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, 37 insertions, 0 deletions

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 \