[sundials] 06/10: patches
Dima Kogan
dima at secretsauce.net
Mon May 29 23:37:39 UTC 2017
This is an automated email from the git hooks/post-receive script.
dkogan pushed a commit to branch master
in repository sundials.
commit 552a0d3f12a7cafe1a06ca13308880ccb150f16b
Author: Dima Kogan <dima at secretsauce.net>
Date: Mon May 29 15:04:12 2017 -0700
patches
---
.../0001-Added-missing-linkages-to-the-DSOs.patch | 54 +++++++++++++++++++---
.../0002-Fix-library-paths-for-multiarch.patch | 30 ++++++------
...-CMakeLists.txt-have-a-minumum-requested.patch} | 2 +-
.../0015-Not-building-CVODE-with-mpicc.patch | 29 ++++++++++++
debian/patches/series | 3 +-
5 files changed, 95 insertions(+), 23 deletions(-)
diff --git a/debian/patches/0001-Added-missing-linkages-to-the-DSOs.patch b/debian/patches/0001-Added-missing-linkages-to-the-DSOs.patch
index 5dc397e..5626145 100644
--- a/debian/patches/0001-Added-missing-linkages-to-the-DSOs.patch
+++ b/debian/patches/0001-Added-missing-linkages-to-the-DSOs.patch
@@ -10,11 +10,13 @@ The shared libraries should link against their dependencies
src/ida/CMakeLists.txt | 6 ++++++
src/idas/CMakeLists.txt | 6 ++++++
src/kinsol/CMakeLists.txt | 6 ++++++
+ src/nvec_openmp/CMakeLists.txt | 2 ++
src/nvec_par/CMakeLists.txt | 2 ++
src/nvec_parhyp/CMakeLists.txt | 1 +
- src/nvec_pthreads/CMakeLists.txt | 1 +
+ src/nvec_petsc/CMakeLists.txt | 1 +
+ src/nvec_pthreads/CMakeLists.txt | 2 ++
src/nvec_ser/CMakeLists.txt | 2 ++
- 10 files changed, 42 insertions(+)
+ 12 files changed, 46 insertions(+)
diff --git a/src/arkode/CMakeLists.txt b/src/arkode/CMakeLists.txt
index cfed8e6..935502a 100644
@@ -160,6 +162,26 @@ index d22ed62..27b5f4a 100644
# Install the KINSOL library
INSTALL(TARGETS sundials_kinsol_shared DESTINATION lib)
+diff --git a/src/nvec_openmp/CMakeLists.txt b/src/nvec_openmp/CMakeLists.txt
+index eab8451..f28f5c9 100644
+--- a/src/nvec_openmp/CMakeLists.txt
++++ b/src/nvec_openmp/CMakeLists.txt
+@@ -65,6 +65,7 @@ IF(BUILD_SHARED_LIBS)
+ PROPERTIES OUTPUT_NAME sundials_nvecopenmp CLEAN_DIRECT_OUTPUT 1)
+ SET_TARGET_PROPERTIES(sundials_nvecopenmp_shared
+ PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
++ TARGET_LINK_LIBRARIES(sundials_nvecopenmp_shared -lm)
+ INSTALL(TARGETS sundials_nvecopenmp_shared DESTINATION lib)
+ ENDIF(BUILD_SHARED_LIBS)
+
+@@ -86,6 +87,7 @@ IF(FCMIX_ENABLE AND F77_FOUND)
+ PROPERTIES OUTPUT_NAME sundials_fnvecopenmp CLEAN_DIRECT_OUTPUT 1)
+ SET_TARGET_PROPERTIES(sundials_fnvecopenmp_shared
+ PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
++ TARGET_LINK_LIBRARIES(sundials_fnvecopenmp_shared sundials_nvecopenmp_shared)
+ INSTALL(TARGETS sundials_fnvecopenmp_shared DESTINATION lib)
+ ENDIF(BUILD_SHARED_LIBS)
+ ENDIF(FCMIX_ENABLE AND F77_FOUND)
diff --git a/src/nvec_par/CMakeLists.txt b/src/nvec_par/CMakeLists.txt
index 8477fb4..f60b795 100644
--- a/src/nvec_par/CMakeLists.txt
@@ -181,29 +203,49 @@ index 8477fb4..f60b795 100644
ENDIF(BUILD_SHARED_LIBS)
ENDIF(FCMIX_ENABLE AND MPIF_FOUND)
diff --git a/src/nvec_parhyp/CMakeLists.txt b/src/nvec_parhyp/CMakeLists.txt
-index 9255489..973f2c3 100644
+index 9255489..b5d8948 100644
--- a/src/nvec_parhyp/CMakeLists.txt
+++ b/src/nvec_parhyp/CMakeLists.txt
@@ -67,6 +67,7 @@ IF(BUILD_SHARED_LIBS)
PROPERTIES OUTPUT_NAME sundials_nvecparhyp CLEAN_DIRECT_OUTPUT 1)
SET_TARGET_PROPERTIES(sundials_nvecparhyp_shared
PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
-+ TARGET_LINK_LIBRARIES(sundials_nvecparhyp_shared ${HYPRE_LIBRARIES})
++ TARGET_LINK_LIBRARIES(sundials_nvecparhyp_shared ${HYPRE_LIBRARIES} -lm)
INSTALL(TARGETS sundials_nvecparhyp_shared DESTINATION lib)
ENDIF(BUILD_SHARED_LIBS)
+diff --git a/src/nvec_petsc/CMakeLists.txt b/src/nvec_petsc/CMakeLists.txt
+index a98867c..73dab6c 100644
+--- a/src/nvec_petsc/CMakeLists.txt
++++ b/src/nvec_petsc/CMakeLists.txt
+@@ -67,6 +67,7 @@ IF(BUILD_SHARED_LIBS)
+ PROPERTIES OUTPUT_NAME sundials_nvecpetsc CLEAN_DIRECT_OUTPUT 1)
+ SET_TARGET_PROPERTIES(sundials_nvecpetsc_shared
+ PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
++ TARGET_LINK_LIBRARIES(sundials_nvecpetsc_shared ${PETSC_LIBRARIES} -lm)
+ INSTALL(TARGETS sundials_nvecpetsc_shared DESTINATION lib)
+ ENDIF(BUILD_SHARED_LIBS)
+
diff --git a/src/nvec_pthreads/CMakeLists.txt b/src/nvec_pthreads/CMakeLists.txt
-index b711d3a..a476ec0 100644
+index b711d3a..dfc8fb0 100644
--- a/src/nvec_pthreads/CMakeLists.txt
+++ b/src/nvec_pthreads/CMakeLists.txt
@@ -58,6 +58,7 @@ IF(BUILD_SHARED_LIBS)
PROPERTIES OUTPUT_NAME sundials_nvecpthreads CLEAN_DIRECT_OUTPUT 1)
SET_TARGET_PROPERTIES(sundials_nvecpthreads_shared
PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
-+ TARGET_LINK_LIBRARIES(sundials_nvecpthreads_shared -lpthread)
++ TARGET_LINK_LIBRARIES(sundials_nvecpthreads_shared -lpthread -lm)
INSTALL(TARGETS sundials_nvecpthreads_shared DESTINATION lib)
ENDIF(BUILD_SHARED_LIBS)
+@@ -79,6 +80,7 @@ IF(FCMIX_ENABLE AND F77_FOUND)
+ PROPERTIES OUTPUT_NAME sundials_fnvecpthreads CLEAN_DIRECT_OUTPUT 1)
+ SET_TARGET_PROPERTIES(sundials_fnvecpthreads_shared
+ PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
++ TARGET_LINK_LIBRARIES(sundials_fnvecpthreads_shared sundials_nvecpthreads_shared)
+ INSTALL(TARGETS sundials_fnvecpthreads_shared DESTINATION lib)
+ ENDIF(BUILD_SHARED_LIBS)
+ ENDIF(FCMIX_ENABLE AND F77_FOUND)
diff --git a/src/nvec_ser/CMakeLists.txt b/src/nvec_ser/CMakeLists.txt
index de9fb12..8b60809 100644
--- a/src/nvec_ser/CMakeLists.txt
diff --git a/debian/patches/0002-Fix-library-paths-for-multiarch.patch b/debian/patches/0002-Fix-library-paths-for-multiarch.patch
index b84c74c..8067adc 100644
--- a/debian/patches/0002-Fix-library-paths-for-multiarch.patch
+++ b/debian/patches/0002-Fix-library-paths-for-multiarch.patch
@@ -230,7 +230,7 @@ index 16377cf..7d2f5e8 100644
#
MESSAGE(STATUS "Added KINSOL FCMIX module")
diff --git a/src/nvec_openmp/CMakeLists.txt b/src/nvec_openmp/CMakeLists.txt
-index eab8451..c1831b9 100644
+index f28f5c9..a2533b4 100644
--- a/src/nvec_openmp/CMakeLists.txt
+++ b/src/nvec_openmp/CMakeLists.txt
@@ -51,7 +51,7 @@ IF(BUILD_STATIC_LIBS)
@@ -242,16 +242,16 @@ index eab8451..c1831b9 100644
ENDIF(BUILD_STATIC_LIBS)
# Rules for building and installing the shared library:
-@@ -65,7 +65,7 @@ IF(BUILD_SHARED_LIBS)
- PROPERTIES OUTPUT_NAME sundials_nvecopenmp CLEAN_DIRECT_OUTPUT 1)
+@@ -66,7 +66,7 @@ IF(BUILD_SHARED_LIBS)
SET_TARGET_PROPERTIES(sundials_nvecopenmp_shared
PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
+ TARGET_LINK_LIBRARIES(sundials_nvecopenmp_shared -lm)
- INSTALL(TARGETS sundials_nvecopenmp_shared DESTINATION lib)
+ INSTALL(TARGETS sundials_nvecopenmp_shared DESTINATION ${CMAKE_INSTALL_LIBDIR})
ENDIF(BUILD_SHARED_LIBS)
# Install the NVECOPENMP header files
-@@ -78,7 +78,7 @@ IF(FCMIX_ENABLE AND F77_FOUND)
+@@ -79,7 +79,7 @@ IF(FCMIX_ENABLE AND F77_FOUND)
ADD_LIBRARY(sundials_fnvecopenmp_static STATIC ${fnvecopenmp_SOURCES})
SET_TARGET_PROPERTIES(sundials_fnvecopenmp_static
PROPERTIES OUTPUT_NAME sundials_fnvecopenmp CLEAN_DIRECT_OUTPUT 1)
@@ -260,10 +260,10 @@ index eab8451..c1831b9 100644
ENDIF(BUILD_STATIC_LIBS)
IF(BUILD_SHARED_LIBS)
ADD_LIBRARY(sundials_fnvecopenmp_shared ${fnvecopenmp_SOURCES})
-@@ -86,7 +86,7 @@ IF(FCMIX_ENABLE AND F77_FOUND)
- PROPERTIES OUTPUT_NAME sundials_fnvecopenmp CLEAN_DIRECT_OUTPUT 1)
+@@ -88,7 +88,7 @@ IF(FCMIX_ENABLE AND F77_FOUND)
SET_TARGET_PROPERTIES(sundials_fnvecopenmp_shared
PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
+ TARGET_LINK_LIBRARIES(sundials_fnvecopenmp_shared sundials_nvecopenmp_shared)
- INSTALL(TARGETS sundials_fnvecopenmp_shared DESTINATION lib)
+ INSTALL(TARGETS sundials_fnvecopenmp_shared DESTINATION ${CMAKE_INSTALL_LIBDIR})
ENDIF(BUILD_SHARED_LIBS)
@@ -310,7 +310,7 @@ index f60b795..3381ed2 100644
ENDIF(FCMIX_ENABLE AND MPIF_FOUND)
#
diff --git a/src/nvec_parhyp/CMakeLists.txt b/src/nvec_parhyp/CMakeLists.txt
-index 973f2c3..0a1378e 100644
+index b5d8948..9ed5b4b 100644
--- a/src/nvec_parhyp/CMakeLists.txt
+++ b/src/nvec_parhyp/CMakeLists.txt
@@ -53,7 +53,7 @@ IF(BUILD_STATIC_LIBS)
@@ -325,14 +325,14 @@ index 973f2c3..0a1378e 100644
@@ -68,7 +68,7 @@ IF(BUILD_SHARED_LIBS)
SET_TARGET_PROPERTIES(sundials_nvecparhyp_shared
PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
- TARGET_LINK_LIBRARIES(sundials_nvecparhyp_shared ${HYPRE_LIBRARIES})
+ TARGET_LINK_LIBRARIES(sundials_nvecparhyp_shared ${HYPRE_LIBRARIES} -lm)
- INSTALL(TARGETS sundials_nvecparhyp_shared DESTINATION lib)
+ INSTALL(TARGETS sundials_nvecparhyp_shared DESTINATION ${CMAKE_INSTALL_LIBDIR})
ENDIF(BUILD_SHARED_LIBS)
# Install the NVECPARHYP header files
diff --git a/src/nvec_petsc/CMakeLists.txt b/src/nvec_petsc/CMakeLists.txt
-index a98867c..52f2b5b 100644
+index 73dab6c..0320b19 100644
--- a/src/nvec_petsc/CMakeLists.txt
+++ b/src/nvec_petsc/CMakeLists.txt
@@ -53,7 +53,7 @@ IF(BUILD_STATIC_LIBS)
@@ -344,17 +344,17 @@ index a98867c..52f2b5b 100644
ENDIF(BUILD_STATIC_LIBS)
# Rules for building and installing the shared library:
-@@ -67,7 +67,7 @@ IF(BUILD_SHARED_LIBS)
- PROPERTIES OUTPUT_NAME sundials_nvecpetsc CLEAN_DIRECT_OUTPUT 1)
+@@ -68,7 +68,7 @@ IF(BUILD_SHARED_LIBS)
SET_TARGET_PROPERTIES(sundials_nvecpetsc_shared
PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
+ TARGET_LINK_LIBRARIES(sundials_nvecpetsc_shared ${PETSC_LIBRARIES} -lm)
- INSTALL(TARGETS sundials_nvecpetsc_shared DESTINATION lib)
+ INSTALL(TARGETS sundials_nvecpetsc_shared DESTINATION ${CMAKE_INSTALL_LIBDIR})
ENDIF(BUILD_SHARED_LIBS)
# Install the NVECPARHYP header files
diff --git a/src/nvec_pthreads/CMakeLists.txt b/src/nvec_pthreads/CMakeLists.txt
-index a476ec0..a176ff7 100644
+index dfc8fb0..6661614 100644
--- a/src/nvec_pthreads/CMakeLists.txt
+++ b/src/nvec_pthreads/CMakeLists.txt
@@ -44,7 +44,7 @@ IF(BUILD_STATIC_LIBS)
@@ -369,7 +369,7 @@ index a476ec0..a176ff7 100644
@@ -59,7 +59,7 @@ IF(BUILD_SHARED_LIBS)
SET_TARGET_PROPERTIES(sundials_nvecpthreads_shared
PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
- TARGET_LINK_LIBRARIES(sundials_nvecpthreads_shared -lpthread)
+ TARGET_LINK_LIBRARIES(sundials_nvecpthreads_shared -lpthread -lm)
- INSTALL(TARGETS sundials_nvecpthreads_shared DESTINATION lib)
+ INSTALL(TARGETS sundials_nvecpthreads_shared DESTINATION ${CMAKE_INSTALL_LIBDIR})
ENDIF(BUILD_SHARED_LIBS)
@@ -384,10 +384,10 @@ index a476ec0..a176ff7 100644
ENDIF(BUILD_STATIC_LIBS)
IF(BUILD_SHARED_LIBS)
ADD_LIBRARY(sundials_fnvecpthreads_shared ${fnvecpthreads_SOURCES})
-@@ -80,7 +80,7 @@ IF(FCMIX_ENABLE AND F77_FOUND)
- PROPERTIES OUTPUT_NAME sundials_fnvecpthreads CLEAN_DIRECT_OUTPUT 1)
+@@ -81,7 +81,7 @@ IF(FCMIX_ENABLE AND F77_FOUND)
SET_TARGET_PROPERTIES(sundials_fnvecpthreads_shared
PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION})
+ TARGET_LINK_LIBRARIES(sundials_fnvecpthreads_shared sundials_nvecpthreads_shared)
- INSTALL(TARGETS sundials_fnvecpthreads_shared DESTINATION lib)
+ INSTALL(TARGETS sundials_fnvecpthreads_shared DESTINATION ${CMAKE_INSTALL_LIBDIR})
ENDIF(BUILD_SHARED_LIBS)
diff --git a/debian/patches/0014-All-example-CMakeLists.txt-have-a-minumum-requested-.patch b/debian/patches/0014-Examples-all-CMakeLists.txt-have-a-minumum-requested.patch
similarity index 99%
rename from debian/patches/0014-All-example-CMakeLists.txt-have-a-minumum-requested-.patch
rename to debian/patches/0014-Examples-all-CMakeLists.txt-have-a-minumum-requested.patch
index 003b593..b3d4c87 100644
--- a/debian/patches/0014-All-example-CMakeLists.txt-have-a-minumum-requested-.patch
+++ b/debian/patches/0014-Examples-all-CMakeLists.txt-have-a-minumum-requested.patch
@@ -1,6 +1,6 @@
From: Dima Kogan <dima at secretsauce.net>
Date: Mon, 29 May 2017 02:49:45 -0700
-Subject: All example CMakeLists.txt have a minumum requested CMake version
+Subject: Examples: all CMakeLists.txt have a minumum requested CMake version
This is just to pacify a cmake warning
---
diff --git a/debian/patches/0015-Not-building-CVODE-with-mpicc.patch b/debian/patches/0015-Not-building-CVODE-with-mpicc.patch
new file mode 100644
index 0000000..8de9b27
--- /dev/null
+++ b/debian/patches/0015-Not-building-CVODE-with-mpicc.patch
@@ -0,0 +1,29 @@
+From: Dima Kogan <dima at secretsauce.net>
+Date: Mon, 29 May 2017 14:54:44 -0700
+Subject: Not building CVODE with mpicc
+
+CVODE doesn't use or NOT use MPI: this is up to the underlying nvec
+implementation
+---
+ src/cvode/CMakeLists.txt | 8 --------
+ 1 file changed, 8 deletions(-)
+
+diff --git a/src/cvode/CMakeLists.txt b/src/cvode/CMakeLists.txt
+index c6238c9..ab7ae8b 100644
+--- a/src/cvode/CMakeLists.txt
++++ b/src/cvode/CMakeLists.txt
+@@ -18,14 +18,6 @@
+
+ INSTALL(CODE "MESSAGE(\"\nInstall CVODE\n\")")
+
+-IF(MPI_MPICC)
+- # use MPI_MPICC as the compiler
+- SET(CMAKE_C_COMPILER ${MPI_MPICC})
+-ELSE(MPI_MPICC)
+- # add MPI_INCLUDE_PATH to include directories
+- INCLUDE_DIRECTORIES(${MPI_INCLUDE_PATH})
+-ENDIF(MPI_MPICC)
+-
+ # Add variable cvode_SOURCES with the sources for the CVODE library
+ SET(cvode_SOURCES
+ cvode.c
diff --git a/debian/patches/series b/debian/patches/series
index 2f28d32..cf65721 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -11,4 +11,5 @@
0011-Examples-nvector-examples-use-shipped-copy-of-sundia.patch
0012-Examples-fortran-examples-CMake-knows-to-do-its-fort.patch
0013-Examples-pthread-example-assumes-we-have-pthread-sup.patch
-0014-All-example-CMakeLists.txt-have-a-minumum-requested-.patch
+0014-Examples-all-CMakeLists.txt-have-a-minumum-requested.patch
+0015-Not-building-CVODE-with-mpicc.patch
--
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