Experimental FAH client to work with newer glibc.

svn path=/; revision=300

7 files changed, 381 insertions, 0 deletions

diff --git a/sci-biology/foldingathome/ChangeLog b/sci-biology/foldingathome/ChangeLog
new file mode 100644
index 0000000..71026fc
--- /dev/null
+++ b/sci-biology/foldingathome/ChangeLog
@@ -0,0 +1,246 @@
+# ChangeLog for sci-biology/foldingathome
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/foldingathome/ChangeLog,v 1.30 2010/06/24 11:47:44 jlec Exp $
+
+  24 Jun 2010; Justin Lecher <jlec@gentoo.org>
+  -foldingathome-5.0.2-r3.ebuild:
+  Cleaned uneeded version
+
+  22 Jun 2010; Justin Lecher <jlec@gentoo.org> foldingathome-6.29.ebuild:
+  Dropping ~x86 as upstream only provides 64bit for this version, 324611
+
+
+*foldingathome-6.29 (17 Jun 2010)
+
+  17 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/6.29/fah-init,
+  +files/6.29/folding-conf.d, +files/6.29/initfolding,
+  +foldingathome-6.29.ebuild:
+  Version Bump, 270458, fixes for prestripped files. #252033
+
+  30 Nov 2008; Jeff Gardner <je_fro@gentoo.org> files/6.02/folding-conf.d:
+  Removing smp from default opts to hopefully fix bug #248896
+  Thanks to Vladimir Berezhnoy.
+
+  22 Nov 2008; Jeff Gardner <je_fro@gentoo.org>
+  foldingathome-6.02-r1.ebuild:
+  Add shameless plug for my folding group.
+
+*foldingathome-6.02-r1 (22 Nov 2008)
+
+  22 Nov 2008; Jeff Gardner <je_fro@gentoo.org> -foldingathome-6.02.ebuild,
+  +foldingathome-6.02-r1.ebuild:
+  Bumping for init script fix and add back ~x86.
+
+  22 Nov 2008; Jeff Gardner <je_fro@gentoo.org> files/6.02/fah-init:
+  Changing to use init script from Constantin Baranov on bug #218331
+
+  03 Aug 2008; Jeff Gardner <je_fro@gentoo.org> -files/6.02_beta1/fah-init,
+  -files/6.02_beta1/folding-conf.d, -files/6.02_beta1/initfolding,
+  -foldingathome-6.02_beta1.ebuild:
+  remove dead beta
+
+*foldingathome-6.02 (03 Aug 2008)
+
+  03 Aug 2008; Jeff Gardner <je_fro@gentoo.org> +files/6.02/fah-init,
+  +files/6.02/folding-conf.d, +files/6.02/initfolding,
+  +foldingathome-6.02.ebuild:
+  Latest version, thanks to Nicolas Schlumberger, closes bug #233751
+
+  15 Jun 2008; Jeff Gardner <je_fro@gentoo.org>
+  files/6.02_beta1/folding-conf.d:
+  Add smp option thanks to Timon Van Overveldt in bug #194423
+
+*foldingathome-6.02_beta1 (14 Jun 2008)
+
+  14 Jun 2008; Jeff Gardner <je_fro@gentoo.org> -files/5.91_beta/fah-init,
+  -files/5.91_beta/initfolding, -files/5.91_beta/folding-conf.d,
+  +files/6.02_beta1/fah-init, +files/6.02_beta1/folding-conf.d,
+  +files/6.02_beta1/initfolding, -foldingathome-5.91_beta.ebuild,
+  +foldingathome-6.02_beta1.ebuild:
+  Latest beta client
+
+  12 Jul 2007; Christoph Mende <angelos@gentoo.org>
+  foldingathome-5.0.2-r5.ebuild:
+  Stable on amd64 wrt bug #164823
+
+  12 Jul 2007; Christian Faulhammer <opfer@gentoo.org>
+  foldingathome-5.0.2-r5.ebuild:
+  stable x86, bug 164823
+
+  03 Jul 2007; Jeff Gardner <je_fro@gentoo.org>
+  foldingathome-5.91_beta.ebuild:
+  foldingathome-5.91_beta has expired. Removing KEYWORDS until the next
+  release arrives.
+
+  02 Jul 2007; Piotr Jaroszyński <peper@gentoo.org>
+  foldingathome-5.0.2-r3.ebuild, foldingathome-5.0.2-r5.ebuild:
+  (QA) RESTRICT clean up.
+
+  21 Apr 2007; Jeff Gardner <je_fro@gentoo.org>
+  foldingathome-5.0.2-r3.ebuild, foldingathome-5.0.2-r5.ebuild:
+  Use newconfd wrt bug #174266
+
+  11 Apr 2007; Jeff Gardner <je_fro@gentoo.org>
+  foldingathome-5.91_beta.ebuild:
+  Fixed to better install files under /etc.
+
+*foldingathome-5.91_beta (10 Apr 2007)
+
+  10 Apr 2007; Jeff Gardner <je_fro@gentoo.org> +files/5.91_beta/fah-init,
+  +files/5.91_beta/folding-conf.d, +files/5.91_beta/initfolding,
+  +foldingathome-5.91_beta.ebuild:
+  Adding the amd64-smp client for testing. Thanks to John Gibson.
+
+  03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -files/init-5.0.2-r4,
+  -foldingathome-5.0.2-r4.ebuild:
+  Pruned old version.
+
+*foldingathome-5.0.2-r5 (16 Jun 2006)
+
+  16 Jun 2006; Patrick Kursawe <phosphan@gentoo.org> +files/init-5.0.2-r5,
+  +foldingathome-5.0.2-r5.ebuild:
+  Adding --chdir to start-stop-daemon because of bug #109707
+
+*foldingathome-5.0.2-r4 (14 Aug 2005)
+
+  14 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +files/init-5.0.2-r4,
+  +foldingathome-5.0.2-r4.ebuild:
+  Fixed bug #95697: license is now correct and the binaries are no longer
+  stripped since we are not allowed to modify them. Thanks to Ian Kelly
+  <kellyia@udel.edu>. Fixed bugs #90247 and #93047: Foldingathome init script
+  now uses start-stop-daemon. Thanks to James Lademann
+  <jwlademann@myrealbox.com>.
+
+  22 Apr 2005; Danny van Dyk <kugelfang@gentoo.org>
+  foldingathome-5.0.2-r3.ebuild:
+  Marked stable on amd64.
+
+  03 Mar 2005; Brandon Low <lostlogic@gentoo.org> -files/folding-conf.d,
+  -files/folding-init.d, -files/folding-init.d-r1, -files/folding-init.d-r3,
+  -files/folding.sh, files/init-5.0.2-r3, -files/initfolding,
+  -files/initfolding-r1, -foldingathome-4.0.0-r2.ebuild,
+  -foldingathome-4.0.0.ebuild:
+  Fix bug 82345, nice 20 doesn't exist.
+  Remove old ebuilds and files.
+
+  08 Feb 2005; Brandon Low <lostlogic@gentoo.org>
+  foldingathome-5.0.2-r3.ebuild:
+  Mark stable on x86
+
+  05 Feb 2005; Brandon Low <lostlogic@gentoo.org> -files/copy_client_config,
+  -files/folding-init.d-r2, -files/folding-init.d-r4, -files/init-5.0.2-r1,
+  -files/init-5.0.2-r2, -foldingathome-5.0.2-r1.ebuild,
+  -foldingathome-5.0.2-r2.ebuild, -foldingathome-5.0.2.ebuild:
+  Clean up some cruft
+
+*foldingathome-5.0.2-r3 (05 Feb 2005)
+
+  05 Feb 2005; Brandon Low <lostlogic@gentoo.org> +files/init-5.0.2-r3,
+  +foldingathome-5.0.2-r3.ebuild:
+  Fix bug #80778
+
+*foldingathome-5.0.2-r2 (04 Feb 2005)
+
+  04 Feb 2005; Brandon Low <lostlogic@gentoo.org> +files/init-5.0.2-r2,
+  +foldingathome-5.0.2-r2.ebuild:
+  Fix bug #79574. Add unitinfo target to initscript to get the status of each
+  core on the system. Thanks to Yosef Meller <yosefm@gmail.com> for the idea
+  and initial patch
+
+*foldingathome-5.0.2-r1 (03 Feb 2005)
+
+  03 Feb 2005; Brandon Low <lostlogic@gentoo.org>
+  +files/copy_client_config-5.0.2-r1, +files/init-5.0.2-r1,
+  +foldingathome-5.0.2-r1.ebuild:
+  Fix bug 71700 hopefully. Use bash not python for copy_client_config. Update
+  the init script to do more sane things and not fail to stop on multi-cpu
+  systems.
+
+*foldingathome-4.0.0-r2 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +files/copy_client_config, +files/folding-conf.d, +files/folding-conf.d-r1,
+  +files/folding-init.d, +files/folding-init.d-r1, +files/folding-init.d-r2,
+  +files/folding-init.d-r3, +files/folding-init.d-r4, +files/folding.sh,
+  +files/initfolding, +files/initfolding-r1, +files/initfolding-r2,
+  +foldingathome-4.0.0-r2.ebuild, +foldingathome-4.0.0.ebuild,
+  +foldingathome-5.0.2.ebuild:
+  Moved from app-sci/foldingathome to sci-biology/foldingathome.
+
+  13 Dec 2004; Patrick Kursawe <phosphan@gentoo.org>
+  -foldingathome-4.0.0-r1.ebuild:
+  Cleanup
+
+*foldingathome-5.0.2 (09 Nov 2004)
+
+  09 Nov 2004; Steve Arnold <nerdboy@gentoo.org> +files/copy_client_config,
+  +files/folding-conf.d-r1, +files/folding-init.d-r4, +files/initfolding-r2,
+  +foldingathome-5.0.2.ebuild:
+  bumped to current version (bug 60318) with ebuild from Gregory P. Smith
+  <greg-gentoo@electricrain.com>.  Gentoo team config.
+
+  12 Jun 2004; Danny van Dyk <kugelfang@gentoo.org>
+  foldingathome-4.0.0-r2.ebuild:
+  Marked ~amd64.
+
+*foldingathome-4.0.0-r2 (07 Jun 2004)
+
+  07 Jun 2004; Patrick Kursawe <phosphan@gentoo.org>
+  foldingathome-3.24-r1.ebuild, foldingathome-3.24.ebuild,
+  foldingathome-4.0.0-r2.ebuild, files/folding-init.d-r3:
+  No longer redirecting output to a redundand log file, see bug #51489
+  Cleanup, removing 3.x versions.
+
+  23 Apr 2004; David Holm <dholm@gentoo.org> foldingathome-4.0.0-r1.ebuild:
+  Added to ~ppc.
+
+*foldingathome-4.0.0-r1 (22 Apr 2004)
+
+  22 Apr 2004; Patrick Kursawe <phosphan@gentoo.org>
+  foldingathome-4.0.0-r1.ebuild, files/folding-conf.d,
+  files/folding-init.d-r2, files/initfolding-r1:
+  Added support to run multiple clients for those with multiprocessors
+  and the ability to pass options to the Folding clients.
+  Based on bug #47526 (by Mike Caley <mjcaley@darkarctic.com>)
+
+  26 Mar 2004; Patrick Kursawe <phosphan@gentoo.org>
+  foldingathome-3.14.ebuild, foldingathome-3.24-r1.ebuild,
+  foldingathome-3.24.ebuild, foldingathome-4.0.0.ebuild:
+  Setting IUSE, removing S= where not necessary, declaring 4.0.0 stable for x86
+
+  09 Mar 2004; Daniel Ahlberg <aliz@gentoo.org> foldingathome-4.0.0.ebuild:
+  Adding amd64 keyword. Closing #43779.
+
+*foldingathome-4.0.0 (03 Mar 2004)
+
+  03 Mar 2004; Patrick Kursawe <phosphan@gentoo.org>
+  foldingathome-4.0.0.ebuild:
+  Version bump inspired by bug #34859
+
+*foldingathome-3.24-r1 (01 Mar 2004)
+
+  01 Mar 2004; Patrick Kursawe <phosphan@gentoo.org>
+  foldingathome-3.24-r1.ebuild, files/folding-init.d-r1, files/folding.sh,
+  files/initfolding:
+  Running as seperate user now.
+
+  05 May 2003; Daniel Ahlberg <aliz@gentoo.org> files/folding-init.d :
+  Fixed stop() in init script. Fix by 
+  Roderick van Domburg <r.s.a.vandomburg@student.utwente.nl> in #20327.
+
+  23 Apr 2003; Daniel Ahlberg <aliz@gentoo.org> foldingathome-3.2.4.ebuild, files/folding-init.d :
+  Now has the version number in SRC_URI and also uses the newer client if we're running >=glibc-2.3.0. 
+  Also updated init script. Closes #19709 and #17715.
+
+*foldingathome-3.24 (27 Feb 2003)
+
+  27 Feb 2003; Daniel Ahlberg <aliz@gentoo.org> foldingathome-3.24.ebuild :
+  Version bump.
+
+  27 Feb 2003; Daniel Ahlberg <aliz@gentoo.org> files/folding-init.d :
+  Start the daemon with nice, closes #12950.
+  
+*foldingathome-3.14 (04 Nov 2002)
+
+  04 Nov 2002; Daniel Ahlberg <aliz@gentoo.org> :
+  Initial import. Ebuild contributed by Ryan Shaw <ryan.shaw@stanfordalumni.org> in #9535.
diff --git a/sci-biology/foldingathome/Manifest b/sci-biology/foldingathome/Manifest
new file mode 100644
index 0000000..1a19e93
--- /dev/null
+++ b/sci-biology/foldingathome/Manifest
@@ -0,0 +1,7 @@
+AUX 999/fah-init 713 RMD160 c4adb8438be73b0679df04422795c6ec88ce4f97 SHA1 a8288e186a83309656703f932950f71ef7846ccc SHA256 4e8ef7f2ae9c5ee22cb9ea246ec69a6676b7225c9729539aa940be2337a8fc3d
+AUX 999/folding-conf.d 855 RMD160 fdcaa327b7b95c9c2e14b9ffd57d02d9a090d0ad SHA1 494ba9f6cc6fc171dc087851e25d95973080de19 SHA256 820a75fb733d06143ed87ad3c1a72f981f440c4ea5904c7c48c0da414788e2f7
+AUX 999/initfolding 129 RMD160 54291b21086999899b4a3706527efb75b0ab4683 SHA1 16705be6fb8cc4078ae84d2dace88426718ba0df SHA256 68cc48a8bd068d10204d2a74d8717baa62ba50567ab2a89c2f27fc27de635c4c
+DIST fah6_alt 312024 RMD160 b9e06ce2961f53aea0695628e04f482c831a34cd SHA1 3481e1a242b18a9a67a5fa4fa3cbcf30d3e1af45 SHA256 db61af58c2b0987244720d1ef5eabb397f182a0be3dee543449492f0457e4574
+EBUILD foldingathome-999.ebuild 1542 RMD160 be12f18e3227363e35d4635b271eae720119d3ac SHA1 0c59548963f86a3fbbe5e592b94b43c45d1954ee SHA256 fefc8004dc024c3e3fd90b72de8c24b325d36cbb089d50e4316b4ad08a235d77
+MISC ChangeLog 9477 RMD160 ede14b11a236de115dee926031a4485b6ca69eed SHA1 a0784b391215455b5498a8477ae3f6253e8f4353 SHA256 52b6b66d1a017eb05eb97debc3df90200c3ffa3e3d7e4ac547704f97166e4a31
+MISC metadata.xml 424 RMD160 18ef625a4315017ead1428c69f1628be0e05a3e3 SHA1 e74c4608795112735b11b3f9053d82e1e351d7ab SHA256 30b75cafd9fda04b994ab9eb0d77c44135479d3373fc0b899b9bde7efebfed12
diff --git a/sci-biology/foldingathome/files/999/fah-init b/sci-biology/foldingathome/files/999/fah-init
new file mode 100644
index 0000000..6f55454
--- /dev/null
+++ b/sci-biology/foldingathome/files/999/fah-init
@@ -0,0 +1,27 @@
+#!/sbin/runscript
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $
+
+opts="${opts} unitinfo"
+
+unitinfo() {
+	einfo "$(head -n1 /opt/foldingathome/unitinfo.txt):"
+	sed -e '1,2d' /opt/foldingathome/unitinfo.txt
+}
+
+start() {
+	ebegin "Starting Folding@Home"
+	cd /opt/foldingathome
+	start-stop-daemon --chdir ${PWD} --chuid foldingathome --nicelevel 19 \
+		--make-pidfile --pidfile "${PIDFILE}" \
+		--start --background --exec ./fah6_alt -- ${FOLD_OPTS}
+	eend $?
+}
+
+stop() {
+	ebegin "Stopping Folding@Home"
+	start-stop-daemon --stop --user foldingathome --pidfile "${PIDFILE}"
+	eend $?
+	[[ -f ${PIDFILE} ]] && killall --user foldingathome --signal SIGKILL
+}
diff --git a/sci-biology/foldingathome/files/999/folding-conf.d b/sci-biology/foldingathome/files/999/folding-conf.d
new file mode 100644
index 0000000..72d211f
--- /dev/null
+++ b/sci-biology/foldingathome/files/999/folding-conf.d
@@ -0,0 +1,21 @@
+# Config file for /etc/init.d/foldingathome
+#
+# The f@h client configuration can be found in /opt/foldingathome/client.cfg
+# Run /opt/foldingathome/initfolding to reconfigure that.
+#
+# Enter options here to be passed to the Folding client:
+#
+#  -oneunit		Instruct the client to quit following the completion of one work unit.
+#  -verbosity x		Sets the output level, from 1 to 9 (max). The default is 3
+#  -forceasm		Force core assembly optimizations to be used if available
+#  -advmethods		Request to be assigned any new Cores or work units.
+#  -smp x		Set the client to run on x cores in SMP mode
+#
+# A full listing of options can be found here:
+# http://www.stanford.edu/group/pandegroup/folding/console-userguide.html
+# But use of other options are not recommended when using the Folding client
+# as a service.
+#
+FOLD_OPTS=""
+PIDFILE=/var/run/folding
+
diff --git a/sci-biology/foldingathome/files/999/initfolding b/sci-biology/foldingathome/files/999/initfolding
new file mode 100644
index 0000000..5fe4830
--- /dev/null
+++ b/sci-biology/foldingathome/files/999/initfolding
@@ -0,0 +1,6 @@
+#!/bin/sh
+
+cd /opt/foldingathome
+/opt/foldingathome/fah6_alt -configonly
+/bin/chown -R foldingathome:nogroup /opt/foldingathome
+
diff --git a/sci-biology/foldingathome/foldingathome-999.ebuild b/sci-biology/foldingathome/foldingathome-999.ebuild
new file mode 100644
index 0000000..e5d3645
--- /dev/null
+++ b/sci-biology/foldingathome/foldingathome-999.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="3"
+
+inherit eutils
+
+DESCRIPTION="Folding@Home is a distributed computing project for protein folding."
+HOMEPAGE="http://folding.stanford.edu/FAQ-SMP.html"
+SRC_URI="http://www.stanford.edu/~kasson/folding/linux/fah6_alt"
+
+LICENSE="folding-at-home"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="mpi"
+
+RDEPEND="mpi? ( >=sys-cluster/openmpi-1.4.3 )"
+
+S="${WORKDIR}"
+
+I="opt/foldingathome"
+
+QA_DT_HASH="${I}/.*"
+QA_PRESTRIPPED="${I}/fah6_alt"
+
+pkg_setup() {
+	I="${EPREFIX}/${I}"
+}
+
+src_install() {
+	exeinto ${I}
+	doexe "${FILESDIR}/${PV}"/initfolding || die
+	doexe fah6_alt || die
+	newconfd "${FILESDIR}/${PV}"/folding-conf.d foldingathome || die
+	newinitd "${FILESDIR}/${PV}"/fah-init foldingathome || die
+}
+
+pkg_preinst() {
+	# the bash shell is important for "su -c" in init script
+	enewuser foldingathome -1 /bin/bash /opt/foldingathome
+}
+
+pkg_postinst() {
+	chown -R foldingathome:nogroup "${EPREFIX}"/opt/foldingathome
+	einfo "To run Folding@home in the background at boot:"
+	einfo " rc-update add foldingathome default"
+	einfo ""
+	einfo "Please run ${I}/initfolding to configure your client"
+	einfo "and edit ${EPREFIX}/etc/conf.d/foldingathome for options"
+	einfo ""
+	einfo "I encourage you to acquire a username and join team 36480."
+	einfo "http://folding.stanford.edu/English/Download#ntoc2"
+	einfo ""
+}
+
+pkg_postrm() {
+	einfo "Folding@home data files were not removed."
+	einfo " Remove them manually from ${I}"
+	einfo ""
+}
diff --git a/sci-biology/foldingathome/metadata.xml b/sci-biology/foldingathome/metadata.xml
new file mode 100644
index 0000000..e6a0858
--- /dev/null
+++ b/sci-biology/foldingathome/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+<maintainer>
+<email>je_fro@gentoo.org</email>
+<name>Jeff Gardner</name>
+</maintainer>
+<longdescription lang="en">
+Folding@home is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
+</longdescription>
+</pkgmetadata>
+