dev-db/scylla: apply read amplification patch

Package-Manager: Portage-2.3.80, Repoman-2.3.19
Manifest-Sign-Key: 34FCB257983BA23A8CEC5EB7EB9E6405C24BFAE5
Signed-off-by: Alexys Jacob <ultrabug@gentoo.org>

3 files changed, 277 insertions, 8 deletions

diff --git a/dev-db/scylla/Manifest b/dev-db/scylla/Manifest
index 6a7d9ee..cf489ed 100644
--- a/dev-db/scylla/Manifest
+++ b/dev-db/scylla/Manifest
@@ -6,6 +6,7 @@ AUX 0001-thrift-support-version-0.11-after-THRIFT-2221.patch 40277 BLAKE2B 4296b
 AUX 10-scylla.conf 64 BLAKE2B 31ce1b2173214bcac351b71cf19e5506ab08cefbca446ce23ad753c98c5e4fd7fbb89b0f79703ea4dcf1f6233e7929268365eeaab1b4e2e7b31553aa7928a969 SHA512 c24b3ec2f0ea3b1ad0792c05a8eb044b3a157862b59759e020586ae872f9789a558d423fe1dff1a8c6d8342049cf4d919faf31a1439a6a1c69af915365b4ec82
 AUX 3.1-revert-64-bit-gc_clock.patch 1132 BLAKE2B 7ed59d5f898babc4940bcd10a8aaf467545c80fd8c7417e481d80abc07fc27b4859396cafa5b1d1da4d386f8c490e6f417c0ce63064eea7177ce869869387480 SHA512 8ff0019080687993939fb5c0bb24945214799dfe0942982d8154769155159c02bc75e448978343c1b08a162a6670bede3721247a70c6fabfe1cd9730dbf4f77a
 AUX 3.1-thrift-support.patch 39980 BLAKE2B 7de8bde052186b8a62ea83b7082e9828d4c320ed86381a93d5136906ba014631dc3b5e2a2b1dfd33bec21c6bd7d685fa3f1f270c97f233934cca24473d0e52b5 SHA512 d33e50dbef01dfd4845a093c160b5cbedc658770c1b5a5de063c56b43df0731329fe0cdb3ddfa5d72020ab25573682e4d14a3c39ad366a208694062a3fd49155
+AUX 3.1.2-fix-read-amplification.patch 962 BLAKE2B bacd95cf99097254a3aca2a034ac38c6133039ab0487cb2880ef4fb3ed960c066bf96470a4c07cf800cd01810b7841c9740ea8204aa0ecd73b2b71489dfcc591 SHA512 59b8646378cc6ec9468920093169f1f537e9855e6b1f4a83f4abaaf15c1c2c66566877d3bae88b4f5b75ab0fb8958527f9a13f13f6a98e839c56bb0418b20c27
 AUX boost-1.65.0-icl-ttp-matching.patch 1427 BLAKE2B de9c77253963656f85ed2d05babd600bc5b59b567bc889ed815dfba97f2a1334df48dbb1e67879dea1419fb439c513c54a66531d4e8ec28a7848385f70471334 SHA512 aaa7959df631c17a80486e5b6724d76bf2193694f5559443350c74567506f36c133f740adcbb1b2d3a5a2760730f498f0fd655ec6eff6d20393b6e49549c6ec8
 AUX fix-fmt-3.5.0-compilation.patch 3785 BLAKE2B 3cd23ccffe1ec33d5f7e2c6c3583631b294fc0e6d36e49eef582598fd168968805dd7ca4cc786c02cb20ae1e758a814e1b761dbd41a86330906cd4b5af5d6666 SHA512 d7606559fb2aef9ea009e8c417397dcc94d0c708da8283d4c1c6393c059ecca50d9806cfb19d1fe69b8d7898da2b8d194fbc8b8dd1aa9c12e0d6120d52bc2518
 AUX scylla-server.confd 396 BLAKE2B dc522b308985e51c24449a333d793eaa777a74b8b5594f1ff4a092aae003202791019a255ea478c4e794a83ca0e01d2c49aac3d267501624f461fa3edfe1c41f SHA512 51739cdeedaedb1a73a345ec6a4a2761d29fac1b9cf61f02937559aed43f02112109464254213118d40af1fb7e8491c22f8cb88908c9c88523dfe1b78b8430c7
@@ -32,20 +33,21 @@ EBUILD scylla-3.1.0.ebuild 7051 BLAKE2B 282b4221655c0156d3a39f7245c8b6023a1f4352
 EBUILD scylla-3.1.1-r1.ebuild 7571 BLAKE2B 999faabaf0a6d2b8de9f555c0170288a1add0ac69d05afd3ab2b1976deb6e560e3046edede9caefcf56f38cd9995aa0e40f184ba14e15cec35b1f3ccf47e3b7c SHA512 fb6442b55e8152ed6c99f7473dd3b5075521f46e23d3124bfa01a13d6d134df872273c9eae207d96d09a7056f2496867c74deca37090c762c1af026708e55394
 EBUILD scylla-3.1.1-r2.ebuild 7630 BLAKE2B 3593fb08d50353daae99dcabfca109a4abd06853bcdff91b7613faf37fab0bc538413957a0aca3015be86748ab9dc0b10defd62115704399b189715695fce4ba SHA512 b5c6b9263b292a2830ea209676ee2dfddaf44f7b22be61bbdaae7c1a776246bdea92e4780dc14e1df68428cd95a8a777eea41efc27c9203e44d4a7f73b354e5e
 EBUILD scylla-3.1.1.ebuild 7505 BLAKE2B 1f3e068c6688c9f3a420102da25966a142dfd3be1f90d94c77c2d744274df4d0eaa82e4af1eeef53d7b6594d940f188263428befd018a4da9aa9ef0896f5799b SHA512 8769a7fd5f69038f958eddd38a70da8cdc76d606638422224394164be09b4b3c0f72c5aac807bcc199a3f56d05b1c3baf48d7dfd1523602b0aca00681fa8a0c4
+EBUILD scylla-3.1.2-r1.ebuild 7680 BLAKE2B e19a665cce5469d956f45e60aa5dbcedd9e7b25ff8d81a3877306b338befa5741f68cd9c805b39fded300560d5999a0d782e36a91f3adb6974388b88baf53f61 SHA512 f3c0ea58ace690d68bbc0646828183a93730ebbede14b7200391aa967f0249b9f8a55c8146b407b5834b4401bb12b192ddbb61c9115148997fc56792d5cedefc
 EBUILD scylla-3.1.2.ebuild 7630 BLAKE2B 3593fb08d50353daae99dcabfca109a4abd06853bcdff91b7613faf37fab0bc538413957a0aca3015be86748ab9dc0b10defd62115704399b189715695fce4ba SHA512 b5c6b9263b292a2830ea209676ee2dfddaf44f7b22be61bbdaae7c1a776246bdea92e4780dc14e1df68428cd95a8a777eea41efc27c9203e44d4a7f73b354e5e
 EBUILD scylla-9999.ebuild 6833 BLAKE2B c21b0db85ca5b2dbe90a7523b739fa6614d40fd0264d8cd5bf77f1c1b37b31f1f042c946b76d5c1e74907badf931c188f7f5112105089658ff6acfc80f440021 SHA512 e5237eddd44fa0f4f88a6aa4bd2d6015dc6c61597636e03957ea932cce240de05533e223aae0abb68d37d16c7734e64267f2b77aedb3913c24b6b73210629972
 MISC metadata.xml 249 BLAKE2B 40afa233e18ae5678e52194be8b1235d8deda4810e55b33ea192ded6b09a158f1bc941544f90a1b9e396db00bc0fe277c072d267568473ae4aa2dec8bc5c2f89 SHA512 6eae78a65db44c8f7ef2d20c10c8612cd2072c0204c6294798e4bf94f1283c684c22d1ad28e0f68e78e82a0c60526d6786492c9dacc438d83405218e51c1bf9c
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diff --git a/dev-db/scylla/files/3.1.2-fix-read-amplification.patch b/dev-db/scylla/files/3.1.2-fix-read-amplification.patch
new file mode 100644
index 0000000..c0dceef
--- /dev/null
+++ b/dev-db/scylla/files/3.1.2-fix-read-amplification.patch
@@ -0,0 +1,13 @@
+diff --git a/table.cc b/table.cc
+index eec65689f2..596c312854 100644
+--- a/table.cc
++++ b/table.cc
+@@ -2518,7 +2518,7 @@ future<row_locker::lock_holder> table::do_push_view_replica_updates(const schema
+         std::move(slice),
+         std::move(m),
+         [base, views = std::move(views), lock = std::move(lock), this, timeout, source = std::move(source), &io_priority] (auto& pk, auto& slice, auto& m) mutable {
+-            auto reader = source.make_reader(base, pk, slice, io_priority);
++            auto reader = source.make_reader(base, pk, slice, io_priority, nullptr, streamed_mutation::forwarding::no, mutation_reader::forwarding::no);
+             return this->generate_and_propagate_view_updates(base, std::move(views), std::move(m), std::move(reader)).then([lock = std::move(lock)] () mutable {
+                 // return the local partition/row lock we have taken so it
+                 // remains locked until the caller is done modifying this
diff --git a/dev-db/scylla/scylla-3.1.2-r1.ebuild b/dev-db/scylla/scylla-3.1.2-r1.ebuild
new file mode 100644
index 0000000..86e46aa
--- /dev/null
+++ b/dev-db/scylla/scylla-3.1.2-r1.ebuild
@@ -0,0 +1,254 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+MY_PV="${PV/_beta/}"
+EGIT_CLONE_TYPE="mirror"
+EGIT_COMMIT="scylla-${PV}"
+EGIT_REPO_URI="https://github.com/scylladb/scylla.git"
+inherit git-r3
+
+PYTHON_COMPAT=( python3_{4,5,6} )
+
+inherit autotools flag-o-matic linux-info python-r1 toolchain-funcs systemd user
+
+DESCRIPTION="NoSQL data store using the seastar framework, compatible with Apache Cassandra"
+HOMEPAGE="http://scylladb.com/"
+
+KEYWORDS="~amd64"
+LICENSE="AGPL-3"
+SLOT="0"
+IUSE="doc systemd"
+
+# NOTE:
+# if you want to debug using backtraces, enable the 'splitdebug' FEATURE:
+# https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Backtraces
+#
+# then check out:
+# https://github.com/scylladb/scylla/wiki/How-to-resolve-backtrace
+
+RESTRICT="test"
+
+RDEPEND="
+	>=dev-libs/thrift-0.11.0
+	<dev-util/ragel-7.0
+	<sys-apps/hwloc-2.0.0
+	~app-admin/scylla-jmx-${PV}
+	~app-admin/scylla-tools-${PV}
+	>=virtual/jdk-1.8.0:*
+	app-arch/lz4
+	app-arch/snappy
+	app-arch/zstd
+	dev-cpp/antlr-cpp:3.5
+	dev-cpp/yaml-cpp
+	dev-java/antlr:3.5
+	~dev-libs/boost-1.65.0[icu]
+	dev-libs/crypto++
+	dev-libs/jsoncpp
+	dev-libs/libaio
+	>=dev-libs/libfmt-3.2.1
+	dev-libs/libxml2
+	dev-libs/protobuf
+	dev-python/psutil[${PYTHON_USEDEP}]
+	dev-python/pyparsing[${PYTHON_USEDEP}]
+	dev-python/pystache[${PYTHON_USEDEP}]
+	dev-python/pyudev[${PYTHON_USEDEP}]
+	>=dev-python/pyyaml-5.1[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	dev-python/urwid[${PYTHON_USEDEP}]
+	dev-util/systemtap
+	net-libs/gnutls
+	net-misc/lksctp-tools
+	sys-apps/ethtool
+	sys-fs/xfsprogs
+	sys-libs/libunwind
+	sys-libs/zlib
+	sys-process/numactl
+	x11-libs/libpciaccess
+	systemd? ( sys-apps/systemd )
+"
+DEPEND="${RDEPEND}
+	>=sys-kernel/linux-headers-3.5
+	dev-util/ninja
+"
+
+# Discussion about kernel configuration:
+# https://groups.google.com/forum/#!topic/scylladb-dev/qJu2zrryv-s
+CONFIG_CHECK="~NUMA_BALANCING ~SYN_COOKIES ~TRANSPARENT_HUGEPAGE"
+ERROR_NUMA_BALANCING="${PN} recommends support for Memory placement aware NUMA scheduler (NUMA_BALANCING)."
+ERROR_SYN_COOKIES="${PN} recommends support for TCP syncookie (SYN_COOKIES)."
+ERROR_TRANSPARENT_HUGEPAGE="${PN} recommends support for Transparent Hugepage (TRANSPARENT_HUGEPAGE)."
+
+# NOTE: maybe later depending on upstream energy, support DPDK
+# For DPDK, removed HUGETLBFS PROC_PAGE_MONITOR UIO_PCI_GENERIC in favor of VFIO
+# CONFIG_CHECK="~NUMA_BALANCING ~SYN_COOKIES ~TRANSPARENT_HUGEPAGE ~VFIO"
+# ERROR_VFIO="${PN} running with DPDK recommends support for Non-Privileged userspace driver framework (VFIO)."
+
+DOCS=( LICENSE.AGPL NOTICE.txt ORIGIN README.md README-DPDK.md )
+PATCHES=(
+	"${FILESDIR}/fix-fmt-3.5.0-compilation.patch"
+	"${FILESDIR}/3.1-thrift-support.patch"
+	"${FILESDIR}/v1-0001-repair-Add-a-timer-for-repair-reader.patch"
+	"${FILESDIR}/0001-repair-Repair-tables-in-parallel.patch"
+	"${FILESDIR}/3.1.2-fix-read-amplification.patch"
+)
+
+pkg_setup() {
+	linux-info_pkg_setup
+	enewgroup scylla
+	enewuser scylla -1 -1 /var/lib/${PN} scylla
+}
+
+src_prepare() {
+	default
+
+	# set version
+	local git_commit=$(git log --pretty=format:'%h' -n 1)
+	echo "${PV}-${git_commit}" > version
+
+	# fix jsoncpp detection
+	sed -e 's@json/json.h@jsoncpp/json/json.h@g' -i json.hh || die
+
+	# QA: no -Werror (tho it does not propagate)
+	sed -e 's/\-Werror//g' -i configure.py || die
+
+	# QA NOTE: respect -O3 as it is upstream recommended
+	# and because we would kill the RAM of the machine with lower optimization
+	# since some files can take up to 8GB of RAM to compile!
+	# sed -e 's/\-O3//g' -i configure.py || die
+
+	# I don't agree with the old 4GB of RAM per job, it's more about 8GB now
+	sed -e 's/4000000000/8000000000/g' -i scripts/jobs || die
+
+	# TODO: contribute me
+	# fix pyyaml vulnerability #659348
+	# seastar/scripts/perftune.py
+	# dist/docker/redhat/scyllasetup.py
+	# dist/common/scripts/scylla_io_setup
+	# dist/common/scripts/scylla_fstrim
+	# dist/common/scripts/scylla_blocktune.py
+	# dist/common/scripts/scylla_util.py
+	# dist/common/scripts/scylla_config_get.py
+	find "${S}/dist" -type f -exec sed -e 's/yaml.load(/yaml.full_load(/g' -i {} \+ || die
+	sed -e 's/yaml.load(/yaml.safe_load(/g' -i seastar/scripts/perftune.py || die
+}
+
+src_configure() {
+	python_setup
+
+	# copied from dist/redhat/scylla.spec.mustache
+	# we want a package compiled with old kernel headers to
+	# support nowait aio if the user upgrades their kernel
+	if ! grep -qwr RWF_NOWAIT /usr/include/linux; then
+	    append-cflags "-DRWF_NOWAIT=8"
+	fi
+	if ! grep -qwr aio_rw_flags /usr/include/linux; then
+	    append-cflags "-Daio_rw_flags=aio_reserved1"
+	fi
+
+	# native CPU CFLAGS are strongly enforced by upstreams, respect that
+	replace-cpu-flags "*" "native"
+
+	append-cflags "-Wno-attributes -Wno-array-bounds"
+
+	${EPYTHON} configure.py --enable-gcc6-concepts --mode=release --with=scylla --disable-xen --c-compiler "$(tc-getCC)" --compiler "$(tc-getCXX)" --ldflags "${LDFLAGS}" --cflags "${CFLAGS}" --python ${EPYTHON} --with-antlr3 /usr/bin/antlr3.5 || die
+}
+
+src_compile() {
+	# we use the provided 'scripts/jobs' to figure out how many parallel
+	# compilation jobs we can sustain
+	einfo "Compiling using $(scripts/jobs) jobs"
+	ninja -v build/release/scylla build/release/iotune -j$(scripts/jobs) || die
+}
+
+src_install() {
+	# NOTE:
+	# I base myself on upstream's install.sh file
+
+	default
+
+	local MUSTACHE_DIST="\"debian\": true"
+	pystache dist/common/systemd/scylla-server.service.mustache "{ $MUSTACHE_DIST }" > build/scylla-server.service
+	pystache dist/common/systemd/scylla-housekeeping-daily.service.mustache "{ $MUSTACHE_DIST }" > build/scylla-housekeeping-daily.service
+	pystache dist/common/systemd/scylla-housekeeping-restart.service.mustache "{ $MUSTACHE_DIST }" > build/scylla-housekeeping-restart.service
+
+	insinto /etc/default
+	doins dist/common/sysconfig/scylla-server
+
+	insinto /etc/security/limits.d
+	doins dist/common/limits.d/scylla.conf
+
+	insinto /etc/scylla.d
+	doins dist/common/scylla.d/*.conf
+
+	insinto /etc/sysctl.d
+	doins dist/common/sysctl.d/*.conf
+
+	insinto /etc/scylla
+	for config_file in scylla.yaml cassandra-rackdc.properties; do
+		doins conf/${config_file}
+	done
+
+	systemd_dounit build/*.service
+	systemd_dounit dist/common/systemd/*.service
+	systemd_dounit dist/common/systemd/*.timer
+
+	exeinto /usr/lib/scylla
+	doexe dist/common/scripts/*
+	doexe seastar/scripts/*
+	doexe scylla-gdb.py
+
+	dobin build/release/iotune
+	dobin build/release/scylla
+
+	insinto /usr/lib/scylla
+	doins dist/common/scripts/scylla_blocktune.py
+
+	exeinto /usr/lib/scylla
+	doexe dist/common/scripts/scylla-blocktune
+	doexe dist/common/scripts/scylla-housekeeping
+
+	insinto /etc/scylla.d
+	doins conf/housekeeping.cfg
+
+	newinitd "${FILESDIR}/scylla-server.initd" ${PN}-server
+	newconfd "${FILESDIR}/scylla-server.confd" ${PN}-server
+
+	dodoc -r licenses
+
+	for x in /var/lib/${PN} /var/lib/${PN}/{data,commitlog,hints,coredump} /var/lib/scylla-housekeeping /var/log/scylla; do
+		keepdir "${x}"
+		fowners scylla:scylla "${x}"
+	done
+
+	insinto /usr/lib/scylla/swagger-ui
+	doins -r swagger-ui/dist
+
+	insinto /usr/lib/scylla/api
+	doins -r api/api-doc
+
+	insinto /usr/lib/scylla/scyllatop
+	doins -r tools/scyllatop/*
+	fperms +x /usr/lib/scylla/scyllatop/scyllatop.py
+	dosym /usr/lib/scylla/scyllatop/scyllatop.py /usr/sbin/scyllatop
+
+	for util in $(ls dist/common/sbin/); do
+		dosym /usr/lib/scylla/${util} /usr/sbin/${util}
+	done
+
+	insinto /etc/sudoers.d
+	newins "${FILESDIR}"/scylla.sudoers scylla
+
+	insinto /etc/rsyslog.d
+	doins "${FILESDIR}/10-scylla.conf"
+}
+
+pkg_postinst() {
+	elog "You should run 'emerge --config dev-db/scylla' to finalize your ScyllaDB installation."
+}
+
+pkg_config() {
+	elog "Running 'scylla_setup'..."
+	scylla_setup
+}