New software: Valgrind and Patch

With this commit, Maneage now includes instructions to build the memory
tracing tool Valgrind and the program 'patch' (to apply corrections/patches
in text files and in particular the sources of programs).

For this version of Valgrind, some patches were necessary for an interface
with OpenMPI 2.x (which is the case now). Also note that this version of
Valgrind's checks can fail with GCC 10.1.x (when using '--host-cc'), and
the failures aren't due to internal problems but due to how the tests are
designed (https://bugs.gentoo.org/707598). So currently if any of
Valgrind's checks fail, Maneage still assumes that Valgrind was built and
installed successfully.

While testing on macOS, we noticed that it needs the macOS-specific 'mig'
program which we can't build in Maneage. DESCRIPTION: The mig command
invokes the Mach Interface Generator to generate Remote Procedure Call
(RPC) code for client-server style Mach IPC from specification files. So a
symbolic link to the system's 'mig' is now added to the project's programs
on macOS systems.

This commit's build of Patch and Valgrind has been tested on two GNU/Linux
distributions (Debian and ArchLinux) as well as macOS.

Work on this commit started by Boud Roukema, but also involved tests and
corrections by Mohammad Akhlaghi and Raul Infante-Sainz.

2 files changed, 60 insertions, 0 deletions

diff --git a/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch b/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch
new file mode 100644
index 0000000..94dcab5
--- /dev/null
+++ b/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch
@@ -0,0 +1,37 @@
+---
+ mpi/libmpiwrap.c |   12 +++++++++++-
+ 1 file changed, 11 insertions(+), 1 deletion(-)
+ Patch by Samuel Thibault:
+ https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329;msg=10
+ and hacked further by Boud Roukema 2020-05-10.
+--- a/mpi/libmpiwrap.c
++++ b/mpi/libmpiwrap.c
+@@ -278,8 +278,12 @@ static void showTy ( FILE* f, MPI_Dataty
+    else if (ty == MPI_LONG_INT)       fprintf(f,"LONG_INT");
+    else if (ty == MPI_SHORT_INT)      fprintf(f,"SHORT_INT");
+    else if (ty == MPI_2INT)           fprintf(f,"2INT");
++#  if defined(MPI_UB_ENABLED_IN_MPI1)
+    else if (ty == MPI_UB)             fprintf(f,"UB");
++#  endif
++#  if defined(MPI_LB_ENABLED_IN_MPI1)
+    else if (ty == MPI_LB)             fprintf(f,"LB");
++#  endif
+ #  if defined(MPI_WCHAR)
+    else if (ty == MPI_WCHAR)          fprintf(f,"WCHAR");
+ #  endif
+@@ -733,8 +737,14 @@ void walk_type ( void(*f)(void*,long), c
+          f(base + offsetof(Ty,loc), sizeof(int));
+          return;
+       }
+-      if (ty == MPI_LB || ty == MPI_UB)
++#if defined(MPI_LB_ENABLED_IN_MPI1)
++      if (ty == MPI_LB)
++         return; /* have zero size, so nothing needs to be done */
++#endif
++#if defined(MPI_UB_ENABLED_IN_MPI1)
++      if (ty == MPI_UB)
+          return; /* have zero size, so nothing needs to be done */
++#endif
+       goto unhandled;
+       /*NOTREACHED*/
+    }
diff --git a/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch b/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch
new file mode 100644
index 0000000..12b50a2
--- /dev/null
+++ b/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch
@@ -0,0 +1,23 @@
+Index: valgrind-3.15.0/mpi/Makefile.am
+===================================================================
+ Patch by Samuel Thibault:
+ https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329;msg=22
+--- valgrind-3.15.0.orig/mpi/Makefile.am
++++ valgrind-3.15.0/mpi/Makefile.am
+@@ -42,14 +42,14 @@ libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@
+ libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_CPPFLAGS = -I$(top_srcdir)/include
+ libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_CFLAGS   = \
+ 	$(CFLAGS_MPI) $(MPI_FLAG_M3264_PRI) -Wno-deprecated-declarations
+-libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_LDFLAGS  = $(LDFLAGS_MPI)
++libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_LDADD  = $(LDFLAGS_MPI)
+ endif
+ if BUILD_MPIWRAP_SEC
+ libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_SOURCES  = libmpiwrap.c
+ libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_CPPFLAGS = -I$(top_srcdir)/include
+ libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_CFLAGS   = \
+ 	$(CFLAGS_MPI) $(MPI_FLAG_M3264_SEC) -Wno-deprecated-declarations
+-libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_LDFLAGS  = $(LDFLAGS_MPI)
++libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_LDADD  = $(LDFLAGS_MPI)
+ endif
+ 
+ #----------------------------------------------------------------------------