Merge pull request #35 from seamplex/feature/gsl-optional

Feenox can be compied without GSL (but features are reduced A LOT)

Author: gtheler

config.h.ac

@@ -1,6 +1,7 @@
 #undef HAVE_ASPRINTF
 #undef HAVE_CLOCK_GETTIME
 #undef HAVE_GETRUSAGE
+#undef HAVE_GSL
 #undef HAVE_PETSC
 #undef HAVE_SLEPC
 #undef HAVE_SUNDIALS

configure.ac

@@ -313,7 +313,15 @@ AM_CONDITIONAL([INCLUDE_SLEPC], [test "x${have_slepc}" = "xyes"])
 
 
 ######################
-# see if we have --enable-download-gsl
+# check for GSL (optional)
+AC_ARG_WITH([gsl],
+  [AS_HELP_STRING([--with-gsl],
+    [use GSL for advanced math features @<:@default=check@:>@])],
+  [],
+  [with_gsl=check]
+)
+
+have_gsl="no"
 gslver=2.8
 gsldist=gsl-${gslver}
 gslmirror=http://ftpmirror.gnu.org/gsl/${gsldist}.tar.gz
@@ -323,59 +331,92 @@ AC_ARG_ENABLE([download-gsl],
  [download_gsl=yes],
  [download_gsl=no])
 
-# if gsl directory does not exist, see if we have to uncompress and/or download
-AS_IF([test ! -e ${gsldist}],[
- AS_IF([test ! -e ${gsldist}.tar.gz],[
-  AS_IF([test "x$download_gsl" = "xyes"],[
-   AS_IF([test "x$(which wget)" != "x"],[
-    AC_MSG_NOTICE([downloading ${gslmirror}])
-    wget -c ${gslmirror}
+AS_IF([test "x${with_gsl}" != "xno"], [
+  # if gsl directory does not exist, see if we have to uncompress and/or download
+  AS_IF([test ! -e ${gsldist}],[
+   AS_IF([test ! -e ${gsldist}.tar.gz],[
+    AS_IF([test "x$download_gsl" = "xyes"],[
+     AS_IF([test "x$(which wget)" != "x"],[
+      AC_MSG_NOTICE([downloading ${gslmirror}])
+      wget -c ${gslmirror}
+     ],[
+      AS_IF([test "x${with_gsl}" != "xcheck"], [
+        AC_MSG_ERROR([file ${gsldist}.tar.gz not found and wget not installed])
+      ])
+     ])
+     AS_IF([test ! -e ${gsldist}.tar.gz],[
+      AS_IF([test "x${with_gsl}" != "xcheck"], [
+        AC_MSG_ERROR([file ${gsldist}.tar.gz could not be downloaded])
+      ])
+     ])
+    ])
+   ])
+   
+   AS_IF([test -e ${gsldist}.tar.gz],[
+    AC_MSG_NOTICE([uncompressing ${gsldist}.tar.gz])
+    tar xzf ${gsldist}.tar.gz
+   ])
+  ])
+
+  # if gsl directory exists, see if we have to compile it
+  AS_IF([test -e ${gsldist}],[
+   AS_IF([test -e ${gsldist}/.libs/libgsl.a],[
+    AC_MSG_NOTICE([using already-compiled GSL library ${gsldist}/.libs/libgsl.a])
    ],[
-    AC_MSG_ERROR([file ${gsldist}.tar.gz not found and wget not installed])
+    AC_MSG_NOTICE([configuring ${gsldist}])
+    cd ${gsldist} 
+    ./configure --prefix=${prefix} --host=${host}
+    AC_MSG_NOTICE([compiling ${gsldist}])
+    make
+    cd ..
    ])
-   AS_IF([test ! -e ${gsldist}.tar.gz],[
-    AC_MSG_ERROR([file ${gsldist}.tar.gz could not be downloaded, copy it manually and re-try.])
+   
+   AC_SUBST([DOWNLOADED_GSL_LIBS], ["../${gsldist}/.libs/libgsl.a ../${gsldist}/cblas/.libs/libgslcblas.a"])
+   AC_SUBST([DOWNLOADED_GSL_INCLUDES], ["-I ../${gsldist} -I ../../${gsldist}"])
+   gsl_version="${gslver} (downloaded and statically linked)"
+   have_gsl="yes"
+  ],[ 
+   # traditional test for GSL
+   # check for GSL & CBLAS
+   AC_CHECK_HEADER([gsl/gsl_vector.h], [], [
+    AS_IF([test "x${with_gsl}" != "xcheck"], [
+      AC_MSG_FAILURE([--with-gsl was given but GSL headers libgsl-dev not found])
+    ])
+   ])
+
+   # TODO: the original idea is that
+   # if we found PETSc, we use whatever BLAS it has, otherwise we use GSL's CBLAS
+   # but this does not work in Fedora since even though the library flexiblas
+   # that is used by PETSc does contain cblas_dgemm, it is not found by the linker
+   #AS_IF([test "x${have_petsc}" != "xyes"],
+    AC_CHECK_LIB([gslcblas],[cblas_dgemm], [], [
+      AS_IF([test "x${with_gsl}" != "xcheck"], [
+        AC_MSG_FAILURE([--with-gsl was given but GSL CBLAS libgsl-dev not found])
+      ])
+    ])
+   #)
+   AC_CHECK_LIB([gsl],[gsl_blas_dgemm], [], [
+    AS_IF([test "x${with_gsl}" != "xcheck"], [
+      AC_MSG_FAILURE([--with-gsl was given but GSL library libgsl-dev not found])
+    ])
    ])
+   
+   # check if we have everything
+   AS_IF([test "x${ac_cv_lib_gsl_gsl_blas_dgemm}" = "xyes" -a \
+               "x${ac_cv_header_gsl_gsl_vector_h}" = "xyes"],
+     [
+       gsl_version="from system"
+       have_gsl="yes"
+     ]
+   )
   ])
- ])
- 
- AS_IF([test -e ${gsldist}.tar.gz],[
-  AC_MSG_NOTICE([uncompressing ${gsldist}.tar.gz])
-  tar xzf ${gsldist}.tar.gz
- ])
-])
 
-# if gsl directory exists, see if we have to compile it
-AS_IF([test -e ${gsldist}],[
- AS_IF([test -e ${gsldist}/.libs/libgsl.a],[
-  AC_MSG_NOTICE([using already-compiled GSL library ${gsldist}/.libs/libgsl.a])
- ],[
-  AC_MSG_NOTICE([configuring ${gsldist}])
-  cd ${gsldist} 
-  ./configure --prefix=${prefix} --host=${host}
-  AC_MSG_NOTICE([compiling ${gsldist}])
-  make
-  cd ..
- ])
- 
- AC_SUBST([DOWNLOADED_GSL_LIBS], ["../${gsldist}/.libs/libgsl.a ../${gsldist}/cblas/.libs/libgslcblas.a"])
- AC_SUBST([DOWNLOADED_GSL_INCLUDES], ["-I ../${gsldist} -I ../../${gsldist}"])
- gsl_version="${gslver} (downloaded and statically linked)"
-],[ 
- # traditional test for GSL
- # check for GSL & CBLAS (required)
- AC_CHECK_HEADER([gsl/gsl_vector.h],    [], AC_MSG_ERROR([GNU Scientific library headers libgsl-dev not found.
-Either install them with your package manager or configure with --enable-download-gsl]))
-
- # TODO: the original idea is that
- # if we found PETSc, we use whatever BLAS it has, otherwise we use GSL's CBLAS
- # but this does not work in Fedora since even though the library flexiblas
- # that is used by PETSc does contain cblas_dgemm, it is not found by the linker
- #AS_IF([test "x${have_petsc}" != "xyes"],
-  AC_CHECK_LIB([gslcblas],[cblas_dgemm], [], AC_MSG_ERROR([GNU Scientific library CBLAS libgsl-dev not found]))
- #)
- AC_CHECK_LIB([gsl],[gsl_blas_dgemm],   [], AC_MSG_ERROR([GNU Scientific library libgsl-dev not found]))
- gsl_version="from system"
+  # Define HAVE_GSL if we found it
+  AS_IF([test "x${have_gsl}" = "xyes"],
+    [
+      AC_DEFINE([HAVE_GSL], [1], [GSL is available])
+    ]
+  )
 ])
 
 
@@ -424,22 +465,32 @@ AS_IF([test "x${enable_fee2ccx}" = "xyes"] , [
 
 
 AS_BOX([Summary of dependencies])
-AS_ECHO(  ["  GNU Scientific Library  ${gsl_version}"])
+AS_ECHO_N(  ["  GNU Scientific Library  ${have_gsl}"])
+AS_IF([test "x${have_gsl}" = "xyes"],
+ AS_ECHO([" ${gsl_version}"]),
+ AS_ECHO
+)
+
 # AS_ECHO(  ["  Readline                ${have_readline}"])
+
 AS_ECHO(  ["  SUNDIALS                ${have_sundials}"])
+
 AS_ECHO_N(["  PETSc                   ${have_petsc}"])
 AS_IF([test "x${have_petsc}" = "xyes"],
  AS_ECHO([" ${PETSC_DIR} ${PETSC_ARCH}"]),
  AS_ECHO
 )
+
 AS_ECHO_N(["  SLEPc                   ${have_slepc}"])
 AS_IF([test "x${have_slepc}" = "xyes"],
  AS_ECHO([" ${SLEPC_DIR}"]),
  AS_ECHO
 )
+
 AS_ECHO(  ["  Compile fee2ccx         ${enable_fee2ccx}"])
 AS_ECHO(  ["  Compiler                ${compiler_show}"])
 AS_ECHO(  ["  Compiler flags          ${CFLAGS}"])
+AS_ECHO(  ["  Compiler version        ${compiler_version}"])
 # AS_ECHO(  ["  Linker flags            ${LDFLAGS}"])
 
 AC_OUTPUT

src/feenox.h

@@ -41,38 +41,17 @@
 #endif
 
 // for inlining as much as possible GSL
+#ifdef HAVE_GSL
 #define HAVE_INLINE
 #define GSL_RANGE_CHECK_OFF
+#endif
 
 #ifndef sunrealtype
 #define sunrealtype realtype
 #endif
 
-// we need all the includes here so they all follow the inline directive above
-#include <gsl/gsl_blas.h>
-#include <gsl/gsl_errno.h>
-#include <gsl/gsl_deriv.h>
-#include <gsl/gsl_heapsort.h>
-#include <gsl/gsl_integration.h>
-#include <gsl/gsl_interp.h>
-#include <gsl/gsl_linalg.h>
-#include <gsl/gsl_math.h>
-#include <gsl/gsl_matrix.h>
-#include <gsl/gsl_min.h>
-#include <gsl/gsl_multifit_nlinear.h>
-#include <gsl/gsl_multimin.h>
-#include <gsl/gsl_multiroots.h>
-#include <gsl/gsl_qrng.h>
-#include <gsl/gsl_randist.h>
-#include <gsl/gsl_rng.h>
-#include <gsl/gsl_roots.h>
-#include <gsl/gsl_spline.h>
-#include <gsl/gsl_sf.h>
-#include <gsl/gsl_statistics.h>
-#include <gsl/gsl_sort_double.h>
-#include <gsl/gsl_sort_vector_double.h>
-#include <gsl/gsl_vector.h>
-#include <gsl/gsl_version.h>
+// Include linear algebra layer (GSL or compatibility implementation)
+#include "math/linalg.h"
 
 #ifdef HAVE_SUNDIALS
  #include <ida/ida.h>
@@ -162,7 +141,11 @@ extern "C++" {
 // reasonable defaults
 #define DEFAULT_DT                         1.0/16.0
 #define DEFAULT_DAE_RTOL                   1e-6
+#ifdef HAVE_GSL
 #define DEFAULT_RANDOM_METHOD              gsl_rng_mt19937
+#else
+#define DEFAULT_RANDOM_METHOD              NULL
+#endif
 
 #define DEFAULT_PRINT_FORMAT               "%g"
 #define DEFAULT_PRINT_SEPARATOR            "\t"
@@ -187,7 +170,11 @@ extern "C++" {
 #define DEFAULT_FIT_GTOL                   1e-8
 #define DEFAULT_FIT_FTOL                   0.0
 
+#ifdef HAVE_GSL
 #define DEFAULT_SOLVE_METHOD               gsl_multiroot_fsolver_dnewton
+#else
+#define DEFAULT_SOLVE_METHOD               NULL
+#endif
 #define DEFAULT_SOLVE_EPSREL               0   // zero means do not look for deltas in derivatives
 #define DEFAULT_SOLVE_EPSABS               1e-6
 #define DEFAULT_SOLVE_MAX_ITER             128
@@ -231,7 +218,9 @@ extern "C++" {
 #define ELEMENT_TYPE_PRISM15        18
 #define NUMBER_ELEMENT_TYPE         19
 
+#ifndef M_SQRT5
 #define M_SQRT5 2.23606797749978969640917366873127623544061835961152572427089
+#endif
 
 #define FEENOX_SOLUTION_NOT_GRADIENT  0
 #define FEENOX_SOLUTION_GRADIENT      1
@@ -1430,8 +1419,8 @@ struct mesh_write_t {
 
   int (*write_header)(mesh_t *mesh, FILE *file);
   int (*write_mesh)(mesh_t *mesh, FILE *file, int no_physical_names);
-  int (*write_data)(mesh_write_t *this, mesh_write_dist_t *dist);
-  int (*write_footer)(mesh_write_t *this);
+  int (*write_data)(mesh_write_t *mesh, mesh_write_dist_t *dist);
+  int (*write_footer)(mesh_write_t *mesh);
 
   // these two are to know if we have to change the type in VTK
   int point_init;
@@ -1538,7 +1527,11 @@ struct solve_t {
   int max_iter;
   int verbose;
 
+#ifdef HAVE_GSL
   const gsl_multiroot_fsolver_type *type;
+#else
+  const void *type;
+#endif
 
   solve_t *next;  
 };
@@ -2130,7 +2123,7 @@ extern int feenox_read_arguments(char *string, int n_arguments, char ***arg, siz
 
 
 // file.c
-char *feenox_evaluate_string(const char *restrict format, int n_args, expr_t *arg);
+char *feenox_evaluate_string(const char *restrict fmt, int n_args, expr_t *arg);
 extern int feenox_instruction_file(void *arg);
 FILE *feenox_fopen(const char *filepath, const char *mode);
 extern int feenox_instruction_file_open(void *arg);
@@ -2303,7 +2296,7 @@ extern double feenox_gsl_function(double x, void *params);
 // mesh.c
 extern int feenox_instruction_mesh_read(void *arg);
 extern int feenox_mesh_create_nodes_argument(mesh_t *);
-extern int feenox_mesh_create_index2tag(mesh_t *this);
+extern int feenox_mesh_create_index2tag(mesh_t *mesh);
 extern int feenox_mesh_free(mesh_t *);
 
 extern int feenox_mesh_read_vtk(mesh_t *);
@@ -2427,13 +2420,13 @@ extern int feenox_mesh_write_header_vtk(mesh_t *mesh, FILE *file);
 extern int feenox_mesh_write_vtk_cells(mesh_t *mesh, FILE * file, int with_size);
 extern int feenox_mesh_write_vtk_types(mesh_t *mesh, FILE * file);
 extern int feenox_mesh_write_mesh_vtk(mesh_t *mesh, FILE *file, int dummy);
-extern int feenox_mesh_write_data_vtk(mesh_write_t *this, mesh_write_dist_t *dist);
+extern int feenox_mesh_write_data_vtk(mesh_write_t *mesh, mesh_write_dist_t *dist);
 
 // vtu.c
 extern int feenox_mesh_write_header_vtu(mesh_t *mesh, FILE *file);
 extern int feenox_mesh_write_mesh_vtu(mesh_t *, FILE *file, int dummy);
-extern int feenox_mesh_write_data_vtu(mesh_write_t *this, mesh_write_dist_t *dist);
-extern int feenox_mesh_write_footer_vtu(mesh_write_t *this);
+extern int feenox_mesh_write_data_vtu(mesh_write_t *mesh, mesh_write_dist_t *dist);
+extern int feenox_mesh_write_footer_vtu(mesh_write_t *mesh);
 
 // neighbors.c
 extern element_t *feenox_mesh_find_element_volumetric_neighbor(element_t *e)  __attribute__((noinline));