stateless.sh reWORK (nfs nodes now boot)

Imported sci-chemistry/gromacs from Bug 193532

9 files changed, 316 insertions, 44 deletions

diff --git a/catalyst/livecd/2008.0/specs/amd64/livecd-stage1.spec b/catalyst/livecd/2008.0/specs/amd64/livecd-stage1.spec
index 2241595..082e699 100644
--- a/catalyst/livecd/2008.0/specs/amd64/livecd-stage1.spec
+++ b/catalyst/livecd/2008.0/specs/amd64/livecd-stage1.spec
@@ -9,7 +9,7 @@ source_subpath: default/stage3-amd64-desktop-2008.0
 # Kyron:
 portage_confdir: /var/git/clustering-livecd/profiles/hpc-clustering/
 pkgcache_path: /var/tmp/catalyst/packages/amd64_desktop
-portage_overlay: /var/git/clustering-livecd/overlay/
+portage_overlay: /var/git/clustering-livecd/overlay/ /usr/local/portage/alexxy
 ### end
 
 # Kyron: added 
@@ -196,4 +196,6 @@ livecd/packages:
 	app-admin/eselect-cblas
 	app-admin/eselect-blas
 	app-admin/eselect-lapack
-
+# Added growmacs as per Alexey Shvetsov's request ;)
+# from: Bug 193532	
+	sci-chemistry/gromacs
diff --git a/catalyst/nfsroot/2008.0/overlay/boot/stateless.sh b/catalyst/nfsroot/2008.0/overlay/boot/stateless.sh
index 0cd3ffd..ed18b92 100755
--- a/catalyst/nfsroot/2008.0/overlay/boot/stateless.sh
+++ b/catalyst/nfsroot/2008.0/overlay/boot/stateless.sh
@@ -7,20 +7,19 @@
 
 MODPROBE=/sbin/modprobe
 IFCONFIG=/sbin/ifconfig
-MYHOST=$(/sbin/dhcpcd -H; /bin/hostname) # By default, we'll use the DHCP assigned hostname
+#MYHOST=$(/sbin/dhcpcd -H; /bin/hostname) # By default, we'll use the DHCP assigned hostname
 
 NODE_NAME="node"
 
 ahostname(){
 	if [ -z ${MYHOST} ]; then
 		echo "DHCP didn't tell me my name. Generating my own hostname..."
-	MYHOST="${NODE_NAME}`$IFCONFIG eth0 | awk '/inet addr/ {print $2}' | tr -t . ' ' | awk '{print $4}'`"
+		MYHOST="${NODE_NAME}${IP##*.}"
+		echo "I proclaim that I am $MYHOST !!"
 	else
 		echo DHCP told me my hostname is ${MYHOST}...
 		echo "Setting domainname to DHCP's settings"
-		# Unfortunately, this doesn't work anymore so we have to chaet: 
-		#/sbin/dhcpcd -D
-		#/bin/domainname cluster.local
+		/bin/domainname $DOMAIN
 	fi
 
 	echo "STATELESS: Setting Hostname to $MYHOST"
@@ -28,21 +27,23 @@ ahostname(){
 	/bin/hostname "$MYHOST"
 }
 
-getparams() {
-	local cmdline=$(dmesg | grep '^Kernel command line' | sed 's/^Kernel command line://g')
-	for pp in $cmdline; do
-		echo $pp | grep '^softlevel=' >/dev/null 2>&1
-		if [ $? -eq 0 ]; then
-			echo $pp | sed 's/softlevel=//g'
-			return 0
-		fi
-	done
-	echo ""
-	return 1
-}
+#getparams() {
+#	#local cmdline=$(dmesg | grep '^Kernel command line' | sed 's/^Kernel command line://g')
+#	cmdline=$(cat /proc/cmdline)
+#	for pp in $cmdline; do
+#		echo $pp | grep '^softlevel=' >/dev/null 2>&1
+#		if [ $? -eq 0 ]; then
+#			echo $pp | sed 's/softlevel=//g'
+#			return 0
+#		fi
+#	done
+#	echo ""
+#	return 1
+#}
 
 isset() {
-	for p in $(getparams | tr ',' ' '); do
+	#for p in $(getparams | tr ',' ' '); do
+	for p in $(get_param softlevel); do
 		if [ "$p" == "$1" ]; then
 			return 0
 		fi
@@ -51,20 +52,14 @@ isset() {
 }
 
 aunionfs() {
-	isset unionfs
-	if [ $? -eq 0 ]; then
-		echo "STATELESS: Loading module unionfs ..."
-#		$MODPROBE unionfs
-		while [ "$1" != "" ]; do
-			echo "STATELESS: Mounting tmpfs $1 ..."
-			mount -n -t tmpfs -o defaults none /mnt/unionfs/$1
-			echo "STATELESS: Mounting $1 unionfs ..."
-			mount -n -t unionfs -o dirs=/mnt/unionfs/$1=rw:/$1=ro none /$1
-			shift
-		done
-	else
-		echo "STATELESS: Not using unionfs as requested ..."
-	fi
+#	$MODPROBE unionfs
+	while [ "$1" != "" ]; do
+		echo "STATELESS: Mounting tmpfs $1 ..."
+		mount -n -t tmpfs -o defaults none /mnt/unionfs/$1
+		echo "STATELESS: Mounting $1 unionfs ..."
+		mount -n -t unionfs -o dirs=/mnt/unionfs/$1=rw:/$1=ro none /$1
+		shift
+	done
 }
 
 # ahosts was added so that we could dynamically change the NFS server address
@@ -72,11 +67,59 @@ aunionfs() {
 # when you want to split the load onto different NIC interfaces within a same
 # logical network.
 ahosts() {
-	local SERV_IP=$(dmesg | egrep -oe 'rootserver=([0-9]+\.?){1,4}')
-	echo "Setting rootserver to ${SERV_IP#*=} in /etc/hosts file..."
-	echo "rootserver ${SERV_IP#*=}" >> /etc/hosts
+	echo "Setting rootserver to $ROOTSERV in /etc/hosts file..."
+	echo "rootserver $ROOTSERV" >> /etc/hosts
+	echo "Setting up fstab"
+	echo "$ROOTSERV:$ROOTPATH     /  nfs   ro,defaults,hard,intr,actimeo=120,timeo=14,tcp 0 1" > /etc/fstab
+}
+
+# get_param: parses parameters in PARSELINE which could be, for example, the kernel's command line
+# (This implies PARSELINE=$(cat /proc/cmdline) 
+# Example:
+# 	ip=dhcp nfsroot=192.168.1.2:/tftproot/nfsroot/x86_64/,hard,intr init=/boot/stateless.sh softlevel=unionfs
+# IN: 
+#	$1: parameter we want (ie: nfsroot)
+#	$2: which token # we want, ie: the IP address of nfsroot it token 1
+get_param() {
+    PARAM=$2
+    for opt in $PARSELINE
+    do
+        case $opt in
+            ${1}=*) set $(echo $opt | sed -e's/[=:,]/ /g' )
+                    if [[ -z $PARAM ]]; then
+                        shift
+                        echo $*
+                    else
+                        shift $PARAM
+                        echo $1
+                    fi
+                    return 0
+            ;;
+        esac
+    done
+    echo "Parameter '$1' not found" >2
+    return 1
+}
+
+# Used to extract useful information for the rest of the configuration
+# It's a horrible hack that parses dmesg but, unfortunately, /proc/net/pnp
+# is insufficient even with /proc/cmdline
+# Here is an example output of dmesg (partial)
+#IP-Config: Complete:
+#      device=eth0, addr=10.0.1.140, mask=255.255.255.0, gw=10.0.1.129,
+#     host=thinkbig24, domain=cluster.local, nis-domain=(none),
+#     bootserver=10.0.1.129, rootserver=10.0.1.129, rootpath=/tftproot/AthlonXP
+
+import_dhcp_info() {
+	PARSELINE=$(dmesg | grep -A3 'IP-Config: Complete:' | sed -e 's/[:,]/ /g' | tr -d '\n')
+	MYIP=$(get_param addr 1)
+	MYHOST=$(get_param host 1)
+	DOMAIN=$(get_param domain 1)
+	ROOTPATH=$(get_param rootpath 1)
+	ROOTSERV=$(get_param rootserver 1)
 }
 
+import_dhcp_info
 aunionfs etc var tmp
 ahostname
 ahosts
diff --git a/catalyst/nfsroot/2008.0/scripts/nfsroot_setup.sh b/catalyst/nfsroot/2008.0/scripts/nfsroot_setup.sh
index 4ac5cd4..164838c 100644
--- a/catalyst/nfsroot/2008.0/scripts/nfsroot_setup.sh
+++ b/catalyst/nfsroot/2008.0/scripts/nfsroot_setup.sh
@@ -10,6 +10,7 @@ kernel_links()
 	cd /boot
 	ln -s kernel-* vmlinuz
 	ln -s initramfs-* initramfs
+	
 }
 
 unionfs_prep()
@@ -17,7 +18,7 @@ unionfs_prep()
 	echo "====================================="
 	echo "=adding unionfs required dirs========"
 	echo "====================================="
-	for I in etc va tmp
+	for I in etc var tmp
 	do
 		mkdir -p /mnt/unionfs/$I
 	done
@@ -25,9 +26,14 @@ unionfs_prep()
 
 set_runlevel()
 {
-	# maybe something to do here...can't remember...
-	#sed -i -e's:l3:3:wait:/sbin/rc nfsmount::' etc/inittab
+	ln -s /etc/runlevels/default /etc/runlevels/unionfs
 }
+
+run_depmod() {
+	depmod -a -b /usr/src/linux
+}
+
 kernel_links
 unionfs_prep
+run_depmod
 
diff --git a/catalyst/nfsroot/2008.0/specs/amd64/nfsroot_stage4.spec b/catalyst/nfsroot/2008.0/specs/amd64/nfsroot_stage4.spec
index ff60864..f28f70d 100644
--- a/catalyst/nfsroot/2008.0/specs/amd64/nfsroot_stage4.spec
+++ b/catalyst/nfsroot/2008.0/specs/amd64/nfsroot_stage4.spec
@@ -54,13 +54,13 @@ distcc_hosts:
 # targets to minimize problems.
 # example:
 # portage_confdir: /etc/portage
-portage_confdir: /var/git/clustering-livecd/profiles/hpc-clustering/
+portage_confdir: /var/git/clustering-livecd/profiles/hpc-clustering/ 
 
 # This option specifies the location to a portage overlay that you would like to
 # have used when building this target.
 # example:
 # portage_overlay: /usr/local/portage
-portage_overlay: /var/git/clustering-livecd/overlay/
+portage_overlay: /var/git/clustering-livecd/overlay/ 
 
 # This allows the optional directory containing the output packages for
 # catalyst.  Mainly used as a way for different spec files to access the same
@@ -174,6 +174,9 @@ stage4/rcadd:
 # the runlevel off to remove the script from any runlevels detected.  We do not
 # use this on the official media, so it is left blank.
 stage4/rcdel:
+	root
+	fsck
+	mtab
 
 # This overlay is dropped onto the filesystem within the loop.  This can be used
 # for such things as updating configuration files or adding anything else you
diff --git a/overlay/sci-chemistry/gromacs/Manifest b/overlay/sci-chemistry/gromacs/Manifest
new file mode 100644
index 0000000..abdf9c1
--- /dev/null
+++ b/overlay/sci-chemistry/gromacs/Manifest
@@ -0,0 +1,2 @@
+DIST gromacs-3.3.3.tar.gz 8013789 RMD160 c7b495423eb07682e88bd7d5c61e0aa9156a17d1 SHA1 318802e39f3ca3e847261a3b96906266e32deba2 SHA256 b95becbe410b71fe9bc19b91dfeb98b940dbb2d66613c9e1de7f6d21fb7534fa
+EBUILD gromacs-3.3.3.ebuild 6083 RMD160 c4d9109897552655932a06c22fab2121e400433f SHA1 f933a478376aaca8b6dcf1d38616b8fed924d598 SHA256 52a227049f109e255e6b5819ac48fd90c8c7f2731c5bfd167f18c42f8d6c5691
diff --git a/overlay/sci-chemistry/gromacs/gromacs-3.3.3.ebuild b/overlay/sci-chemistry/gromacs/gromacs-3.3.3.ebuild
new file mode 100644
index 0000000..1197744
--- /dev/null
+++ b/overlay/sci-chemistry/gromacs/gromacs-3.3.3.ebuild
@@ -0,0 +1,213 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+LIBTOOLIZE="true"
+inherit autotools eutils flag-o-matic fortran multilib
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
+IUSE="3dnow X altivec blas double-precision gsl lapack mpi +single-precision sse sse2 static xml"
+
+# mopac7 qm/mm is broken until we can get files from
+# http://md.chem.rug.nl/~groenhof/qmmm.html
+# or somewhere else...
+
+DEPEND=">=sci-libs/fftw-3.0.1
+	app-shells/tcsh
+	X? ( x11-libs/libX11
+		x11-libs/libXt
+		x11-libs/libXp
+		x11-libs/libXext
+		x11-proto/xproto
+		x11-libs/openmotif )
+	blas? ( virtual/blas )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2 )"
+
+FORTRAN="g77 gfortran ifc"
+
+src_unpack() {
+
+	unpack ${A}
+	cd "${S}"
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	# Fix a sandbox violation that occurs when re-emerging with mpi.
+	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed -e "s:\$\$libdir:\$temp_libdir:" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	# Rename disco manpage to fix bug #210083.
+	sed "s:disco.1:g_disco.1:" \
+	-i "${S}"/man/man1/Makefile.am \
+	|| die "sed failed to rename disco"
+
+	mv "${S}"/man/man1/disco.1 "${S}"/man/man1/g_disco.1
+
+	eautoreconf
+
+	cd "${WORKDIR}"
+	mv "${P}" "${P}-single"
+	if ( use double-precision ) ; then
+		einfo "Moving sources for Multiprecision Build"
+		cp -prP "${P}-single" "${P}-double"
+	fi
+}
+
+src_compile() {
+
+	# static should work but something's broken.
+	# gcc spec file may be screwed up.
+	# Static linking should try -lgcc instead of -lgcc_s.
+	# For more info:
+	# http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html
+
+	# if we don't set C[XX]FLAGS configure will set: -O3 -finline-functions
+	# -funroll-all-loops
+	# append-flags "-O3 -finline-functions -funroll-all-loops"
+	# use x86 && append-flags "-malign-double"
+
+	# We will compile single precision by default, and suffix double-precision with _d.
+	# Sparc is the only arch I can test on that needs to use fortran.
+	local myconf ;
+
+	case "${ARCH}" in
+
+		x86)
+			if ( use sse || use sse2 ) ; then
+				myconf="${myconf} --enable-ia32-sse"
+			fi
+			myconf="$myconf $(use_enable 3dnow ia32-3dnow)"
+
+			if ( ! use sse && ! use sse2 && ! use 3dnow ) ; then
+				if ! has_version "=sys-devel/gcc-3*" ; then
+					die "If you must run gromacs without sse (not recommended) gfortran will not work."
+				else
+					myconf="${myconf} --enable-fortran" && fortran_pkg_setup
+				fi
+			else
+				myconf="${myconf} --disable-fortran"
+			fi
+			;;
+
+		amd64)
+			myconf="$myconf --enable-x86-64-sse --disable-fortran"
+			;;
+
+		ppc*)
+			if use altivec ; then
+				myconf="${myconf} --enable-ppc-altivec --disable-fortran"
+			else
+				if ! has_version "=sys-devel/gcc-3*" ; then
+					die "If you must run gromacs without sse (not recommended) gfortran will not work."
+				else
+					myconf="${myconf} --enable-fortran" && fortran_pkg_setup
+				fi
+			fi
+			;;
+
+		ia64)
+			myconf="$myconf --enable-ia64-asm --disable-fortran"
+			;;
+
+		alpha)
+			if ! has_version "=sys-devel/gcc-3*" ; then
+				die "If you must run gromacs without sse (not recommended) gfortran will not work."
+			else
+				myconf="$myconf --enable-fortran" && fortran_pkg_setup
+			fi
+			;;
+
+		sparc)
+			if ! has_version "=sys-devel/gcc-3*" ; then
+				die "If you must run gromacs without sse (not recommended) gfortran will not work."
+			else
+				myconf="${myconf} --enable-fortran" && fortran_pkg_setup
+			fi
+			;;
+	esac
+
+	# if we need external blas
+	if use blas; then
+		export LIBS="${LIBS} -lblas"
+		myconf="${myconf} $(use_with blas external-blas)"
+	fi
+
+	# if we need external lapack
+	if use lapack; then
+		export LIBS="${LIBS} -llapack"
+		myconf="${myconf} $(use_with lapack external-lapack)"
+	fi
+
+	myconf="--datadir=/usr/share \
+			--bindir=/usr/bin \
+			--libdir=/usr/$(get_libdir) \
+			--with-fft=fftw3 \
+			$(use_with gsl) \
+			$(use_enable mpi) \
+			$(use_with X x) \
+			$(use_with xml) \
+			$(use_enable static all-static) \
+			${myconf}"
+
+	if ( use double-precision && use single-precision ); then
+		einfo "Building Single Precison Gromacs"
+		cd "${WORKDIR}"/"${P}"-single
+		myconf="${myconf}  --enable-float"
+		econf ${myconf} || die "Single Precision econf failed"
+		emake || die "Single Precision emake failed"
+
+		einfo "Building Double Precision Gromacs"
+		cd "${WORKDIR}"/"${P}"-double
+		myconf="${myconf} --enable-double --program-suffix=_d"
+		econf ${myconf} || die "Double Precision econf failed"
+		emake || die "Double Precision emake failed"
+	else
+		use single-precision && cd "${WORKDIR}"/"${P}"-single
+		use double-precision && cd "${WORKDIR}"/"${P}"-double
+		cd "${WORKDIR}"/"${P}"
+		myconf="${myconf} $(use_enable double-precision double) \
+				$(use_enable single-precision float) --program-suffix='' "
+		econf ${myconf} || die "configure failed"
+		emake || die "emake failed"
+	fi
+}
+
+src_install() {
+	if ( use single-precision ); then
+		einfo "Installing Single Precision"
+		cd "${WORKDIR}"/"${P}"-single
+		emake DESTDIR="${D}" install || die "Installing Single Precision failed"
+	fi
+
+	if ( use double-precision ) ; then
+	einfo "Installing Double Precision"
+		cd "${WORKDIR}"/"${P}"-double
+		emake DESTDIR="${D}" install || die "Installing Double Precision failed"
+	fi
+
+	dodoc AUTHORS INSTALL README
+	# Move html and leave examples and templates under /usr/share/gromacs.
+	mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/
+}
diff --git a/overlay/sys-cluster/beowulf-head/Manifest b/overlay/sys-cluster/beowulf-head/Manifest
index 449637a..dc2f003 100644
--- a/overlay/sys-cluster/beowulf-head/Manifest
+++ b/overlay/sys-cluster/beowulf-head/Manifest
@@ -1,3 +1,3 @@
-AUX cluster.conf 1592 RMD160 58464c00571c6c84e7ed1d63686f0d02f88b1597 SHA1 1d35aaba87de3a40de6a5922777f0760453cbf75 SHA256 8065a6610621e233d966b5c45f154fcba1ca1c699f42c86af7ae9f5b16053d65
-EBUILD beowulf-head-0.1.ebuild 4120 RMD160 3d3fcbe754d847355b51b8a2d069ab360f5ef6a9 SHA1 ffcf9be5d4c3cb7333ec55be0323a0aa2789fcfb SHA256 cc174265ba8eb540bac2b476f3ce27466af325c8752bf12d6ae1113a7c6e01d5
+AUX cluster.conf 2401 RMD160 e5f37c56b03791f6a884bfad6b37ec17f27045cf SHA1 685c32c8deab47c326e7e05f41caa127e11de863 SHA256 e0142db68ecb9182161b9818d1a8cf944cf316ae694c095123c6d4f8a6f0ce10
+EBUILD beowulf-head-0.1.ebuild 4558 RMD160 c7f9a2e729524d7fb600ef1ae709cb8e56be5f86 SHA1 da07cdbaa572424a387f897fc0b0bf48d37dfc09 SHA256 9c45ca4868bd4ec12622020a49b1eedac03ffd289fb7ad71c06b0831a80a53ca
 MISC ChangeLog 101 RMD160 d735719ccc09237e68e4e984eb5451000b06c382 SHA1 79098d1e8ae451f0430d363da6b717966ade6e78 SHA256 8dd010e2772026c4a6b86839842931b99c85c44a5e9f380864cc275b55587ac2
diff --git a/profiles/hpc-clustering/package.keywords/baselayout2 b/profiles/hpc-clustering/package.keywords/baselayout2
new file mode 100644
index 0000000..aa526a1
--- /dev/null
+++ b/profiles/hpc-clustering/package.keywords/baselayout2
@@ -0,0 +1,2 @@
+=sys-apps/baselayout-2.0.0 **
+=sys-apps/openrc-0.2.5 **
diff --git a/profiles/hpc-clustering/package.keywords/gromacs b/profiles/hpc-clustering/package.keywords/gromacs
new file mode 100644
index 0000000..0b00576
--- /dev/null
+++ b/profiles/hpc-clustering/package.keywords/gromacs
@@ -0,0 +1 @@
+=sci-chemistry/gromacs-3.3.3 **