapack -lm -lc -lgfortran -lstdc++
+gfortran ql-balance_mod.f90 wave_code_data_64bit.f90 bessel.f90 amn_of_r.f90 test_interface.f90 -L$kilca_lib_path -l$kilca_64bit -L$cvode_lib_path -lsundials_cvode -lsundials_nvecserial -L$slatec_lib_path -lslatec -lfortnum -lblas -llapack -lm -lc -lgfortran -lstdc++

KiLCA/math/fourier/mk_fourier

@@ -64,7 +64,7 @@ cvode_lib_path = /usr/local/lib
 libs = -L$(LINKER_PATH) \
 -L$(math_lib_path) -lslatec_gf_430 -llapack_gf_430 -lblas_gf_430 \
 -L$(cvode_lib_path) -lsundials_cvode -lsundials_nvecserial \
--lgsl -lgslcblas \
+-lfortnum \
 -lgfortran \
 -lstdc++
 

KiLCA/math/hyper/Makefile

@@ -47,13 +47,13 @@ LINKER_PATH = /usr/local/gcc$(COMPILER_PREFIX)/lib
 math_lib_path = /usr/local/lib/math_lib
 cvode_lib_path = /usr/local/lib
 
-libs = -lgsl -lstdc++
+libs = -lfortnum -lstdc++
 
 
 # libs = -L$(LINKER_PATH) \
 # -L$(math_lib_path) -lslatec_gf_430 -llapack_gf_430 -lblas_gf_430 \
 # -L$(cvode_lib_path) -lsundials_cvode -lsundials_nvecserial \
-# -lgsl -lgslcblas \
+# -lfortnum \
 # -lgfortran \
 # -lstdc++
 

QL-Balance/CMakeLists.txt

@@ -154,8 +154,6 @@ target_link_libraries(ql-balance_lib PUBLIC
     SUNDIALS::nvecserial
     blas
     fortnum
-    gsl
-    gslcblas
     hdf5::hdf5
     hdf5::hdf5_fortran
     hdf5::hdf5_hl

README.md

@@ -29,7 +29,7 @@ The framework consists of three main codes:
 
 ### Auto-Fetched Libraries
 The following are automatically downloaded and built if not found on the system:
-- **GSL** - GNU Scientific Library
+- **fortnum** - Numerical core (special functions, quadrature, ODE, root finding)
 - **SuiteSparse** - Sparse matrix operations (UMFPACK)
 - **SUNDIALS** - Numerical differential equation solvers
 - **NetCDF** - Network Common Data Form (with Fortran bindings)
@@ -60,7 +60,7 @@ make QL-Balance
 make clean
 ```
 
-**Note:** External dependencies (LAPACK, SuiteSparse, GSL, SUNDIALS) are automatically downloaded and built during the first compilation if not found on the system.
+**Note:** External dependencies (LAPACK, SuiteSparse, fortnum, SUNDIALS) are automatically downloaded and built during the first compilation if not found on the system.
 
 To pin libneo to a specific branch, tag, or commit, pass `-DLIBNEO_REF=<ref>` to cmake or `LIBNEO_REF=<ref>` to make. To use a local checkout instead of fetching, pass `-DLIBNEO_PATH=<dir>` / `LIBNEO_PATH=<dir>`.
 

cmake/Dependencies.cmake

@@ -5,7 +5,6 @@
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
 
 # Core dependencies
-include(FetchGSL)
 include(FetchLapack)
 include(FetchNetcdf)
 include(FetchSuiteSparse)

python/susc_functions/f2py_Ifuncs.sh

@@ -9,8 +9,7 @@ f2py -c src/getIfunc.f90 src/W2_arr.f90 $curr_loc/../../KiLCA/flre/conductivity/
     -L$libs_path/sundials/build/src/nvector/serial/ -lsundials_nvecserial \
     -L$libs_path/slatec/ -lslatec \
     -L$libs_path/bessel/lib/ -lbessel \
-    -lgsl \
-    -lgslcblas \
+    -L$libs_path -lfortnum \
     -lm \
     -lc \
     --verbose

utility_scripts/setup_arch.sh

@@ -8,7 +8,6 @@ sudo pacman -Sy \
     gcc \
     gcc-fortran \
     git \
-    gsl \
     make \
     netcdf \
     netcdf-cxx \

utility_scripts/setup_debian.sh

@@ -2,5 +2,5 @@
 
 sudo apt update && apt install -y wget git cmake make gcc g++ gfortran \
     libnetcdf-dev libnetcdff-dev openmpi-bin libopenmpi-dev libfftw3-dev \
-    python3 python3-pip python3-numpy python3-scipy ninja-build libgsl-dev \
+    python3 python3-pip python3-numpy python3-scipy ninja-build \
     libopenblas-dev