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.

7 files changed, 105 insertions, 1 deletions

diff --git a/.file-metadata b/.file-metadata
index 1b9ba37..3a4122f 100644
--- a/.file-metadata
+++ b/.file-metadata
diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf
index f19d831..643be9c 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -53,6 +53,7 @@ sed-checksum = e0be5db4cdf8226b34aaa9071bc5ae0eafde1c52227cee3512eea7fe2520d6c5c
 tar-checksum = 4be18afeac54aec4af074cf2358cfade5aaebe2041c5075c5764a81114df4d002e90b28f4444bd1430783e7d6bed82abd0440ef5cb244695f2e56a9a41b42fbc
 texinfo-checksum = 96e0764d0808152d3662e65c3287fb0f86ed918912cdc036380637dbadaacd6a489b516543c07b08105686575e8d495a945f73e23ff0909d5a0f12026e4131e0
 unzip-checksum = 0694e403ebc57b37218e00ec1a406cae5cc9c5b52b6798e0d4590840b6cdbf9ddc0d9471f67af783e960f8fa2e620394d51384257dca23d06bcd90224a80ce5d
+valgrind-checksum = 5695d1355226fb63b0c80809ed43bb077b6eed4d427792d9d7ed944c38b557a84fe3c783517b921e32f161228e10e4625bea0550faa4685872bb4454450cfa7f
 wget-checksum = 95fb064f0d79b0a3178a83322f58a85a3a036fb300ed759eb67a538f0bbacdd552f6cbeb60d63b4f0113e8467d923a5ce7ac5570b7a4ce1733b3dfd559bb33b2
 which-checksum = d2f04a5c5291f2d7d1226982da7cf999d36cfe24d3f7bda145508efcfb359511251d3c68b860c0ddcedd66b15a0587b648a35ab6d1f173707565305c506dfc61
 xz-checksum = e5bf6eb88365d2dbdc774db49261fb9fae0544ed297891fc20f1ed223f4072cb0357cbd98146ac35b6d29410a12b6739bbd111cd57d4a225bef255ed46988578
@@ -110,6 +111,7 @@ netpbm-checksum = 064720f8a9d0a502488e1af4daecdbf3936910996507ca6f311073a0ad8423
 openblas-checksum = 91b3074eb922453bf843158b4281cde65db9e8bbdd7590e75e9e6cdcb486157f7973f2936f327bb3eb4f1702ce0ba51ae6729d8d4baf2d986c50771e8f696df0
 openmpi-checksum = 760716974cb6b25ad820184622e1ee7926bc6fda87db6b574f76792bc1ca99522e52195866c14b7cb2df5a4981efdaf9f71d2c5533cc0e8e45c2c4b3b74cbacc
 openssh-checksum = e280fa2d56f550efd37c5d2477670326261aa8b94d991f9eb17aad90e0c6c9c939efa90fe87d33260d0f709485cb05c379f0fd1bd44fc0d5190298b6398c9982
+patch-checksum = 75d4e1544484da12185418cd4a1571994398140a91ac606fa08dd067004187dad77d1413f0eb3319b3fe4df076714615c98b29df06af052bb65960fa8b0c86bf
 pixman-checksum = 1b0205dbe9d9185c68813ce577a889f3c83e83fbd9955c3a72d411c3b476e6be93fc246b5b6ef4ee17e2bb8eb6fb5559e01dff7feb6a6c4c6314f980e960d690
 python-checksum = c25a72ad792f7c1b4c2f79faebbe9608d04b04b2fe58ab804cb4732cdaa75ea93d175f5e52b38e91cb6ae0559ea6b645d802c8b6a869584e8bb9b5018367ce3d
 R-checksum = 17513e9f4dd27c61c11f7aa45227aeeeefb375bf5d4e193b471724f379a1b2da33e127cbe91aa175cbbbb048b892047e2f610280585c8159242a6c94790b07f9
diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 7df4539..e9aad2e 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -104,6 +104,7 @@ missfits-version = 2.8.0
 openblas-version = 0.3.5
 openmpi-version = 4.0.1
 openssh-version = 8.0p1
+patch-version = 2.7.6
 pixman-version = 0.38.0
 python-version = 3.7.4
 R-version = 3.6.2
@@ -216,4 +217,8 @@ minizip-version = $(zlib-version)
 # From version 1.2 OpenSSL may not need a manual addition, as described in
 # its comments and `https://savannah.nongnu.org/bugs/?58263'. If it doesn't
 # cause problems, put it back in the list of "Basic/low-level" tools.
-openssl-version = 1.1.1a
\ No newline at end of file
+openssl-version = 1.1.1a
+
+# Version 3.15.0 needs two patches, please check if they are necessary on
+# any future release.
+valgrind-version = 3.15.0
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 9119930..8b216fe 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -311,6 +311,7 @@ $(ibidir)/low-level-links: | $(ibdir) $(ildir)
 	$(call makelink,clang++)
 
         # Mac OS specific
+	$(call makelink,mig)
 	$(call makelink,sysctl)
 	$(call makelink,sw_vers)
 	$(call makelink,dsymutil)
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 7e9c723..3ad4468 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -42,6 +42,7 @@ ibdir   = $(BDIR)/software/installed/bin
 ildir   = $(BDIR)/software/installed/lib
 iidir   = $(BDIR)/software/installed/include
 dtexdir = $(shell pwd)/reproduce/software/bibtex
+patchdir= $(shell pwd)/reproduce/software/patches
 itidir  = $(BDIR)/software/installed/version-info/tex
 ictdir  = $(BDIR)/software/installed/version-info/cite
 ipydir  = $(BDIR)/software/installed/version-info/python
@@ -188,6 +189,7 @@ tarballs = $(foreach t, apachelog4cxx-$(apachelog4cxx-version).tar.lz \
                         openblas-$(openblas-version).tar.gz \
                         openmpi-$(openmpi-version).tar.gz \
                         openssh-$(openssh-version).tar.gz \
+                        patch-$(patch-version).tar.gz \
                         pixman-$(pixman-version).tar.gz \
                         R-$(R-version).tar.gz \
                         scamp-$(scamp-version).tar.lz \
@@ -198,6 +200,7 @@ tarballs = $(foreach t, apachelog4cxx-$(apachelog4cxx-version).tar.lz \
                         rpcsvc-proto-$(rpcsvc-proto-version).tar.xz \
                         tides-$(tides-version).tar.gz \
                         tiff-$(libtiff-version).tar.gz \
+                        valgrind-$(valgrind-version).tar.bz2 \
                         wcslib-$(wcslib-version).tar.bz2 \
                         xlsxio-$(xlsxio-version).tar.gz \
                         yaml-$(yaml-version).tar.gz \
@@ -294,6 +297,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	  majorver=$$(echo $(openmpi-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}')
 	  w=https://download.open-mpi.org/release/open-mpi/v$$majorver/$*
 	elif [ $$n = openssh     ]; then c=$(openssh-checksum); w=https://artfiles.org/openbsd/OpenSSH/portable
+	elif [ $$n = patch       ]; then c=$(patch-checksum); w=http://ftp.gnu.org/gnu/patch
 	elif [ $$n = pixman      ]; then c=$(pixman-checksum); w=https://www.cairographics.org/releases
 	elif [ $$n = R           ]; then c=$(R-checksum);
 	  majver=$$(echo $(R-version) | sed -e's/\./ /g' | awk '{print $$1}')
@@ -309,6 +313,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	elif [ $$n = swig        ]; then c=$(swig-checksum); w=https://sourceforge.net/projects/swig/files/swig/swig-$(swig-version)
 	elif [ $$n = tides       ]; then c=$(tides-checksum); w=http://akhlaghi.org/maneage-software
 	elif [ $$n = tiff        ]; then c=$(libtiff-checksum); w=https://download.osgeo.org/libtiff
+	elif [ $$n = valgrind    ]; then c=$(valgrind-checksum); w=https://sourceware.org/pub/valgrind
 	elif [ $$n = wcslib      ]; then c=$(wcslib-checksum); w=ftp://ftp.atnf.csiro.au/pub/software/wcslib
 	elif [ $$n = xlsxio      ]; then
 	  mergenames=0
@@ -737,6 +742,33 @@ $(ibidir)/tides: $(tdir)/tides-$(tides-version).tar.gz
 	&& cp $(dtexdir)/tides.tex $(ictdir)/ \
 	&& echo "TIDES $(tides-version) \citep{tides}" > $@
 
+$(ibidir)/valgrind: $(ibidir)/patch \
+                    $(ibidir)/autoconf \
+                    $(ibidir)/automake \
+                    $(tdir)/valgrind-$(valgrind-version).tar.bz2
+        # For valgrind-3.15.0, see
+        # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329 for a
+        # report on an MPI-related compile bug and the two patches
+        # below. These two patches and `automake` should allow valgrind to
+        # compile with gcc-9.2.0.
+	cd $(ddir) \
+	&& tar -x -f $(word 1,$(filter $(tdir)/%,$^)) \
+	&& valgrinddir=valgrind-$(valgrind-version) \
+	&& cd $${valgrinddir} \
+	&& printf "valgrindir=$${valgrinddir} ; pwd = %s .\n" $$($(ibdir)/pwd) \
+	&& if [ "x$(valgrind-version)" = "x3.15.0" ]; then \
+	     patch --verbose -p1 < $(patchdir)/valgrind-3.15.0-mpi-fix1.patch; \
+	     patch --verbose -p1 < $(patchdir)/valgrind-3.15.0-mpi-fix2.patch; \
+	   fi \
+	&& autoreconf \
+	&& ./configure --prefix=$(idir) \
+	&& make -j$(numthreads) \
+	&& if ! make check -j$(numthreads); then \
+	     echo; echo "Valgrind's 'make check' failed!"; echo; \
+	   fi \
+	&& make install \
+	&& echo "Valgrind $(valgrind-version)" > $@
+
 $(ibidir)/yaml: $(tdir)/yaml-$(yaml-version).tar.gz
 	$(call gbuild, yaml-$(yaml-version), static) \
 	&& echo "LibYAML $(yaml-version)" > $@
@@ -1099,6 +1131,10 @@ $(ibidir)/netpbm: $(ibidir)/unzip \
 	&& rm -rf $$unpackdir \
 	&& echo "Netpbm $(netpbm-version)" > $@
 
+$(ibidir)/patch: $(tdir)/patch-$(patch-version).tar.gz
+	$(call gbuild, patch-$(patch-version), static, ,V=1) \
+	&& echo "GNU Patch $(patch-version)" > $@
+
 # R programming language
 $(ibidir)/R: $(ibidir)/libpng \
              $(ibidir)/libjpeg \
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
+ 
+ #----------------------------------------------------------------------------