CONFIG: update link to mpc version

ENH: makeVTK -mpi also define VTK_Group_MPI=ON
- this pulls in the other bits (Module_vtkParallelMPI, Module_vtkRenderingParallel, ...)
2018-12-14 12:17:49 +01:00 · 2018-12-05 23:37:00 +01:00 · 2018-12-04 18:33:45 +01:00 · 2018-12-03 08:45:29 +01:00 · 2018-12-03 08:44:27 +01:00 · 2018-07-31 11:20:37 +02:00
27 changed files with 954 additions and 75 deletions
--- a/BUILD.md
+++ b/BUILD.md
@ -243,17 +243,17 @@ and save some disk space.
  sources that are bundled with ParaView.
  For example, by using a symbolic link:

-      ln -s ParaView-v5.5.2/VTK VTK-9.0.0
+      ln -s ParaView-v5.6.0/VTK VTK-8.2.0

  The appropriate VTK version number can be found from the contents of
  the `vtkVersion.cmake` file.
  For example,

-      $ cat ParaView-v5.5.2/VTK/CMake/vtkVersion.cmake
+      $ cat ParaView-v5.6.0/VTK/CMake/vtkVersion.cmake

      # VTK version number components.
-      set(VTK_MAJOR_VERSION 9)
-      set(VTK_MINOR_VERSION 0)
+      set(VTK_MAJOR_VERSION 8)
+      set(VTK_MINOR_VERSION 2)
      set(VTK_BUILD_VERSION 0)

 ### ParaView
@ -273,7 +273,7 @@ source pack. This, however, has never been tested in combination with
 the OpenFOAM Catalyst insitu visualization.


-#### 5.5.x binary package
+#### 5.6.x, 5.5.x binary packages

 For general functionality, the paraview version distributed with
 the operating system or a [binary package][download ParaView]])
@ -322,7 +322,7 @@ may not be important for you):

 3. Build ParaView using this third-party QT. For example,

-       ./makeParaView -qt-5.9.3  5.5.2
+       ./makeParaView -qt-5.9.3  5.6.0

 - ParaView versions prior to 5.3.0 do not properly support QT5.

@ -412,7 +412,7 @@ you may have additional hurdles to using the newest versions of clang.
 |-----------------------|------------------------
 | [openmpi][page openmpi] | [download][link openmpi]. The newer [openmpi][newer openmpi] make exhibit stability issues.
 | [adios][page adios]   | [repo][repo adios] or [github download][link adios] or [alt download][altlink adios]
-| [scotch, ptscotch][page scotch] | [download][link scotch]
+| [scotch, ptscotch][page scotch] | [download][link scotch] or older: [6.0.3][link scotch603]
 | [kahip][page kahip] | [download][link kahip]
 | [metis][page metis] | [download][link metis]

@ -422,7 +422,7 @@ you may have additional hurdles to using the newest versions of clang.
 | Name                  | Location
 |-----------------------|------------------------
 | [MESA][page mesa]     | [download][link mesa] or [older 13][link mesa13], [older 11][link mesa11]
-| [ParaView][page ParaView] | [download][link ParaView] or [older paraview-54][link ParaView54] or [binaries][download ParaView]
+| [ParaView][page ParaView] | [download][link ParaView] or [older paraview-55][link ParaView55], [older paraview-54][link ParaView54] or [binaries][download ParaView]
 | [Qt][page Qt]         | [QT5][link Qt5] for ParaView-5.3.0 and later, or the [older qt-56][link Qt56] for older systems.


@ -436,7 +436,7 @@ The minimum CMake requirements for building various components.
    2.8.12.2    llvm-3.7.0
    2.8.12.2    llvm-3.8.0
    2.8.4       cmake-3.6.0
-    3.3         ParaView-5.5.2
+    3.3         ParaView-5.6.0
    3.4.3       llvm-3.9.1
    3.4.3       llvm-4.0.0 - llvm-6.0.0
    3.6         ADIOS2
@ -463,9 +463,9 @@ that clang compiler for building the newer llvm/clang version.
 [page mpc]:       http://www.multiprecision.org/

 [link gcc]:       http://gcc.gnu.org/releases.html
-[link gmp]:       ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.0.tar.bz2
-[link mpfr]:      ftp://ftp.gnu.org/gnu/mpfr/mpfr-3.1.4.tar.bz2
-[link mpc]:       ftp://ftp.gnu.org/gnu/mpc/mpc-1.0.3.tar.gz
+[link gmp]:       ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.xz
+[link mpfr]:      ftp://ftp.gnu.org/gnu/mpfr/mpfr-4.0.1.tar.xz
+[link mpc]:       ftp://ftp.gnu.org/gnu/mpc/mpc-1.1.0.tar.gz


 <!-- clang-related -->
@ -490,8 +490,9 @@ that clang compiler for building the newer llvm/clang version.
 [page zfp]:       http://computation.llnl.gov/projects/floating-point-compression/zfp-versions

 [page scotch]:    https://www.labri.fr/perso/pelegrin/scotch/
-[link scotch]:    https://gforge.inria.fr/frs/download.php/file/34099/scotch_6.0.3.tar.gz
-[link scotch]:    https://gforge.inria.fr/frs/download.php/file/37398/scotch_6.0.5a.tar.gz
+[link scotch603]: https://gforge.inria.fr/frs/download.php/file/34099/scotch_6.0.3.tar.gz
+[link scotch605]: https://gforge.inria.fr/frs/download.php/file/37398/scotch_6.0.5a.tar.gz
+[link scotch]:    https://gforge.inria.fr/frs/download.php/file/37622/scotch_6.0.6.tar.gz

 [page kahip]:     http://algo2.iti.kit.edu/documents/kahip/
 [link kahip]:     http://algo2.iti.kit.edu/schulz/software_releases/KaHIP_2.00.tar.gz
@ -530,7 +531,8 @@ that clang compiler for building the newer llvm/clang version.
 [page ParaView]:  http://www.paraview.org/
 [download ParaView]: https://www.paraview.org/download/
 [link ParaView54]: http://www.paraview.org/files/v5.4/ParaView-v5.4.1.tar.gz
-[link ParaView]:   http://www.paraview.org/files/v5.5/ParaView-v5.5.2.tar.gz
+[link ParaView55]:   http://www.paraview.org/files/v5.5/ParaView-v5.5.2.tar.gz
+[link ParaView]: http://www.paraview.org/files/v5.6/ParaView-v5.6.0.tar.gz

 [page mesa]:  http://mesa3d.org/
 [link mesa]:  ftp://ftp.freedesktop.org/pub/mesa/mesa-17.1.1.tar.xz
--- a/SOURCES.txt
+++ b/SOURCES.txt
@ -1,5 +1,17 @@
 Short summary of third-party software versions for recent OpenFOAM versions.

+OpenFOAM-1812
+---------------
+
+CGAL-4.9.1
+ParaView-5.6.0      *update*
+boost_1_64_0
+fftw-3.3.7
+openmpi-1.10.4
+scotch_6.0.6        *minor*
+kahip-2.00d
+
+
 OpenFOAM-1806
 ---------------
 CGAL-4.9.1
--- a/etc/patches/gcc-4.8.5-with-gcc-7
+++ b/etc/patches/gcc-4.8.5-with-gcc-7
@ -0,0 +1,155 @@
+#
+# Patch for building older gcc versions with gcc-7
+#
+--- gcc-4.8.5/gcc/cp/cfns.gperf.orig	2013-01-10 21:38:27.000000000 +0100
+++ gcc-4.8.5/gcc/cp/cfns.gperf	2016-02-25 16:36:41.000000000 +0100
+@@ -1,5 +1,7 @@
+%language=C++
+%define class-name libc_name
+ %{
+-/* Copyright (C) 2000-2013 Free Software Foundation, Inc.
+/* Copyright (C) 2000-2014 Free Software Foundation, Inc.
+ 
+ This file is part of GCC.
+ 
+@@ -16,14 +18,6 @@
+ You should have received a copy of the GNU General Public License
+ along with GCC; see the file COPYING3.  If not see
+ <http://www.gnu.org/licenses/>.  */
+-#ifdef __GNUC__
+-__inline
+-#endif
+-static unsigned int hash (const char *, unsigned int);
+-#ifdef __GNUC__
+-__inline
+-#endif
+-const char * libc_name_p (const char *, unsigned int);
+ %}
+ %%
+ # The standard C library functions, for feeding to gperf; the result is used
+--- gcc-4.8.5/gcc/cp/cfns.h.orig	2013-01-10 21:38:27.000000000 +0100
+++ gcc-4.8.5/gcc/cp/cfns.h	2016-02-25 16:36:41.000000000 +0100
+@@ -1,5 +1,5 @@
+-/* ANSI-C code produced by gperf version 3.0.3 */
+-/* Command-line: gperf -o -C -E -k '1-6,$' -j1 -D -N libc_name_p -L ANSI-C cfns.gperf  */
+/* C++ code produced by gperf version 3.0.4 */
+/* Command-line: gperf -o -C -E -k '1-6,$' -j1 -D -N libc_name_p -L C++ --output-file cfns.h cfns.gperf  */
+ 
+ #if !((' ' == 32) && ('!' == 33) && ('"' == 34) && ('#' == 35) \
+       && ('%' == 37) && ('&' == 38) && ('\'' == 39) && ('(' == 40) \
+@@ -28,9 +28,9 @@
+ #error "gperf generated tables don't work with this execution character set. Please report a bug to <bug-gnu-gperf@gnu.org>."
+ #endif
+ 
+-#line 1 "cfns.gperf"
+#line 3 "cfns.gperf"
+ 
+-/* Copyright (C) 2000-2013 Free Software Foundation, Inc.
+/* Copyright (C) 2000-2014 Free Software Foundation, Inc.
+ 
+ This file is part of GCC.
+ 
+@@ -47,25 +47,18 @@
+ You should have received a copy of the GNU General Public License
+ along with GCC; see the file COPYING3.  If not see
+ <http://www.gnu.org/licenses/>.  */
+-#ifdef __GNUC__
+-__inline
+-#endif
+-static unsigned int hash (const char *, unsigned int);
+-#ifdef __GNUC__
+-__inline
+-#endif
+-const char * libc_name_p (const char *, unsigned int);
+ /* maximum key range = 391, duplicates = 0 */
+ 
+-#ifdef __GNUC__
+-__inline
+-#else
+-#ifdef __cplusplus
+-inline
+-#endif
+-#endif
+-static unsigned int
+-hash (register const char *str, register unsigned int len)
+class libc_name
+{
+private:
+  static inline unsigned int hash (const char *str, unsigned int len);
+public:
+  static const char *libc_name_p (const char *str, unsigned int len);
+};
+
+inline unsigned int
+libc_name::hash (register const char *str, register unsigned int len)
+ {
+   static const unsigned short asso_values[] =
+     {
+@@ -122,14 +115,8 @@
+   return hval + asso_values[(unsigned char)str[len - 1]];
+ }
+ 
+-#ifdef __GNUC__
+-__inline
+-#ifdef __GNUC_STDC_INLINE__
+-__attribute__ ((__gnu_inline__))
+-#endif
+-#endif
+ const char *
+-libc_name_p (register const char *str, register unsigned int len)
+libc_name::libc_name_p (register const char *str, register unsigned int len)
+ {
+   enum
+     {
+--- gcc-4.8.5/gcc/cp/except.c.orig	2013-10-25 15:49:48.000000000 +0200
+++ gcc-4.8.5/gcc/cp/except.c	2018-07-27 13:11:11.825369497 +0200
+@@ -1025,7 +1025,7 @@
+      unless the system headers are playing rename tricks, and if
+      they are, we don't want to be confused by them.  */
+   id = DECL_NAME (fn);
+-  return !!libc_name_p (IDENTIFIER_POINTER (id), IDENTIFIER_LENGTH (id));
+  return !!libc_name::libc_name_p (IDENTIFIER_POINTER (id), IDENTIFIER_LENGTH (id));
+ }
+ 
+ /* Returns nonzero if an exception of type FROM will be caught by a
+--- gcc-4.8.5/libgcc/config/i386/linux-unwind.h.orig	2013-02-04 20:06:20.000000000 +0100
+++ gcc-4.8.5/libgcc/config/i386/linux-unwind.h	2018-07-27 12:51:18.305390871 +0200
+@@ -58,7 +58,7 @@
+   if (*(unsigned char *)(pc+0) == 0x48
+       && *(unsigned long long *)(pc+1) == RT_SIGRETURN_SYSCALL)
+     {
+-      struct ucontext *uc_ = context->cfa;
+      ucontext_t *uc_ = context->cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+          because it does not alias anything.  */
+@@ -138,7 +138,7 @@
+ 	siginfo_t *pinfo;
+ 	void *puc;
+ 	siginfo_t info;
+-	struct ucontext uc;
+	ucontext_t uc;
+       } *rt_ = context->cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+--- gcc-4.8.5/libsanitizer/asan/asan_linux.cc.orig	2013-01-23 12:41:33.000000000 +0100
+++ gcc-4.8.5/libsanitizer/asan/asan_linux.cc	2018-07-27 12:51:45.641390381 +0200
+@@ -25,6 +25,7 @@
+ #include <sys/types.h>
+ #include <fcntl.h>
+ #include <pthread.h>
+#include <signal.h>
+ #include <stdio.h>
+ #include <unistd.h>
+ #include <unwind.h>
+--- gcc-4.8.5/libsanitizer/tsan/tsan_platform_linux.cc.orig	2013-02-21 11:57:10.000000000 +0100
+++ gcc-4.8.5/libsanitizer/tsan/tsan_platform_linux.cc	2018-07-27 13:17:32.417362682 +0200
+@@ -292,7 +292,7 @@
+ #ifndef TSAN_GO
+ int ExtractResolvFDs(void *state, int *fds, int nfd) {
+   int cnt = 0;
+-  __res_state *statp = (__res_state*)state;
+  struct __res_state *statp = (struct __res_state*)state;
+   for (int i = 0; i < MAXNS && cnt < nfd; i++) {
+     if (statp->_u._ext.nsaddrs[i] && statp->_u._ext.nssocks[i] != -1)
+       fds[cnt++] = statp->_u._ext.nssocks[i];
--- a/etc/patches/gcc-4.9.4-with-gcc-7
+++ b/etc/patches/gcc-4.9.4-with-gcc-7
@ -0,0 +1,87 @@
+#
+# Patch for building older gcc versions with gcc-7
+#
+--- gcc-4.9.4/libgcc/config/i386/linux-unwind.h.orig	2014-01-02 23:25:22.000000000 +0100
+++ gcc-4.9.4/libgcc/config/i386/linux-unwind.h	2018-07-27 10:43:46.021527909 +0200
+@@ -58,7 +58,7 @@
+   if (*(unsigned char *)(pc+0) == 0x48
+       && *(unsigned long long *)(pc+1) == RT_SIGRETURN_SYSCALL)
+     {
+-      struct ucontext *uc_ = context->cfa;
+      ucontext_t *uc_ = context->cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+          because it does not alias anything.  */
+@@ -138,7 +138,7 @@
+ 	siginfo_t *pinfo;
+ 	void *puc;
+ 	siginfo_t info;
+-	struct ucontext uc;
+	ucontext_t uc;
+       } *rt_ = context->cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+--- gcc-4.9.4/libsanitizer/asan/asan_linux.cc.orig	2013-12-05 10:18:38.000000000 +0100
+++ gcc-4.9.4/libsanitizer/asan/asan_linux.cc	2018-07-27 11:11:52.085497715 +0200
+@@ -26,6 +26,7 @@
+ #include <sys/types.h>
+ #include <fcntl.h>
+ #include <pthread.h>
+#include <signal.h>
+ #include <stdio.h>
+ #include <unistd.h>
+ #include <unwind.h>
+--- gcc-4.9.4/libsanitizer/sanitizer_common/sanitizer_linux.cc.orig	2013-12-05 10:18:38.000000000 +0100
+++ gcc-4.9.4/libsanitizer/sanitizer_common/sanitizer_linux.cc	2018-07-27 10:43:02.405528690 +0200
+@@ -599,8 +599,7 @@
+   return internal_syscall(__NR_prctl, option, arg2, arg3, arg4, arg5);
+ }
+ 
+-uptr internal_sigaltstack(const struct sigaltstack *ss,
+-                         struct sigaltstack *oss) {
+uptr internal_sigaltstack(const void *ss, void *oss) {
+   return internal_syscall(__NR_sigaltstack, (uptr)ss, (uptr)oss);
+ }
+ 
+--- gcc-4.9.4/libsanitizer/sanitizer_common/sanitizer_linux.h.orig	2013-12-05 10:18:38.000000000 +0100
+++ gcc-4.9.4/libsanitizer/sanitizer_common/sanitizer_linux.h	2018-07-27 10:42:29.845529273 +0200
+@@ -18,7 +18,6 @@
+ #include "sanitizer_platform_limits_posix.h"
+ 
+ struct link_map;  // Opaque type returned by dlopen().
+-struct sigaltstack;
+ 
+ namespace __sanitizer {
+ // Dirent structure for getdents(). Note that this structure is different from
+@@ -28,8 +27,7 @@
+ // Syscall wrappers.
+ uptr internal_getdents(fd_t fd, struct linux_dirent *dirp, unsigned int count);
+ uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5);
+-uptr internal_sigaltstack(const struct sigaltstack* ss,
+-                          struct sigaltstack* oss);
+uptr internal_sigaltstack(const void* ss, void* oss);
+ uptr internal_sigaction(int signum, const __sanitizer_kernel_sigaction_t *act,
+     __sanitizer_kernel_sigaction_t *oldact);
+ uptr internal_sigprocmask(int how, __sanitizer_kernel_sigset_t *set,
+--- gcc-4.9.4/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc.orig	2013-12-05 11:28:59.000000000 +0100
+++ gcc-4.9.4/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc	2018-07-27 10:41:32.053530308 +0200
+@@ -238,7 +238,7 @@
+ 
+   // Alternate stack for signal handling.
+   InternalScopedBuffer<char> handler_stack_memory(kHandlerStackSize);
+-  struct sigaltstack handler_stack;
+  stack_t handler_stack;
+   internal_memset(&handler_stack, 0, sizeof(handler_stack));
+   handler_stack.ss_sp = handler_stack_memory.data();
+   handler_stack.ss_size = kHandlerStackSize;
+--- gcc-4.9.4/libsanitizer/tsan/tsan_platform_linux.cc.orig	2013-12-05 10:18:38.000000000 +0100
+++ gcc-4.9.4/libsanitizer/tsan/tsan_platform_linux.cc	2018-07-27 10:40:13.781531710 +0200
+@@ -351,7 +351,7 @@
+ // closes within glibc. The code is a pure hack.
+ int ExtractResolvFDs(void *state, int *fds, int nfd) {
+   int cnt = 0;
+-  __res_state *statp = (__res_state*)state;
+  struct __res_state *statp = (struct __res_state*)state;
+   for (int i = 0; i < MAXNS && cnt < nfd; i++) {
+     if (statp->_u._ext.nsaddrs[i] && statp->_u._ext.nssocks[i] != -1)
+       fds[cnt++] = statp->_u._ext.nssocks[i];
--- a/etc/patches/gcc-6.3.0-with-gcc-7
+++ b/etc/patches/gcc-6.3.0-with-gcc-7
@ -0,0 +1,82 @@
+#
+# Patch for building older gcc versions with gcc-7
+#
+diff -u gcc-6.3.0/libgcc/config/i386/linux-unwind.h.orig gcc-6.3.0/libgcc/config/i386/linux-unwind.h
+--- gcc-6.3.0/libgcc/config/i386/linux-unwind.h.orig 2016-01-04 23:30:50.000000000 +0900
+++ gcc-6.3.0/libgcc/config/i386/linux-unwind.h 2017-10-29 23:01:21.717240052 +0900
+@@ -58,7 +58,7 @@
+   if (*(unsigned char *)(pc+0) == 0x48
+       &amp;&amp; *(unsigned long long *)(pc+1) == RT_SIGRETURN_SYSCALL)
+     {
+-      struct ucontext *uc_ = context-&gt;cfa;
+      ucontext_t *uc_ = context-&gt;cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+          because it does not alias anything.  */
+@@ -138,7 +138,7 @@
+  siginfo_t *pinfo;
+  void *puc;
+  siginfo_t info;
+- struct ucontext uc;
+ ucontext_t uc;
+       } *rt_ = context-&gt;cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+diff -u gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_linux.cc.orig gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_linux.cc
+--- gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_linux.cc.orig 2015-11-23 18:07:18.000000000 +0900
+++ gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_linux.cc 2017-10-29 23:09:00.490577558 +0900
+@@ -546,8 +546,7 @@
+ }
+ #endif
+
+-uptr internal_sigaltstack(const struct sigaltstack *ss,
+-                         struct sigaltstack *oss) {
+uptr internal_sigaltstack(const void *ss, void *oss) {
+   return internal_syscall(SYSCALL(sigaltstack), (uptr)ss, (uptr)oss);
+ }
+
+diff -u gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_linux.h.orig gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_linux.h
+--- gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_linux.h.orig 2015-10-21 16:32:45.000000000 +0900
+++ gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_linux.h 2017-10-29 23:09:43.907244619 +0900
+@@ -19,7 +19,6 @@
+ #include "sanitizer_platform_limits_posix.h"
+
+ struct link_map;  // Opaque type returned by dlopen().
+-struct sigaltstack;
+
+ namespace __sanitizer {
+ // Dirent structure for getdents(). Note that this structure is different from
+@@ -28,8 +27,7 @@
+
+ // Syscall wrappers.
+ uptr internal_getdents(fd_t fd, struct linux_dirent *dirp, unsigned int count);
+-uptr internal_sigaltstack(const struct sigaltstack* ss,
+-                          struct sigaltstack* oss);
+uptr internal_sigaltstack(const void* ss, void* oss);
+ uptr internal_sigprocmask(int how, __sanitizer_sigset_t *set,
+     __sanitizer_sigset_t *oldset);
+ void internal_sigfillset(__sanitizer_sigset_t *set);
+diff -u gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc.orig gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
+--- gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc.orig 2015-10-21 16:32:45.000000000 +0900
+++ gcc-6.3.0/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc 2017-10-29 23:08:07.260577074 +0900
+@@ -267,7 +267,7 @@
+
+   // Alternate stack for signal handling.
+   InternalScopedBuffer&lt;char&gt; handler_stack_memory(kHandlerStackSize);
+-  struct sigaltstack handler_stack;
+  stack_t handler_stack;
+   internal_memset(&amp;handler_stack, 0, sizeof(handler_stack));
+   handler_stack.ss_sp = handler_stack_memory.data();
+   handler_stack.ss_size = kHandlerStackSize;
+diff -u gcc-6.3.0/libsanitizer/tsan/tsan_platform_linux.cc.orig gcc-6.3.0/libsanitizer/tsan/tsan_platform_linux.cc
+--- gcc-6.3.0/libsanitizer/tsan/tsan_platform_linux.cc.orig 2016-08-12 17:53:46.000000000 +0900
+++ gcc-6.3.0/libsanitizer/tsan/tsan_platform_linux.cc 2017-10-29 23:10:38.817245120 +0900
+@@ -291,7 +291,7 @@
+ int ExtractResolvFDs(void *state, int *fds, int nfd) {
+ #if SANITIZER_LINUX
+   int cnt = 0;
+-  __res_state *statp = (__res_state*)state;
+  struct __res_state *statp = (struct __res_state*)state;
+   for (int i = 0; i &lt; MAXNS &amp;&amp; cnt &lt; nfd; i++) {
+     if (statp-&gt;_u._ext.nsaddrs[i] &amp;&amp; statp-&gt;_u._ext.nssocks[i] != -1)
+       fds[cnt++] = statp-&gt;_u._ext.nssocks[i];
--- a/etc/patches/paraview-5.5.2
+++ b/etc/patches/paraview-5.5.2
@ -1,3 +1,128 @@
+--- ParaView-git/CMake/ParaViewMacros.cmake.orig	2018-07-22 17:38:33.933614131 +0200
+++ ParaView-git/CMake/ParaViewMacros.cmake	2018-07-22 17:42:12.457612519 +0200
+@@ -353,8 +353,9 @@
+     set(qt_binary_dir_hints "${Qt5_DIR}/../../../bin")
+   endif()
+ 
+  # The qhelpgenerator program may be installed as qhelpgenerator-qt5
+   find_program(QT_HELP_GENERATOR
+-    qhelpgenerator
+    NAMES qhelpgenerator qhelpgenerator-qt5
+     HINTS "${qt_binary_dir_hints}"
+     DOC "qhelpgenerator used to compile Qt help project files")
+   mark_as_advanced(QT_HELP_GENERATOR)
+--- ParaView-v5.5.2/VTK/ThirdParty/hdf5/vtkhdf5/src/H5detect.c.orig	2018-06-15 21:09:45.000000000 +0200
+++ ParaView-v5.5.2/VTK/ThirdParty/hdf5/vtkhdf5/src/H5detect.c	2018-07-07 13:20:40.641815285 +0200
+@@ -1360,8 +1360,8 @@
+  *
+  *-------------------------------------------------------------------------
+  */
+-static void
+-detect_C89_integers(void) HDF_NO_UBSAN
+static void HDF_NO_UBSAN
+detect_C89_integers(void)
+ {
+     DETECT_BYTE(signed char,	  SCHAR,        d_g[nd_g]); nd_g++;
+     DETECT_BYTE(unsigned char,	  UCHAR,        d_g[nd_g]); nd_g++;
+@@ -1388,8 +1388,8 @@
+  *
+  *-------------------------------------------------------------------------
+  */
+-static void
+-detect_C89_floats(void) HDF_NO_UBSAN
+static void HDF_NO_UBSAN
+detect_C89_floats(void)
+ {
+     DETECT_F(float,     FLOAT,      d_g[nd_g]); nd_g++;
+     DETECT_F(double,    DOUBLE,     d_g[nd_g]); nd_g++;
+@@ -1410,8 +1410,8 @@
+  *
+  *-------------------------------------------------------------------------
+  */
+-static void
+-detect_C99_integers8(void) HDF_NO_UBSAN
+static void HDF_NO_UBSAN
+detect_C99_integers8(void)
+ {
+ #if H5_SIZEOF_INT8_T>0
+   #if H5_SIZEOF_INT8_T==1
+@@ -1472,8 +1472,8 @@
+  *
+  *-------------------------------------------------------------------------
+  */
+-static void
+-detect_C99_integers16(void) HDF_NO_UBSAN
+static void HDF_NO_UBSAN
+detect_C99_integers16(void)
+ {
+ #if H5_SIZEOF_INT16_T>0
+     DETECT_I(int16_t, 		  INT16,        d_g[nd_g]); nd_g++;
+@@ -1510,8 +1510,8 @@
+  *
+  *-------------------------------------------------------------------------
+  */
+-static void
+-detect_C99_integers32(void) HDF_NO_UBSAN
+static void HDF_NO_UBSAN
+detect_C99_integers32(void)
+ {
+ #if H5_SIZEOF_INT32_T>0
+     DETECT_I(int32_t, 		  INT32,        d_g[nd_g]); nd_g++;
+@@ -1548,8 +1548,8 @@
+  *
+  *-------------------------------------------------------------------------
+  */
+-static void
+-detect_C99_integers64(void) HDF_NO_UBSAN
+static void HDF_NO_UBSAN
+detect_C99_integers64(void)
+ {
+ #if H5_SIZEOF_INT64_T>0
+     DETECT_I(int64_t, 		  INT64,        d_g[nd_g]); nd_g++;
+@@ -1599,8 +1599,8 @@
+  *
+  *-------------------------------------------------------------------------
+  */
+-static void
+-detect_C99_integers(void) HDF_NO_UBSAN
+static void HDF_NO_UBSAN
+detect_C99_integers(void)
+ {
+     /* break it down to more subroutines so that each module subroutine */
+     /* is smaller and takes less time to compile with optimization on.  */
+@@ -1625,8 +1625,8 @@
+  *
+  *-------------------------------------------------------------------------
+  */
+-static void
+-detect_C99_floats(void) HDF_NO_UBSAN
+static void HDF_NO_UBSAN
+detect_C99_floats(void)
+ {
+ #if H5_SIZEOF_DOUBLE == H5_SIZEOF_LONG_DOUBLE
+     /*
+@@ -1656,8 +1656,8 @@
+  *
+  *-------------------------------------------------------------------------
+  */
+-static void
+-detect_alignments(void) HDF_NO_UBSAN
+static void HDF_NO_UBSAN
+detect_alignments(void)
+ {
+     /* Detect structure alignment for pointers, hvl_t, hobj_ref_t, hdset_reg_ref_t */
+     DETECT_M(void *,              POINTER,      m_g[na_g]); na_g++;
+@@ -1744,8 +1744,8 @@
+  *
+  *-------------------------------------------------------------------------
+  */
+-int
+-main(void) HDF_NO_UBSAN
+int HDF_NO_UBSAN
+main(void)
+ {
+ 
+ #if defined(H5_HAVE_SETSYSINFO) && defined(SSI_NVPAIRS)
 --- ParaView-v5.5.0/VTK/ThirdParty/vtkm/vtk-m/CMake/VTKmDetermineVersion.cmake.orig	2018-04-06 22:03:33.000000000 +0200
 +++ ParaView-v5.5.0/VTK/ThirdParty/vtkm/vtk-m/CMake/VTKmDetermineVersion.cmake	2018-04-23 12:00:23.708544206 +0200
@@ -51,6 +51,8 @@
--- a/etc/tools/ParaViewFunctions
+++ b/etc/tools/ParaViewFunctions
@ -137,7 +137,7 @@ addVerbosity()


 #
-# Define options for mpi support
+# MPI support for PARAVIEW
 #
 addMpiSupport()
 {
@ -146,7 +146,7 @@ addMpiSupport()
        return
    fi

-    addCMakeVariable "PARAVIEW_USE_MPI=ON" "VTK_USE_MPI=ON"
+    addCMakeVariable "PARAVIEW_USE_MPI=ON"
    if [ "${MPI_MAX_PROCS:=0}" -gt 1 ]
    then
        addCMakeVariable "VTK_MPI_MAX_NUMPROCS=$MPI_MAX_PROCS"
@ -467,11 +467,13 @@ You may need to update the OpenFOAM environment by running:
 INFO

    # Non-system installation of QT?
-    if [ "$qmake" != /usr/bin/qmake -a -d "$qtLib" ]
+    case "$qtLib" in (/usr/lib | /usr/lib64) unset qtLib ;; esac
+
+    if [ "${qmake%/*}" != /usr/bin -a -d "$qtLib" ]
    then
        /bin/cat<<INFO

-And adjust your LD_LIBRARY_PATH to include the following:
+Your LD_LIBRARY_PATH may require adjustment to include the following:
    $qtLib
 INFO
    fi
--- a/etc/tools/ThirdPartyFunctions
+++ b/etc/tools/ThirdPartyFunctions
@ -20,9 +20,12 @@
 #------------------------------------------------------------------------------

 # The normal locations for source, build and installation (prefix-dir)
-sourceBASE=$WM_THIRD_PARTY_DIR
-buildBASE=$WM_THIRD_PARTY_DIR/build/$WM_ARCH$WM_COMPILER
-installBASE=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER
+sourceBASE="$WM_THIRD_PARTY_DIR"
+buildBASE="$WM_THIRD_PARTY_DIR/build/$WM_ARCH$WM_COMPILER"
+installBASE="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER"
+
+# Synthetic value combining precision and label size (Eg, DPInt32)
+WM_SIZE_OPTIONS="${WM_PRECISION_OPTION}Int${WM_LABEL_SIZE}"

 # Dynamic library endings (default is .so)
 [ "$(uname -s)" = Darwin ] && SO=dylib || SO=so
@ -64,7 +67,7 @@ exportLinker()
 # Force use of gcc/g++
 useGcc()
 {
-    export CC=gcc    # Use gcc/g++
+    export CC=gcc
    export CXX=g++
 }

@ -89,38 +92,59 @@ whichMpicc()
    local mpicc=$(command -v mpicc)
    case "$WM_MPLIB" in
    (INTELMPI)
-        mpicc=$(command -v mpiicc)  # Intel <mpiicc> available?
+        mpicc=$(command -v mpiicc)      # Intel <mpiicc> available?
        ;;
    (CRAY-MPI*)
-        : ${mpicc:=cc}              # Cray <cc> if there is no <mpicc>
+        : ${mpicc:=cc}                  # Cray <cc> if there is no <mpicc>
        ;;
    esac
    echo "${mpicc:-mpicc}"
 }

-# The presence of wmkdep etc required for building with wmake
+
+# Return <mpicc> by default or <mpiicc> if possible for INTELMPI.
+# Cray doesn't have <mpicc>, but its <cc> manages mpi paths directly.
+# NOTE: could further refine based on $CC or $WM_CC, but not yet needed
+whichMpicxx()
+{
+    local mpicxx=$(command -v mpicxx)
+    case "$WM_MPLIB" in
+    (INTELMPI)
+        mpicxx=$(command -v mpiicpc)    # Intel <mpiicpc> available?
+        ;;
+    (CRAY-MPI*)
+        : ${mpicxx:=CC}                 # Cray <CC> if there is no <mpicc>
+        ;;
+    esac
+    echo "${mpicxx:-mpicxx}"
+}
+
+# Require wmkdepend etc when building with wmake
 requireWMakeToolchain()
 {
-    local dir="${WM_DIR:-$WM_PROJECT_DIR/wmake}"
-    local src="$dir/src"
-    local bin="$dir/platforms/$WM_ARCH$WM_COMPILER/wmkdep"
+    local wmDir="${WM_DIR:-$WM_PROJECT_DIR/wmake}"
+    local archDir="$wmDir/platforms/$WM_ARCH$WM_COMPILER"

-    test -x $bin || {
-        echo "Warning: the 'wmkdep' binary is missing - attempting to build it"
-        ( cd $src && make -s )
-    }
+    if [ -x "$archDir/wmkdepend" ] || [ -x "$archDir/wmkdep" ]
+    then
+        echo "Appear to have {wmkdepend,wmkdep} binary" 1>&2
+    else
+        echo "Warning: appear to be missing {wmkdepend,wmkdep} binary ... building" 1>&2
+        ( cd "$wmDir/src" && make -s )

-    test -x $bin || {
-        exec 1>&2
-        echo
-        echo "Error: cannot use wmake build for '${0##*/}"
-        echo "    The 'wmkdep' binary is missing"
-        echo "    Please run the top-level OpenFOAM Allwmake first"
-        echo
-        exit 1
-    }
+        [ -x "$archDir/wmkdepend" ] || [ -x "$archDir/wmkdep" ] || {
+            exec 1>&2
+            echo
+            echo "Error: cannot use wmake build for '${0##*/}"
+            echo "    Missing {wmkdepend,wmkdep} binary"
+            echo "    Please try run the top-level OpenFOAM Allwmake first"
+            echo
+            exit 1
+        }
+    fi
 }

+
 #------------------------------------------------------------------------------
 # Some functions as per OpenFOAM etc/config.sh/functions

@ -143,6 +167,9 @@ fi
 # Source an etc/config.sh file
 _foamConfig() { eval "$($WM_PROJECT_DIR/bin/foamEtcFile -sh -config $@)"; }

+# Source an etc file (as per OpenFOAM functions). Eg, for mpi setup.
+_foamEtc() { eval "$($WM_PROJECT_DIR/bin/foamEtcFile -sh $@)"; }
+
 #------------------------------------------------------------------------------

 #
@ -168,9 +195,7 @@ setBuildSuffix()
 #
 unset WM_HOSTS WM_SCHEDULER

-WM_NCOMPPROCS=$(egrep -c "^processor" /proc/cpuinfo 2>/dev/null) || \
-WM_NCOMPPROCS=$(getconf _NPROCESSORS_ONLN 2>/dev/null) || \
-WM_NCOMPPROCS=1
+WM_NCOMPPROCS=$(getconf _NPROCESSORS_ONLN 2>/dev/null) || WM_NCOMPPROCS=1
 : ${WM_NCOMPPROCS:=1}
 export WM_NCOMPPROCS

--- a/etc/tools/vtkFunctions
+++ b/etc/tools/vtkFunctions
@ -2,7 +2,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
-#   \\  /    A nd           | Copyright (C) 2016-2017 OpenCFD Ltd.
+#   \\  /    A nd           | Copyright (C) 2016-2018 OpenCFD Ltd.
 #    \\/     M anipulation  |
 #------------------------------------------------------------------------------
 # License
@ -148,6 +148,28 @@ configVTK()
 }


+#
+# MPI support for VTK
+#
+unset -f addMpiSupport 2>/dev/null
+addMpiSupport()
+{
+    if [ "${withMPI:=false}" != true ]
+    then
+        return
+    fi
+
+    addCMakeVariable "VTK_Group_MPI=ON"
+    addCMakeVariable "Module_vtkRenderingParallel=ON"
+    addCMakeVariable "Module_vtkParallelMPI=ON"
+
+    if [ "${MPI_MAX_PROCS:=0}" -gt 1 ]
+    then
+        addCMakeVariable "VTK_MPI_MAX_NUMPROCS=$MPI_MAX_PROCS"
+    fi
+}
+
+
 #
 # Invoke make
 # also link bin/ to lib/paraview-* for development without installation
--- a/4
+++ b/4
@ -41,8 +41,8 @@ usage() {

 usage: ${0##*/} [OPTION] [adios-VERSION] [-- configure-options]
 options:
-  -cmake PATH       With cmake from the path given
-  -gcc              Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
+  -cmake PATH   With cmake from the path given
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
  -help

 * Build ADIOS
--- a/4
+++ b/4
@ -39,8 +39,8 @@ usage() {

 usage: ${0##*/} [OPTION] [adios-VERSION]
 options:
-  -cmake PATH       With cmake from the path given
-  -gcc              Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
+  -cmake PATH   With cmake from the path given
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
  -help

 * Build ADIOS2
--- a/2
+++ b/2
@ -51,7 +51,7 @@ usage()

 Usage: ${0##*/} [OPTION] [lib|libso] [libccmio-VERSION]
 options:
-  -gcc              Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
  -help

 * Compile the proprietary libccmio library
--- a/1
+++ b/1
@ -534,6 +534,7 @@ CMAKE_OPTIONS
        -DCMAKE_INSTALL_PREFIX=$CGAL_ARCH_PATH \
        -DCGAL_INSTALL_LIB_DIR=lib$WM_COMPILER_LIB_ARCH \
        -DCMAKE_BUILD_TYPE=Release \
+        -DWITH_CGAL_Core=OFF \
        -DWITH_CGAL_ImageIO=OFF \
        -DWITH_CGAL_Qt5=OFF \
        ${optHeadersOnly:+-DCGAL_HEADER_ONLY=TRUE} \
--- a/4
+++ b/4
@ -42,8 +42,8 @@ usage() {

 usage: ${0##*/} [OPTION] cmake-VERSION
 options:
-  -gcc              Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
-  -link             Create additional symlink as 'cmake-system'
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
+  -link         Create additional symlink as 'cmake-system'
  -help

 * build cmake
--- a/2
+++ b/2
@ -59,7 +59,7 @@ usage() {

 usage: ${0##*/} [OPTION] [fftw-VERSION] [-- configure-options]
 options:
-  -gcc              Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
  -help

 * build FFTW with
--- a/7
+++ b/7
@ -60,6 +60,7 @@ usage() {

 usage: ${0##*/} [OPTION] [gcc-VERSION] [gmp-VERSION] [mpfr-VERSION] [mpc-VERSION]
 options:
+  -clang            Force clang/clang++ for building
  -multilib         for 64-bit systems with 32-bit support required
  -no-multilib      for 64-bit systems without 32-bit support (DEFAULT)
  -no-threadsafe    disable mpfr thread-safe (default is auto-detect)
@ -86,6 +87,10 @@ do
    case "$1" in
    '') ;;      # Ignore empty
    -h | -help) usage   ;;
+    -clang)     # Force use of clang/clang++ for building
+        export CC=clang
+        export CXX=clang++
+        ;;

    -multi*)
        optMultilib=enable
@ -133,6 +138,8 @@ GCC configuration
    MPFR    = $mpfrPACKAGE
    MPC     = $mpcPACKAGE
 ------------------
+Using CC    = $CC $CFLAGS
+Using CXX   = $CXX $CXXFLAGS
 SUMMARY

 # Set 32 or 64 bit ABI
--- a/2
+++ b/2
@ -41,7 +41,7 @@ usage() {

 usage: ${0##*/} [gperftools-VERSION]
 options:
-  -gcc              Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
  -help

 * build gperftools
--- a/172
+++ b/172
@ -0,0 +1,172 @@
+#!/bin/sh
+#------------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2018 OpenCFD Ltd.
+#    \\/     M anipulation  |
+#------------------------------------------------------------------------------
+# License
+#     This file is part of OpenFOAM, licensed under GNU General Public License
+#     <http://www.gnu.org/licenses/>.
+#
+# Script
+#     makeHYPRE
+#
+# Description
+#     Build script for HYPRE
+#
+# ----------------------------------------------
+# NO USER-CONFIGURABLE SETTINGS WITHIN THIS FILE
+#------------------------------------------------------------------------------
+# Dynamic library endings (default is .so)
+[ "$(uname -s)" = Darwin ] && SO=dylib || SO=so
+
+# Short-circuit test for an installation
+if [ "$1" = "-test" ]
+then
+    [ "$#" -eq 2 ] || { echo "${0##*/} -test : needs 1 argument"; exit 1; }
+    dir="$2" # <- HYPRE_ARCH_PATH
+    if [ -d "$dir/include" ]
+    then
+        for lib in \
+            $FOAM_EXT_LIBBIN/libhypre.$SO \
+            $dir/lib/libhypre.a \
+            $dir/lib/libhypre.$SO \
+            $dir/lib$WM_COMPILER_LIB_ARCH/libhypre.a \
+            $dir/lib$WM_COMPILER_LIB_ARCH/libhypre.$SO \
+            ;
+        do
+            if [ -r "$lib" ]
+            then
+                echo "    hypre include: $dir/include"
+                echo "    hypre library: ${lib%/*}"
+                exit 0
+            fi
+        done
+    fi
+    exit 2
+fi
+#------------------------------------------------------------------------------
+# Run from third-party directory only
+cd ${0%/*} && wmakeCheckPwd "$WM_THIRD_PARTY_DIR" 2>/dev/null || {
+    echo "Error (${0##*/}) : not located in \$WM_THIRD_PARTY_DIR"
+    echo "    Check your OpenFOAM environment and installation"
+    exit 1
+}
+[ -n "$FOAM_EXT_LIBBIN" ] || {
+    echo "Error (${0##*/}) : \$FOAM_EXT_LIBBIN not set"
+    echo "    Check your OpenFOAM environment and installation"
+    exit 1
+}
+. etc/tools/ThirdPartyFunctions
+#------------------------------------------------------------------------------
+_foamConfig hypre
+
+hyprePACKAGE=${hypre_version:-hypre-system}
+targetType=libso
+
+#------------------------------------------------------------------------------
+usage() {
+    exec 1>&2
+    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
+    cat<<USAGE
+
+usage: ${0##*/} [OPTION] [lib|libso] [HYPRE-VERSION]
+options:
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
+  -help
+
+* build HYPRE with
+      ${hyprePACKAGE:-'unspecified hypre version'}
+
+USAGE
+    exit 1
+}
+#------------------------------------------------------------------------------
+exportCompiler          # Compiler info for CMake/configure
+
+# Parse options
+while [ "$#" -gt 0 ]
+do
+    case "$1" in
+    '') ;;      # Ignore empty
+    -h | -help) usage   ;;
+    -gcc)       useGcc  ;;
+
+    lib|libso)
+        targetType="$1"
+        ;;
+
+    hypre-[0-9]*)
+        hyprePACKAGE="${1%%/}"
+        unset HYPRE_ARCH_PATH  # Avoid inconsistency
+        ;;
+    *)
+        die "unknown option/argument: '$1'"
+        ;;
+    esac
+    shift
+done
+
+[ -n "$hyprePACKAGE" ] || die "The hypre-VERSION was not specified"
+
+# Nothing to build
+if _foamIsNone $hyprePACKAGE
+then
+    echo "Using hypre-none (skip ThirdParty build of HYPRE)"
+    exit 0
+elif _foamIsSystem $hyprePACKAGE
+then
+    echo "Using hypre-system"
+    exit 0
+fi
+
+#------------------------------------------------------------------------------
+#
+# Build HYPRE
+#
+#   HYPRE_ARCH_PATH  : installation directory
+#   HYPRE_SOURCE_DIR : location of the original sources
+
+HYPRE_SOURCE_DIR=$sourceBASE/$hyprePACKAGE
+: ${HYPRE_ARCH_PATH:=$installBASE$WM_SIZE_OPTIONS/$hyprePACKAGE}
+
+[ -d "$HYPRE_SOURCE_DIR" ] || {
+    echo "Missing sources: '$hyprePACKAGE'"
+    exit 1
+}
+
+
+# Compilers
+CC="$(whichMpicc)"
+CXX="$(whichMpicxx)"
+
+echo "Starting build: $hyprePACKAGE ($targetType)"
+echo
+(
+    # Configuration options:
+    unset configOpt
+
+    cd $HYPRE_SOURCE_DIR/src || exit 1
+    export GIT_DIR=$PWD/.git # Mask seeing our own git-repo
+
+    rm -rf $HYPRE_ARCH_PATH
+    [ -e Makefile ] && make distclean 2>/dev/null
+
+    ./configure \
+       --prefix=$HYPRE_ARCH_PATH \
+       --disable-fortran \
+       --enable-shared \
+       $configOpt \
+    && make -j $WM_NCOMPPROCS \
+    && echo "Built: hypre" \
+    && make install \
+    && echo "Installed: hypre"
+) || {
+    echo "Error building: hypre"
+    exit 1
+}
+
+
+#------------------------------------------------------------------------------
--- a/2
+++ b/2
@ -75,7 +75,7 @@ usage()

 Usage: ${0##*/} [OPTION] [lib|libso] [kahip-VERSION]
 options:
-  -gcc              Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
  -help

 * Compile KaHIP
--- a/4
+++ b/4
@ -74,7 +74,7 @@ usage() {

 usage: ${0##*/} [OPTION] [lib|libso] [METIS-VERSION]
 options:
-  -gcc              Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
  -help

 * build METIS with
@ -130,7 +130,7 @@ fi
 #   METIS_SOURCE_DIR : location of the original sources

 METIS_SOURCE_DIR=$sourceBASE/$metisPACKAGE
-: ${METIS_ARCH_PATH:=$installBASE$WM_PRECISION_OPTION$WM_LABEL_OPTION/$metisPACKAGE}
+: ${METIS_ARCH_PATH:=$installBASE$WM_SIZE_OPTIONS/$metisPACKAGE}

 [ -d "$METIS_SOURCE_DIR" ] || {
    echo "Missing sources: '$metisPACKAGE'"
--- a/4
+++ b/4
@ -42,7 +42,7 @@ usage() {

 usage: ${0##*/} [OPTION] [mgridgen-VERSION]
 options:
-  -gcc              Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
  -help

 * Build MGridGen
@ -96,7 +96,7 @@ fi
 #   MGRIDGEN_ARCH_PATH  : installation directory

 MGRIDGEN_SOURCE_DIR=$WM_THIRD_PARTY_DIR/$mgridgenPACKAGE
-MGRIDGEN_ARCH_PATH=$installBASE$WM_PRECISION_OPTION$WM_LABEL_OPTION/$mgridgenPACKAGE
+MGRIDGEN_ARCH_PATH=$installBASE$WM_SIZE_OPTIONS/$mgridgenPACKAGE

 : ${FOAM_MPI:=dummy}

--- a/2
+++ b/2
@ -49,7 +49,7 @@ usage() {

 usage: ${0##*/} [OPTION] mesa-VERSION [-- configure-options]
 options:
-  -gcc              Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
  -help

 * build Mesa with
--- a/2
+++ b/2
@ -70,7 +70,7 @@ usage() {

 usage: ${0##*/} [OPTION] [openmpi-VERSION] [-- configure-options]
 options:
-  -gcc          Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
  -memcheck     Configure with --enable-memcheck (requires valgrind.h)
  -threaded     Configure with --enable-mpi-thread-multiple
  -no-threaded  Configure with --disable-mpi-thread-multiple
--- a/194
+++ b/194
@ -0,0 +1,194 @@
+#!/bin/sh
+#------------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2018 OpenCFD Ltd.
+#    \\/     M anipulation  |
+#------------------------------------------------------------------------------
+# License
+#     This file is part of OpenFOAM, licensed under GNU General Public License
+#     <http://www.gnu.org/licenses/>.
+#
+# Script
+#     makePETSC
+#
+# Description
+#     Build script for PETSC
+#
+# ----------------------------------------------
+# NO USER-CONFIGURABLE SETTINGS WITHIN THIS FILE
+#------------------------------------------------------------------------------
+# Dynamic library endings (default is .so)
+[ "$(uname -s)" = Darwin ] && SO=dylib || SO=so
+
+# Short-circuit test for an installation
+if [ "$1" = "-test" ]
+then
+    [ "$#" -eq 2 ] || { echo "${0##*/} -test : needs 1 argument"; exit 1; }
+    dir="$2" # <- PETSC_ARCH_PATH
+    if [ -d "$dir/include" ]
+    then
+        for lib in \
+            $FOAM_EXT_LIBBIN/libpetsc.$SO \
+            $dir/lib/libpetsc.a \
+            $dir/lib/libpetsc.$SO \
+            $dir/lib$WM_COMPILER_LIB_ARCH/libpetsc.a \
+            $dir/lib$WM_COMPILER_LIB_ARCH/libpetsc.$SO \
+            ;
+        do
+            if [ -r "$lib" ]
+            then
+                echo "    petsc include: $dir/include"
+                echo "    petsc library: ${lib%/*}"
+                exit 0
+            fi
+        done
+    fi
+    exit 2
+fi
+#------------------------------------------------------------------------------
+# Run from third-party directory only
+cd ${0%/*} && wmakeCheckPwd "$WM_THIRD_PARTY_DIR" 2>/dev/null || {
+    echo "Error (${0##*/}) : not located in \$WM_THIRD_PARTY_DIR"
+    echo "    Check your OpenFOAM environment and installation"
+    exit 1
+}
+[ -n "$FOAM_EXT_LIBBIN" ] || {
+    echo "Error (${0##*/}) : \$FOAM_EXT_LIBBIN not set"
+    echo "    Check your OpenFOAM environment and installation"
+    exit 1
+}
+. etc/tools/ThirdPartyFunctions
+#------------------------------------------------------------------------------
+_foamConfig petsc
+
+petscPACKAGE=${petsc_version:-petsc-system}
+targetType=libso
+
+#------------------------------------------------------------------------------
+usage() {
+    exec 1>&2
+    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
+    cat<<USAGE
+
+usage: ${0##*/} [OPTION] [lib|libso] [PETSC-VERSION]
+options:
+  -gcc          Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
+  -help
+
+* build PETSC with
+      ${petscPACKAGE:-'unspecified petsc version'}
+
+USAGE
+    exit 1
+}
+#------------------------------------------------------------------------------
+exportCompiler          # Compiler info for CMake/configure
+
+# Parse options
+while [ "$#" -gt 0 ]
+do
+    case "$1" in
+    '') ;;      # Ignore empty
+    -h | -help) usage   ;;
+    -gcc)       useGcc  ;;
+
+    lib|libso)
+        targetType="$1"
+        ;;
+
+    petsc-[0-9]*)
+        petscPACKAGE="${1%%/}"
+        unset PETSC_ARCH_PATH  # Avoid inconsistency
+        ;;
+    *)
+        die "unknown option/argument: '$1'"
+        ;;
+    esac
+    shift
+done
+
+[ -n "$petscPACKAGE" ] || die "The petsc-VERSION was not specified"
+
+# Nothing to build
+if _foamIsNone $petscPACKAGE
+then
+    echo "Using petsc-none (skip ThirdParty build of PETSC)"
+    exit 0
+elif _foamIsSystem $petscPACKAGE
+then
+    echo "Using petsc-system"
+    exit 0
+fi
+
+#------------------------------------------------------------------------------
+#
+# Build PETSC
+#
+#   PETSC_ARCH_PATH  : installation directory
+#   PETSC_SOURCE_DIR : location of the original sources
+
+PETSC_SOURCE_DIR=$sourceBASE/$petscPACKAGE
+: ${PETSC_ARCH_PATH:=$installBASE$WM_SIZE_OPTIONS/$petscPACKAGE}
+
+[ -d "$PETSC_SOURCE_DIR" ] || {
+    echo "Missing sources: '$petscPACKAGE'"
+    exit 1
+}
+
+
+echo "Starting build: $petscPACKAGE ($targetType)"
+echo
+(
+    # PETSC arch - same root as WM_OPTIONS (eg, DPInt32)
+    archOpt="$WM_SIZE_OPTIONS"
+
+    # Configuration options:
+    configOpt="--with-cc=$(whichMpicc) --with-cxx=$(whichMpicxx)"
+
+    if [ "$targetType" = libso ]
+    then
+        configOpt="--with-shared-libraries"
+    fi
+
+    if [ "$WM_LABEL_SIZE" = 64 ]
+    then
+        configOpt="$configOpt --with-64-bit-indices=1"
+    else
+        configOpt="$configOpt --with-64-bit-indices=0"
+    fi
+
+    if [ "$WM_PRECISION_OPTION" = SP ]
+    then
+        configOpt="$configOpt --with-precision=single"
+    else
+        configOpt="$configOpt --with-precision=double"
+    fi
+
+    cd $PETSC_SOURCE_DIR || exit 1
+    export GIT_DIR=$PWD/.git # Mask seeing our own git-repo
+
+    rm -rf $PETSC_ARCH_PATH
+
+    ./configure \
+       --prefix=$PETSC_ARCH_PATH \
+       --with-petsc-arch=$archOpt \
+       --with-clanguage=C \
+       --with-scalapack=0 \
+       --with-superlu_dist=0 \
+       --with-suitesparse=0 \
+       --download-f2cblaslapack=1 \
+       $configOpt \
+     && echo "Configured: petsc" \
+     && make PETSC_DIR=$PETSC_SOURCE_DIR PETSC_ARCH="$archOpt" all \
+     && echo "Built: petsc" \
+     && make PETSC_DIR=$PETSC_SOURCE_DIR PETSC_ARCH="$archOpt" install
+     && echo "Installed: petsc"
+) || {
+    echo "Error building: petsc"
+    exit 1
+}
+
+
+#------------------------------------------------------------------------------
--- a/2
+++ b/2
@ -35,7 +35,7 @@ usage() {

 usage: ${0##*/} [OPTION] [qt-VERSION] [-- configure-options]
 options:
-  -gcc              Force gcc/g++ instead of the values from \$WM_CC, \$WM_CXX
+  -gcc              Force gcc/g++ instead of using \$WM_CC, \$WM_CXX
  -help

 * build $qtTYPE, version ${qtVERSION:-undefined}
--- a/2
+++ b/2
@ -71,7 +71,7 @@ options:
  -mesa-include DIR location of mesa headers (current: ${MESA_INCLUDE:-none})
  -mesa-lib PATH    path to mesa library     (current: ${MESA_LIBRARY:-none})
  -osmesa           with off-screen mesa only
-  -mpi              with mpi
+  -mpi              with mpi (VTK_Group_MPI=ON)
  -mpi=N            with max 'N' mpi processes. N=0 for no upper-limit.
  -cmake PATH       with cmake from the path given
  -verbose          verbose output in Makefiles
--- a/makeVTK.example
+++ b/makeVTK.example
@ -7,24 +7,17 @@ vtk=VTK-9.0.0
 # mesa=mesa-13.0.3
 mesa=mesa-17.1.1

-# Request building MPI modules
-# VTK_Group_MPI=ON
+# Module_vtkAcceleratorsVTKm    : Request building vtkAcceleratorsVTKm
 #
-# Request building vtkAcceleratorsVTKm
-# Module_vtkAcceleratorsVTKm=OFF
-#
-# Request building vtkParallelMPI
-# Module_vtkParallelMPI=ON
+# -mpi implies VTK_Group_MPI    : Request building MPI modules

 set -x
 ./makeVTK \
-    -mpi=0 \
+    -mpi  \
    -osmesa \
    -mesa-prefix $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$mesa \
    $vtk "$@" \
-    VTK_Group_MPI=ON \
-    Module_vtkAcceleratorsVTKm=ON \
-    Module_vtkParallelMPI=ON
+    Module_vtkAcceleratorsVTKm=ON


 #------------------------------------------------------------------------------
Author	SHA1	Message	Date
Mark Olesen	3fe5c2beb5	CONFIG: update link to mpc version	2018-12-14 12:17:49 +01:00
Mark Olesen	6e0c9f9d8b	ENH: makeVTK -mpi also define VTK_Group_MPI=ON - this pulls in the other bits (Module_vtkParallelMPI, Module_vtkRenderingParallel, ...)	2018-12-05 23:37:00 +01:00
Mark Olesen	013c7154ff	STYLE: avoid spurious message about non-system qt - arises when update-alternatives or similar are being used.	2018-12-04 18:33:45 +01:00
Mark Olesen	28e7982258	ENH: minor build script improvements - add internal WM_SIZE_OPTIONS variable for reduced typing - check for wmkdepend and wmkdep for wmake builds - avoid egrep for getting processor count.	2018-12-03 08:45:29 +01:00
Mark Olesen	7e5bdfd747	CONFIG: update version information	2018-12-03 08:44:27 +01:00
Mark Olesen	f64c88a1cf	ENH: initial (rudimentary) makeHYPRE, makePETSC scripts	2018-07-31 11:20:37 +02:00
Mark Olesen	b71a60d122	ENH: add whichMpicxx function for C++ programs	2018-07-30 17:18:32 +02:00
Mark Olesen	7aee88cf92	COMP: patches for building older gcc versions with gcc-7 - gcc-4.8.5 : oldest currently supported - gcc-4.9.4 : possibly usable C++11 regex - gcc-6.3.0 : one generation older than gcc-7	2018-07-27 14:09:27 +02:00
Mark Olesen	d2334fe051	COMP: patch ParaView macros to find qhelpgenerator-qt5 (issue #40 )	2018-07-22 17:47:03 +02:00
Mark Olesen	a77852ae18	CONFIG: add download link for scotch 6.0.6	2018-07-19 11:02:18 +02:00
Mark Olesen	0e599b7a64	ENH: add optional -clang flag for building gcc - can be useful when bootstrapping	2018-07-18 09:39:12 +02:00
Mark Olesen	1a1c624422	COMP: add vtkhdf5 patch for compiling with gcc-8.1 (closes #39 )	2018-07-07 13:35:08 +02:00
Mark Olesen	2dd42d8c6c	CONFIG: disable CGAL_Core - not required by OpenFOAM, and provokes cmake issues for CGAL-4.12	2018-07-05 14:12:36 +02:00
Mark Olesen	ff162da2f8	BUG: missing _foamEtc definition (fixes #38 ) - this function definition (as per the OpenFOAM functions) is required for compatibility when sourcing some config files (eg, mpi).	2018-07-02 07:28:51 +02:00