reinit the tree, so we can have metadata

5 files changed, 100 insertions, 0 deletions

diff --git a/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch b/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch
new file mode 100644
index 000000000000..a52c78bf77c8
--- /dev/null
+++ b/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch
@@ -0,0 +1,22 @@
+patch to allow gerris to use hypre without mpi
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -336,7 +336,7 @@
+ 
+ # Build hypre module if HYPRE is installed
+ hypre=no
+-if test "x$use_mpicc" = "xyes" ; then # HYPRE needs MPI
++# hypre does not need mpi
+    AC_CHECK_LIB(HYPRE, HYPRE_IJMatrixCreate, hypre="yes", hypre="no", [-lm])
+    if test x$hypre = xyes; then
+       AC_CHECK_HEADERS(HYPRE.h, hypre="yes", hypre="no")
+@@ -344,7 +344,7 @@
+    if test x$hypre = xno; then
+       AC_MSG_WARN([HYPRE not found. hypre Module won't be available.])
+    fi
+-fi
++
+ AM_CONDITIONAL(BUILD_HYPRE, test x$hypre = xyes)
+ 
+ # Build lis module if lis is installed
diff --git a/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch b/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch
new file mode 100644
index 000000000000..d4c7bfae15bb
--- /dev/null
+++ b/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch
@@ -0,0 +1,11 @@
+--- a/modules/lis.c
++++ b/modules/lis.c
+@@ -45,7 +45,7 @@
+ 			    g_array_index (stencil->coeff, double, j), 
+ 			    A);
+   }
+-  lis_matrix_set_type (A, LIS_MATRIX_CRS);
++  lis_matrix_set_type (A, LIS_MATRIX_CSR);
+   lis_matrix_assemble (A);
+ 
+   LIS_VECTOR b, x;
diff --git a/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch b/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch
new file mode 100644
index 000000000000..1c25a8f516b6
--- /dev/null
+++ b/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch
@@ -0,0 +1,33 @@
+--- a/modules/Makefile.am
++++ b/modules/Makefile.am
+@@ -105,7 +105,7 @@
+ libstokes2D_la_LIBADD = $(GFS2D_LIBS)
+ 
+ libwavewatch2D_la_SOURCES = wavewatch.c
+-libwavewatch2D_la_LIBADD = $(GFS2D_LIBS) -Lwavewatch -lwavewatch -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran
++libwavewatch2D_la_LIBADD = $(GFS2D_LIBS) -Lwavewatch -lwavewatch
+ libwavewatch2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1 \
+   -DW3SRCE=`nm wavewatch/libwavewatch.a | grep w3srce | awk '{ if ($$2 == "T") print $$3; }'` \
+   -DGFSW3INIT=`nm wavewatch/libwavewatch.a | grep gfsw3_init | awk '{ if ($$2 == "T") print $$3; }'`
+@@ -164,17 +164,17 @@
+ 
+ liblis3D_la_SOURCES = lis.c
+ liblis3D_la_CFLAGS = $(AM_CFLAGS)
+-liblis3D_la_LIBADD = $(GFS3D_LIBS) -llis -lgfortran -lm
++liblis3D_la_LIBADD = $(GFS3D_LIBS) -llis -lm
+ liblis2D_la_SOURCES = lis.c
+ liblis2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1
+-liblis2D_la_LIBADD = $(GFS2D_LIBS) -llis -lgfortran -lm
++liblis2D_la_LIBADD = $(GFS2D_LIBS) -llis -lm
+ 
+ libagmg3D_la_SOURCES = agmg.c dagmg.f90
+ libagmg3D_la_CFLAGS = $(AM_CFLAGS)
+-libagmg3D_la_LIBADD = $(GFS3D_LIBS) -llapack -lblas -lgfortran -lm
++libagmg3D_la_LIBADD = $(GFS3D_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) -lm
+ libagmg2D_la_SOURCES = agmg.c dagmg.f90
+ libagmg2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1
+-libagmg2D_la_LIBADD = $(GFS2D_LIBS) -llapack -lblas -lgfortran -lm
++libagmg2D_la_LIBADD = $(GFS2D_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) -lm
+ 
+ libokada3D_la_SOURCES = okada.c
+ libokada3D_la_CFLAGS = $(AM_CFLAGS)
diff --git a/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch b/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch
new file mode 100644
index 000000000000..d20df635512c
--- /dev/null
+++ b/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch
@@ -0,0 +1,16 @@
+Silence warnings due to _BSD_SOURCE being deprecated by glib:
+* /usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and
+* _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
+* # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -108,7 +108,7 @@
+ AC_PROG_CC
+ 
+ # -D_GNU_SOURCE is only necessary for old (< 2.10) glibc implementations of open_memstream()
+-CFLAGS="$CFLAGS -D_XOPEN_SOURCE=700 -D_BSD_SOURCE -D_GNU_SOURCE"
++CFLAGS="$CFLAGS -D_XOPEN_SOURCE=700 -D_DEFAULT_SOURCE -D_GNU_SOURCE"
+ if test x$GCC = xyes ; then
+   CFLAGS="$CFLAGS -Wall -Werror-implicit-function-declaration -Wmissing-prototypes -Wmissing-declarations -pipe -std=c99"
+ fi
diff --git a/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch b/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch
new file mode 100644
index 000000000000..28892ddadedf
--- /dev/null
+++ b/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch
@@ -0,0 +1,18 @@
+sci-libs/lis changed some of its function prototypes by renaming
+lis_solver_get_iters to lis_solver_get_iter in version 1.4.43 from 17 July 2014
+
+See also:
+http://www.ssisc.org/lis/ChangeLog.txt
+https://bugs.gentoo.org/show_bug.cgi?id=593282
+
+--- a/modules/lis.c
++++ b/modules/lis.c
+@@ -67,7 +67,7 @@
+ 
+   lis_solve (A, b, x, solver);
+   int iter;
+-  lis_solver_get_iters (solver, &iter);
++  lis_solver_get_iter (solver, &iter);
+   par->niter = iter;
+ 
+   lis_vector_get_values (x, 0, lp->lhs->len, (double *) lp->lhs->data);