diff options
Diffstat (limited to 'reproduce/software')
-rw-r--r-- | reproduce/software/config/checksums.conf | 2 | ||||
-rw-r--r-- | reproduce/software/config/versions.conf | 7 | ||||
-rw-r--r-- | reproduce/software/make/basic.mk | 1 | ||||
-rw-r--r-- | reproduce/software/make/high-level.mk | 36 | ||||
-rw-r--r-- | reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch | 37 | ||||
-rw-r--r-- | reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch | 23 |
6 files changed, 105 insertions, 1 deletions
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 + + #---------------------------------------------------------------------------- |