From 78af18063cb9a68e4c8eb83f971705dd603dec50 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 13 Mar 2015 15:27:37 +0100
Subject: [PATCH 01/50] scripts/Bootstrap/Pmodules/libpmodules.bash:
 'check_modules_env()' splitted into 'check_pmodules_env_vars()' and
 'check_pmodules_directories()'

---
 scripts/Bootstrap/Pmodules/libpmodules.bash | 22 ++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/scripts/Bootstrap/Pmodules/libpmodules.bash b/scripts/Bootstrap/Pmodules/libpmodules.bash
index 0590835..c54bb78 100644
--- a/scripts/Bootstrap/Pmodules/libpmodules.bash
+++ b/scripts/Bootstrap/Pmodules/libpmodules.bash
@@ -58,7 +58,7 @@ get_options() {
 	"${bindir}/getopt" "$@"
 }
 
-check_pmodules_env() {
+check_pmodules_env_vars() {
 	[[ -n "${PSI_PREFIX}" ]] &&
 	    [[ -n "${PSI_CONFIG_DIR}" ]] &&
 	    [[ -n "${PSI_MODULES_ROOT}" ]] &&
@@ -67,14 +67,22 @@ check_pmodules_env() {
 	    [[ -n "${PMODULES_VERSION}" ]] || die 1 "
 Error: the module environment you are going to use as source has not been
 initialized properly!"
+}
 
-	[[ -d "${PSI_PREFIX}" ]] &&
-	    [[ -d "${PSI_PREFIX}/${PSI_CONFIG_DIR}" ]] &&
-	    [[ -d "${PSI_PREFIX}/${PSI_MODULES_ROOT}" ]] &&
-	    [[ -d "${PSI_PREFIX}/${PSI_TEMPLATES_DIR}" ]] &&
-	    [[ -d "${PMODULES_HOME}" ]] || die 1 "
-Error: the module environment '$PSI_PREFIX' has not been initialized properly!"
+check_pmodules_directories() {
+	local -r src_prefix="$1"
 
+	[[ -d "${src_prefix}" ]] &&
+	    [[ -d "${src_prefix}/${PSI_CONFIG_DIR}" ]] &&
+	    [[ -d "${src_prefix}/${PSI_MODULES_ROOT}" ]] &&
+	    [[ -d "${src_prefix}/${PSI_TEMPLATES_DIR}" ]] &&
+	    [[ -d "${src_prefix}/Tools/Pmodules/${PMODULES_VERSION}" ]] || die 1 "
+Error: the module environment '${src_prefix}' has not been initialized properly!"
+}
+
+check_pmodules_env() {
+	check_pmodules_env_vars
+	check_pmodules_directories "${PSI_PREFIX}"
 }
 
 

From 543f7fa523c15a81c1cc5451d1aad4b075bc0d01 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 13 Mar 2015 15:31:56 +0100
Subject: [PATCH 02/50] scripts/Bootstrap/Pmodules/modmanage.in: create dir
 '/modulefiles'; add installation source to environment.bash

---
 scripts/Bootstrap/Pmodules/modmanage.in | 24 ++++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/scripts/Bootstrap/Pmodules/modmanage.in b/scripts/Bootstrap/Pmodules/modmanage.in
index 6301e31..4ec9b3b 100755
--- a/scripts/Bootstrap/Pmodules/modmanage.in
+++ b/scripts/Bootstrap/Pmodules/modmanage.in
@@ -25,7 +25,7 @@ Switches:
         --force       force overwrite
 
 Available SubCommands and Args:
-        init [--src=<src>] [--user=<user>] --dst=<dst>
+        init [--src=<src>] [--user=<user>] <dst>
                 Initialize a new minimal Pmodule environment.
 
         install <module> [--with=<dep>...]
@@ -197,6 +197,7 @@ environment at '${PSI_PREFIX}'
 "
 
 	init_pmodules_environment() {
+		local -r src_prefix="${PSI_PREFIX}"
 		local -r target_prefix=$1
 		local src=''
 		local dst=''
@@ -212,26 +213,37 @@ environment at '${PSI_PREFIX}'
 		$DRY mkdir -p "${target_prefix}" || die 1 "Error: make directory failed!"
 		echo
 
-		src="${PSI_PREFIX}/${PSI_CONFIG_DIR}/"
+		src="${src_prefix}/${PSI_CONFIG_DIR}/"
 		dst="${target_prefix}/${PSI_CONFIG_DIR}/"
 		echo "Synching configuration from '${src}' to '${dst}'..."
 		$DRY rsync --recursive --links --perms --delete \
 		     "${src}" "${dst}" || die 1 "Error: synch operation failed!"
 		echo
 		
-		src="${PSI_PREFIX}/${PSI_TEMPLATES_DIR}/"
+		src="${src_prefix}/${PSI_TEMPLATES_DIR}/"
 		dst="${target_prefix}/${PSI_TEMPLATES_DIR}/"
 		echo "Synching template files from '${src}' to '${dst}'..."
 		$DRY rsync --recursive --links --perms --delete \
 		     "${src}" "${dst}" || die 1 "Error: synch operation failed!"
 		echo
 
+		dst="${target_prefix}/${PSI_MODULES_ROOT}/"
+		echo "Creating root directory '${dst}' for module hierarchy ..."
+		$DRY mkdir -p "${dst}"
+		echo
+
 		echo "Syncing Pmodules ..."
 		sync_module "Tools/Pmodules/${PMODULES_VERSION}" \
-			    "${PSI_PREFIX}" \
+			    "${src_prefix}" \
 			    "${target_prefix}" || die 1 "Error: sync Pmodules failed!"
 		echo
-		
+
+		dst="${target_prefix}/${PSI_CONFIG_DIR}/environment.bash"
+		echo "Adding installation source '${src_prefix}' to '${dst}'..."
+		sed -i .bak '/PMODULES_INSTALL_SOURCE/d' "${dst}"
+		echo "declare -x PMODULES_INSTALL_SOURCE=\"${src_prefix}\"" >> "${dst}"
+		echo
+
 		if [[ -n "${user}" ]]; then
 	                echo "Changing user of new module environment to '${user}'..."
                         $DRY chown -R "${user}" "${target_prefix}" || die 1 "Error: changing owner failed!"
@@ -287,7 +299,7 @@ subcommand_install() {
 		esac
 		shift
 	done
-	${PMODULES_HOME}/bin/modulecmd bash search "${module_pattern[@]}" "${with[@]/#/--with}" "${releases[@]/#/--release=}" --no-header
+	PSI_PREFIX="${PMODULES_INSTALL_SOURCE}" ${PMODULES_HOME}/bin/modulecmd bash search "${module_pattern[@]}" "${with[@]/#/--with}" "${releases[@]/#/--release=}" --no-header
 }
 
 while (($# > 0)); do

From c537be0ed9b821751eea9e332751ec1cf319d7a9 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 13 Mar 2015 15:33:23 +0100
Subject: [PATCH 03/50] scripts/Bootstrap/Pmodules/modulecmd.in: '--src=<dir>'
 option added to search sub-command

---
 scripts/Bootstrap/Pmodules/modulecmd.in | 44 ++++++++++++++++---------
 1 file changed, 29 insertions(+), 15 deletions(-)

diff --git a/scripts/Bootstrap/Pmodules/modulecmd.in b/scripts/Bootstrap/Pmodules/modulecmd.in
index 9901229..ba1a5f2 100755
--- a/scripts/Bootstrap/Pmodules/modulecmd.in
+++ b/scripts/Bootstrap/Pmodules/modulecmd.in
@@ -10,6 +10,8 @@ declare -rx PSI_LIBMODULES="${PMODULES_DIR}/lib/libmodules.tcl"
 declare -r modulepath_root="${PSI_PREFIX}/${PSI_MODULES_ROOT}"
 declare -ra modulepath=( ${MODULEPATH//:/ } )
 
+source "${PMODULES_DIR}/lib/libpmodules.bash"
+
 if set -o | grep 'xtrace' | grep -q 'on'; then
         declare -r __XTRACE__='on'
 else
@@ -668,22 +670,25 @@ subcommand_avail() {
 }
 
 get_families () {
-	if [[ ! -d "${modulepath_root}" ]]; then
+	local -r module_hierarchy_root="$1"
+	if [[ ! -d "${module_hierarchy_root}" ]]; then
 		echo ""
 	else
 	{
-		cd "${modulepath_root}"
+		cd "${module_hierarchy_root}"
 		ls -1
 	}
 	fi
 }
 
 #
-# $1: family name (not path!)
+# $1: root of modulefile hierarchy
+# $2: family name (not path!)
 compute_family_depth () {
+	local -r module_hierarchy_root="$1"
+	local -r family=$2
 	{
-		local -r family=$1
-		cd "${modulepath_root}"
+		cd "${module_hierarchy_root}"
 		local -r tmp=$(find "${family}" -depth -type f -o -type l | head -1)
 		local -ar tmp2=( ${tmp//\// } )
 		local depth=${#tmp2[@]}
@@ -701,8 +706,8 @@ subcommand_use() {
 			echo -e "\t${f}" 1>&2
 		done
 		echo -e "\nFamilies you may use in addition:" 1>&2
-		for family in $(get_families); do
-			local -i depth=$( compute_family_depth "${family}")
+		for family in $(get_families "${modulepath_root}"); do
+			local -i depth=$( compute_family_depth "${modulepath_root}" "${family}")
 			if ! is_used_family $f && (( depth == 0 )); then
 			    echo -e "\t${f}" 1>&2
 			fi
@@ -739,7 +744,7 @@ subcommand_use() {
 			        # releases are always *appended*
 			        append_path PSI_USED_RELEASES "${arg}"
 			elif [[ ! ${arg} =~ */* ]] && [[ -d ${modulepath_root}/${arg} ]]; then
-				local -i depth=$(compute_family_depth "${arg}")
+				local -i depth=$(compute_family_depth "${modulepath_root}" "${arg}")
 				if (( depth == 0 )); then	
 			        	dirs_to_add+=( ${modulepath_root}/${arg} )
 				else
@@ -816,6 +821,7 @@ subcommand_clear() {
 subcommand_search() {
 	local modules=()
 	local with_modules='//'
+	local src_prefix=''
 	local _print_header='yes'
 	local _print_modulefiles='no'
 	local use_releases=':'
@@ -833,22 +839,23 @@ subcommand_search() {
 	# $1: module name pattern
 	search () {
 		local -r module=$1
+		local -r module_hierarchy_root="${src_prefix}/${PSI_MODULES_ROOT}"
 		# we must write temporary results to a file for sorting
 		local -r tmpfile=$( mktemp /tmp/$(basename $0).XXXXXX ) || exit 1
 		local family
 		# loop over all families
-		for family in $(get_families); do
-			local -i depth=$( compute_family_depth ${family} )
+		for family in $(get_families "${module_hierarchy_root}"); do
+			local -i depth=$( compute_family_depth "${module_hierarchy_root}" "${family}" )
 			# get all potential directories of family $f with module-files 
 			local mpaths=( $(find \
-					     "${modulepath_root}/${family}" \
+					     "${module_hierarchy_root}/${family}" \
 					     -type d \
 					     -mindepth ${depth} -maxdepth ${depth} \
 					     2>/dev/null))
 			local mpath
 			for mpath in "${mpaths[@]}"; do
 				# get dependencies encoded in directory name
-				local p="${mpath/${modulepath_root}}"
+				local p="${mpath/${module_hierarchy_root}}"
 				p=( ${p//\// } )
 				local deps=()
 				local -i i
@@ -870,7 +877,7 @@ subcommand_search() {
 				done
 			done
 		done
-		if [[ "{_print_modulefiles}" == "no" ]]; then
+		if [[ "${_print_modulefiles}" == "no" ]]; then
 			sort -k 1,1 -k 4,4 -k 5,5 "${tmpfile}" | awk "${with_modules}" 1>&2
 		else
 			while read -a line; do
@@ -914,6 +921,10 @@ subcommand_search() {
 			-a | --all-releases )
 				use_releases=${available_releases}
 				;;
+			--src=* )
+				src_prefix=${1/--src=}
+				check_pmodules_directories "${src_prefix}"
+				;;
 			-? | -h | --help )
 				usage
 				;;
@@ -927,9 +938,12 @@ subcommand_search() {
 		esac
 		shift
 	done
-
+	if [[ -z "${src_prefix}" ]]; then
+	        src_prefix="${PSI_PREFIX}"
+	fi
+	
 	if [[ "${use_releases}" == ":" ]]; then
-	    use_releases=":${PSI_USED_RELEASES}:"
+                use_releases=":${PSI_USED_RELEASES}:"
 	fi
 	
 	[[ "${_print_header}" == "yes" ]] && print_header

From 2c2a4f669d68382d250f9c5eb0b54bc165027d90 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 17 Mar 2015 10:05:25 +0100
Subject: [PATCH 04/50] scripts/Bootstrap/Pmodules/modulecmd.in: redirect
 output of sub-command 'search' to stderr if option '--print-modulefiles' is
 used

---
 scripts/Bootstrap/Pmodules/modulecmd.in | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/Bootstrap/Pmodules/modulecmd.in b/scripts/Bootstrap/Pmodules/modulecmd.in
index ba1a5f2..bc47ba7 100755
--- a/scripts/Bootstrap/Pmodules/modulecmd.in
+++ b/scripts/Bootstrap/Pmodules/modulecmd.in
@@ -881,11 +881,11 @@ subcommand_search() {
 			sort -k 1,1 -k 4,4 -k 5,5 "${tmpfile}" | awk "${with_modules}" 1>&2
 		else
 			while read -a line; do
-				echo -n "${line[2]}/"
+				echo -n "${line[2]}/" 1>&2
 				for d in "${line[@]:3}"; do
-					echo -n "$d/"
+					echo -n "$d/" 1>&2
 				done
-				echo "${line[0]}"
+				echo "${line[0]}" 1>&2
 			done < <(sort -k 1,1 -k 4,4 -k 5,5 "${tmpfile}" | awk "${with_modules}")
 		fi
 		rm -f "${tmpfile}"

From 2fb13788e5f834038a1b0866c52bd4900a8d0df5 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 17 Mar 2015 10:59:47 +0100
Subject: [PATCH 05/50] scripts/Bootstrap/Pmodules/modmanage.in: sub-command
 'install' implemented

---
 scripts/Bootstrap/Pmodules/modmanage.in | 40 +++++++++++++++++++++++--
 1 file changed, 37 insertions(+), 3 deletions(-)

diff --git a/scripts/Bootstrap/Pmodules/modmanage.in b/scripts/Bootstrap/Pmodules/modmanage.in
index 4ec9b3b..dfec8d1 100755
--- a/scripts/Bootstrap/Pmodules/modmanage.in
+++ b/scripts/Bootstrap/Pmodules/modmanage.in
@@ -267,8 +267,10 @@ subcommand_install() {
 	local -a with=()
 	local -a releases=()
 	local -a module_pattern=()
+	local -r src_prefix="${PMODULES_INSTALL_SOURCE}"
+	local -r target_prefix="${PSI_PREFIX}"
 
-	opts=$(get_options -o h -l with: -l release: -l help -- "$@")
+	opts=$(get_options -o h -l with: -l release: -l help -l src: -- "$@")
 	if [[ $? != 0 ]]; then
 		subcommand_help_install
 		exit 1
@@ -278,7 +280,10 @@ subcommand_install() {
 		case $1 in
 			--release )
 				releases+=( "$2" )
-				echo $2
+				shift
+				;;
+			--src )
+				src_prefix="$2"
 				shift
 				;;
 			--with )
@@ -299,7 +304,36 @@ subcommand_install() {
 		esac
 		shift
 	done
-	PSI_PREFIX="${PMODULES_INSTALL_SOURCE}" ${PMODULES_HOME}/bin/modulecmd bash search "${module_pattern[@]}" "${with[@]/#/--with}" "${releases[@]/#/--release=}" --no-header
+	local -A modules_to_install
+	local -i n=0
+	while read rel_modulefile; do
+		modules_to_install["${rel_modulefile}"]+='.'
+		let n+=1
+	done < <(${PMODULES_HOME}/bin/modulecmd bash search \
+				 "${module_pattern[@]}" \
+				 "${with[@]/#/--with}" \
+				 "${releases[@]/#/--release=}" \
+				 --no-header --print-modulefiles \
+				 --src="${src_prefix}" 2>&1)
+	(( n == 0 )) && die 0 "Nothing to install..."
+	echo -e "The following modules will be installed/updated:\n" 1>&2
+	for key in "${!modules_to_install[@]}"; do
+		echo "    ${key}" 1>&2
+	done
+	echo 1>&2
+	get_YN_answer "Do you want to continue? [n] " || die 1 "Aborting..."
+	echo 1>&2
+	for rel_modulefile in "${!modules_to_install[@]}"; do
+		if [[ -d "${target_prefix}/${rel_modulefile}" ]]; then
+			echo "    Updating; ${rel_modulefile}..." 1>&2
+		else
+			echo "    Installing: ${rel_modulefile}..."
+		fi
+		sync_module "${rel_modulefile}" \
+			    "${src_prefix}" \
+			    "${target_prefix}"
+	done
+	echo -e "\nDone!\n" 1>&2
 }
 
 while (($# > 0)); do

From 9a745ecfc81a0ec52ddcaeee084af2e4d30c37b3 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 17 Mar 2015 17:22:15 +0100
Subject: [PATCH 06/50] scripts/Bootstrap/Pmodules/environment.bash: renamed

---
 .../Bootstrap/Pmodules/{environment.bash => environment.bash.in}  | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename scripts/Bootstrap/Pmodules/{environment.bash => environment.bash.in} (100%)

diff --git a/scripts/Bootstrap/Pmodules/environment.bash b/scripts/Bootstrap/Pmodules/environment.bash.in
similarity index 100%
rename from scripts/Bootstrap/Pmodules/environment.bash
rename to scripts/Bootstrap/Pmodules/environment.bash.in

From 4faf9f7d29a906ed5864e65ade89afc472c5c74f Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 17 Mar 2015 17:23:34 +0100
Subject: [PATCH 07/50] config/Pmodules.conf: PMODULES_VERSION bumped to 0.99.2

---
 config/Pmodules.conf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/Pmodules.conf b/config/Pmodules.conf
index 15fb32d..15cae9f 100644
--- a/config/Pmodules.conf
+++ b/config/Pmodules.conf
@@ -1,4 +1,4 @@
-declare -x PMODULES_VERSION=0.99.1
+declare -x PMODULES_VERSION=0.99.2
 declare -x MODULES_VERSION=3.2.10
 
 declare -a COMPILER_VERSIONS=( 'gcc/4.7.4' 'gcc/4.8.3' 'gcc/4.8.4' 'gcc/4.9.2' )

From 025180d9fc9fe37b1daf9212b13c079397078f8a Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 17 Mar 2015 17:24:51 +0100
Subject: [PATCH 08/50] scripts/Bootstrap/install_pmodules.sh: run
 'environment.bash.in' throu sed

---
 scripts/Bootstrap/install_pmodules.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/Bootstrap/install_pmodules.sh b/scripts/Bootstrap/install_pmodules.sh
index 76fc0b1..13d301d 100755
--- a/scripts/Bootstrap/install_pmodules.sh
+++ b/scripts/Bootstrap/install_pmodules.sh
@@ -14,6 +14,7 @@ sed_cmd+="s:@PMODULES_VERSION@:${PMODULES_VERSION}:g;"
 sed_cmd+="s:@MODULES_VERSION@:${MODULES_VERSION}:g"
 sed "${sed_cmd}" "${SRC_DIR}/modulecmd.in" > "${SRC_DIR}/modulecmd"
 sed "${sed_cmd}" "${SRC_DIR}/modmanage.in" > "${SRC_DIR}/modmanage.bash"
+sed "${sed_cmd}" "${SRC_DIR}/environment.bash.in" > "${SRC_DIR}/environment.bash"
 
 install -d -m 0755 "${PMODULES_HOME}/bin"
 install -d -m 0755 "${PMODULES_HOME}/config"

From 30e636c03026f49a8fa3e446a1356156879c096f Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 17 Mar 2015 17:29:09 +0100
Subject: [PATCH 09/50] scripts/Bootstrap/Pmodules/bash: set MODULEPATH if
 empty only; remove old PMODUES_HOME in PATH and MANPATH; legacy variables
 MODULE_VERSION, MODULE_VERSION_STACK and MODULESHOME removed

---
 scripts/Bootstrap/Pmodules/bash | 51 ++++++++++++++++++++++++++-------
 1 file changed, 41 insertions(+), 10 deletions(-)

diff --git a/scripts/Bootstrap/Pmodules/bash b/scripts/Bootstrap/Pmodules/bash
index c5085bb..e55b9dc 100644
--- a/scripts/Bootstrap/Pmodules/bash
+++ b/scripts/Bootstrap/Pmodules/bash
@@ -90,6 +90,33 @@ prepend_path () {
 	fi
 }
 
+#
+# Replace or remove a directory in a path variable.
+#
+# To remove a dir:
+#	replace_path PATH <pattern>
+#
+# To replace a dir:
+#	replace_path PATH <pattern> /replacement/path
+#
+# Args:
+#	$1 name of the shell variable to set (e.g. PATH)
+#	$2 a grep pattern identifying the element to be removed/replaced
+#	$3 the replacement string (use "" for removal)
+#
+# Based on solution published here:
+# https://stackoverflow.com/questions/273909/how-do-i-manipulate-path-elements-in-shell-scripts 
+#
+function replace_path () {
+	local -r path=$1
+	local -r removepat=$2
+	local -r replacestr=$3
+
+	local -r removestr=$(echo "${!path}" | tr ":" "\n" | grep -m 1 "^$removepat\$")
+    	export $path=$(echo "${!path}" | tr ":" "\n" | sed "s:^${removestr}\$:${replacestr}:" |
+                   sed '/^\s*$/d' | tr "\n" ":" | sed -e 's|^:||' -e 's|:$||')
+}
+
 #############################################################################
 # setup environment
 #
@@ -99,18 +126,20 @@ fi
 
 if [[ -z ${MODULEPATH} ]]; then
 	declare -x MODULEPATH=''
+	for f in ${PSI_DEFAULT_FAMILIES}; do
+		append_path MODULEPATH "${PSI_PREFIX}/${PSI_MODULES_ROOT}/$f"
+		append_path PSI_LOADEDFAMILIES "${f}"
+	done
 fi
 
 if [[ -z ${PSI_LOADEDFAMILIES} ]]; then
 	declare -x PSI_LOADEDFAMILIES=''
 fi
-for f in ${PSI_DEFAULT_FAMILIES}; do
-	append_path MODULEPATH "${PSI_PREFIX}/${PSI_MODULES_ROOT}/$f"
-	append_path PSI_LOADEDFAMILIES "${f}"
-done
 
-append_path PATH    "${PMODULES_HOME}/bin"
-append_path MANPATH "${PMODULES_HOME}/share/man"
+replace_path PATH    "${PMODULES_HOME%/*}/.*"
+replace_path MANPATH "${PMODULES_HOME%/*}/.*"
+append_path  PATH    "${PMODULES_HOME}/bin"
+append_path  MANPATH "${PMODULES_HOME}/share/man"
 
 #############################################################################
 # initialize bash completion
@@ -122,10 +151,12 @@ fi
 #############################################################################
 # legacy...
 #
-declare -x MODULE_VERSION=${PMODULES_VERSION}
-declare -x MODULE_VERSION_STACK="${PMODULE_VERSION}"
-declare -x MODULESHOME="${PMODULES_HOME}"
-
+#declare -x MODULE_VERSION=${PMODULES_VERSION}
+#declare -x MODULE_VERSION_STACK="${PMODULE_VERSION}"
+#declare -x MODULESHOME="${PMODULES_HOME}"
+unset MODULE_VERSION
+unset MODULE_VERSION_STACK
+unset MODULESHOME
 
 # Local Variables:
 # mode: sh

From 0366201a0bad69bf6613f934985f4d721dd4826a Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 17 Mar 2015 17:30:34 +0100
Subject: [PATCH 10/50] scripts/Bootstrap/Pmodules/environment.bash.in:
 hardcoded version replaced with @PMODULES_VERSION@

---
 scripts/Bootstrap/Pmodules/environment.bash.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/Bootstrap/Pmodules/environment.bash.in b/scripts/Bootstrap/Pmodules/environment.bash.in
index be8bfca..16c9eb9 100644
--- a/scripts/Bootstrap/Pmodules/environment.bash.in
+++ b/scripts/Bootstrap/Pmodules/environment.bash.in
@@ -3,7 +3,7 @@
 declare -x PSI_PREFIX=$(cd $(dirname "${BASH_SOURCE}")/.. && pwd)
 
 if [[ -z ${PMODULES_VERSION} ]]; then
-	declare -x PMODULES_VERSION="0.99.1"
+	declare -x PMODULES_VERSION="@PMODULES_VERSION@"
 fi
 declare -x PMODULES_HOME="${PSI_PREFIX}/Tools/Pmodules/${PMODULES_VERSION}"
 

From 2172a047c10293f63551f9cce01e0312940f68df Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 17 Mar 2015 17:32:24 +0100
Subject: [PATCH 11/50] ignore files edited

---
 scripts/Bootstrap/.gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/Bootstrap/.gitignore b/scripts/Bootstrap/.gitignore
index 11934a7..f3c2f53 100644
--- a/scripts/Bootstrap/.gitignore
+++ b/scripts/Bootstrap/.gitignore
@@ -1,2 +1,3 @@
+environment.bash
 modulecmd
 modmanage.bash

From 861ab772be18eda7617bd46b6af521d1c9f6ffcc Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 14:48:00 +0100
Subject: [PATCH 12/50] config/Pmodules.conf: family configuration removed, did
 not work properly anyway

---
 config/Pmodules.conf | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/config/Pmodules.conf b/config/Pmodules.conf
index 15cae9f..956049e 100644
--- a/config/Pmodules.conf
+++ b/config/Pmodules.conf
@@ -4,14 +4,3 @@ declare -x MODULES_VERSION=3.2.10
 declare -a COMPILER_VERSIONS=( 'gcc/4.7.4' 'gcc/4.8.3' 'gcc/4.8.4' 'gcc/4.9.2' )
 declare -a MPI_VERSIONS=( 'openmpi/1.6.5' 'openmpi/1.8.2' 'openmpi/1.8.4' )
 declare -a HDF5_VERSIONS=( 'hdf5/1.8.12' 'hdf5/1.8.14' )
-
-declare COMPILER='gcc'
-declare COMPILER_VERSION='4.8.4'
-declare GCC_VERSION="${COMPILER_VERSION}"
-
-declare MPI='openmpi'
-declare MPI_VERSION='1.8.4'
-declare OPENMPI_VERSION="${MPI_VERSION}"
-
-declare HDF5='hdf5/1.8.12'
-declare HDF5_serial='hdf5_serial/1.8.12'

From cc7a8100ac7d6333300123e4704d655dd0893c30 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 14:49:09 +0100
Subject: [PATCH 13/50] lib/libem.bash: load modules specified with '--with='
 while sourcing the library

---
 lib/libem.bash | 177 ++++++++++++++++++++++++-------------------------
 1 file changed, 88 insertions(+), 89 deletions(-)

diff --git a/lib/libem.bash b/lib/libem.bash
index f63c895..67fc508 100644
--- a/lib/libem.bash
+++ b/lib/libem.bash
@@ -96,85 +96,6 @@ ENV=VALUE
 	exit 1
 }
 
-
-debug_on='no'
-force_rebuild='no'
-ENVIRONMENT_ARGS=''
-dry_run='no'
-bootstrap='no'
-
-# array collecting all modules specified on the command line via '--with=module'
-with_modules=()
-
-while (( $# > 0 )); do
-	case $1 in
-	-j )
-		JOBS=$2
-		shift
-		;;
-	--jobs=[0-9]* )
-		JOBS=${1/--jobs=}
-		;;
-	-v | --verbose)
-		debug_on='yes'
-		;;
-	-f | --force-rebuild )
-		force_rebuild='yes'
-		;;
-	-b | --bootstrap )
-		bootstrap='yes'
-		force_rebuild='yes'
-		;;
-	-? | -h | --help )
-		usage
-		;;
-	--dry-run )
-		dry_run='yes'
-		;;
-	--release=* )
-		MODULE_RELEASE=${1/--release=}
-		;;
-	--with=*/* )
-		with_modules+=( ${1/--with=} )
-		;;
-	*=* )
-		eval $1
-		ENVIRONMENT_ARGS="${ENVIRONMENT_ARGS} $1"
-		;;
-	* )
-		V=$1
-		;;
-	esac
-	shift
-done
-
-if [[ ${debug_on} == yes ]]; then
-	trap 'echo "$BASH_COMMAND"' DEBUG
-fi
-
-# while bootstraping the module command is not yet available
-if [[ ${bootstrap} == no ]]; then
-        source	"${PSI_PREFIX}/${PSI_CONFIG_DIR}/profile.bash"
-	MODULECMD="${PMODULES_HOME}/bin/modulecmd"
-	[[ -x ${MODULECMD} ]] || die 1 "${MODULECMD}: no such executable"
-	module use unstable
-	module purge
-fi
-
-P=$(basename $(dirname "${BUILDSCRIPT}"))
-_P=$(echo $P | tr [:lower:] [:upper:])
-_P=${_P//-/_}
-_V=${_P}_VERSION
-
-eval "${ENVIRONMENT_ARGS}"
-
-if [[ -n ${PSI_RELEASES} ]]; then
-        declare -r releases="${PSI_RELEASES}"
-else
-	# set defaults, if file doesn't exist or isn't readable
-	declare -r releases=":unstable:stable:deprecated:"
-fi
-
 is_release () {
 	[[ ${releases} =~ :$1: ]]
 }
@@ -223,16 +144,6 @@ function module_is_available() {
 }
 
 function _load_build_dependencies() {
-	# :FIXME: merge this two loops, load only modules which are required
-	#         this merge is not as easy as it looks like at a first glance!
-	for m in "${with_modules[@]}"; do
-		if module_is_available "$m"; then
-			echo "Loading module: ${m}"
-			module load "${m}"
-		else
-			die 44 "$m: module not available!"
-		fi
-	done
 	for m in "${MODULE_BUILD_DEPENDENCIES[@]}"; do
 		[[ -z $m ]] && continue
 		if [[ ! $m =~ "*/*" ]]; then
@@ -719,6 +630,94 @@ function em.make_all() {
 	em.cleanup_build
 }
 
+##############################################################################
+#
+debug_on='no'
+force_rebuild='no'
+ENVIRONMENT_ARGS=''
+dry_run='no'
+bootstrap='no'
+
+# array collecting all modules specified on the command line via '--with=module'
+with_modules=()
+
+while (( $# > 0 )); do
+	case $1 in
+	-j )
+		JOBS=$2
+		shift
+		;;
+	--jobs=[0-9]* )
+		JOBS=${1/--jobs=}
+		;;
+	-v | --verbose)
+		debug_on='yes'
+		;;
+	-f | --force-rebuild )
+		force_rebuild='yes'
+		;;
+	-b | --bootstrap )
+		bootstrap='yes'
+		force_rebuild='yes'
+		;;
+	-? | -h | --help )
+		usage
+		;;
+	--dry-run )
+		dry_run='yes'
+		;;
+	--release=* )
+		MODULE_RELEASE=${1/--release=}
+		;;
+	--with=*/* )
+		with_modules+=( ${1/--with=} )
+		;;
+	*=* )
+		eval $1
+		ENVIRONMENT_ARGS="${ENVIRONMENT_ARGS} $1"
+		;;
+	* )
+		V=$1
+		;;
+	esac
+	shift
+done
+
+if [[ ${debug_on} == yes ]]; then
+	trap 'echo "$BASH_COMMAND"' DEBUG
+fi
+
+# while bootstraping the module command is not yet available
+if [[ ${bootstrap} == no ]]; then
+        source	"${PSI_PREFIX}/${PSI_CONFIG_DIR}/profile.bash"
+	MODULECMD="${PMODULES_HOME}/bin/modulecmd"
+	[[ -x ${MODULECMD} ]] || die 1 "${MODULECMD}: no such executable"
+	module use unstable
+	module purge
+	for m in "${with_modules[@]}"; do
+		if module_is_available "$m"; then
+			echo "Loading module: ${m}"
+			module load "${m}"
+		else
+			die 44 "$m: module not available!"
+		fi
+	done
+fi
+
+P=$(basename $(dirname "${BUILDSCRIPT}"))
+_P=$(echo $P | tr [:lower:] [:upper:])
+_P=${_P//-/_}
+_V=${_P}_VERSION
+
+eval "${ENVIRONMENT_ARGS}"
+
+if [[ -n ${PSI_RELEASES} ]]; then
+        declare -r releases="${PSI_RELEASES}"
+else
+	# set defaults, if file doesn't exist or isn't readable
+	declare -r releases=":unstable:stable:deprecated:"
+fi
+
 # Local Variables:
 # mode: sh
 # sh-basic-offset: 8

From 6a7ae8ed52deef7ddee8ab4a57cb5b9ccc431472 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 14:50:41 +0100
Subject: [PATCH 14/50] scripts/Bootstrap/Pmodules/bash: run module purge and
 re-initialize everything

---
 scripts/Bootstrap/Pmodules/bash | 27 +++++++++------------------
 1 file changed, 9 insertions(+), 18 deletions(-)

diff --git a/scripts/Bootstrap/Pmodules/bash b/scripts/Bootstrap/Pmodules/bash
index e55b9dc..e2276b6 100644
--- a/scripts/Bootstrap/Pmodules/bash
+++ b/scripts/Bootstrap/Pmodules/bash
@@ -117,24 +117,18 @@ function replace_path () {
                    sed '/^\s*$/d' | tr "\n" ":" | sed -e 's|^:||' -e 's|:$||')
 }
 
+module purge
+
 #############################################################################
 # setup environment
 #
-if [[ -z ${LOADEDMODULES} ]]; then
-	declare -x LOADEDMODULES=''
-fi
-
-if [[ -z ${MODULEPATH} ]]; then
-	declare -x MODULEPATH=''
-	for f in ${PSI_DEFAULT_FAMILIES}; do
-		append_path MODULEPATH "${PSI_PREFIX}/${PSI_MODULES_ROOT}/$f"
-		append_path PSI_LOADEDFAMILIES "${f}"
-	done
-fi
-
-if [[ -z ${PSI_LOADEDFAMILIES} ]]; then
-	declare -x PSI_LOADEDFAMILIES=''
-fi
+declare -x LOADEDMODULES=''
+declare -x PSI_LOADEDFAMILIES=''
+declare -x MODULEPATH=''
+for f in ${PSI_DEFAULT_FAMILIES}; do
+	append_path MODULEPATH "${PSI_PREFIX}/${PSI_MODULES_ROOT}/$f"
+	append_path PSI_LOADEDFAMILIES "${f}"
+done
 
 replace_path PATH    "${PMODULES_HOME%/*}/.*"
 replace_path MANPATH "${PMODULES_HOME%/*}/.*"
@@ -151,9 +145,6 @@ fi
 #############################################################################
 # legacy...
 #
-#declare -x MODULE_VERSION=${PMODULES_VERSION}
-#declare -x MODULE_VERSION_STACK="${PMODULE_VERSION}"
-#declare -x MODULESHOME="${PMODULES_HOME}"
 unset MODULE_VERSION
 unset MODULE_VERSION_STACK
 unset MODULESHOME

From 4f3d3c812a415e8e087720316966a3760068b970 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 17:44:12 +0100
Subject: [PATCH 15/50] lib/libem.bash: unset CDPATH added; fix problem with
 --bootstrap

---
 lib/libem.bash | 95 ++++++++++++++++++++++++++------------------------
 1 file changed, 50 insertions(+), 45 deletions(-)

diff --git a/lib/libem.bash b/lib/libem.bash
index 67fc508..5dcb5cb 100644
--- a/lib/libem.bash
+++ b/lib/libem.bash
@@ -2,6 +2,9 @@
 
 PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin
 
+# disable auto-echo feature of 'cd'
+unset CDPATH
+
 shopt -s expand_aliases
 
 
@@ -434,58 +437,56 @@ function _setup_env2() {
 
 }
 
-if [[ ${bootstrap} == yes ]]; then
-    # redefine function for bootstrapping
-    function _setup_env2() {
-	    if [[ -z ${MODULE_FAMILY} ]]; then
+# redefine function for bootstrapping
+function _setup_env2_bootstrap() {
+	if [[ -z ${MODULE_FAMILY} ]]; then
 		die 1 "$P: family not set."
-	    fi
+	fi
 
-            if [[ -z $V ]]; then
+        if [[ -z $V ]]; then
 		V=$(eval echo \$${_P}_VERSION)
-	    fi
+	fi
 
-	    # oops, we need a version
-	    if [[ -z $V ]]; then
+	# oops, we need a version
+	if [[ -z $V ]]; then
 		die 1 "$P: Missing version."
-	    fi
-	    MODULE_SRCDIR="${BUILD_TMPDIR}/src/${P/_serial}-$V"
-	    MODULE_BUILDDIR="${BUILD_TMPDIR}/build/$P-$V"
-	    MODULE_FAMILY='Tools'
-	    MODULE_NAME="Pmodules/${PMODULES_VERSION}"
-	    # set PREFIX of module
-	    PREFIX="${PSI_PREFIX}/${MODULE_FAMILY}/${MODULE_NAME}"
-	    
-	    MODULE_RELEASE='unstable'
-	    info "${MODULE_NAME}: will be released as \"${MODULE_RELEASE}\""
+	fi
+	MODULE_SRCDIR="${BUILD_TMPDIR}/src/${P/_serial}-$V"
+	MODULE_BUILDDIR="${BUILD_TMPDIR}/build/$P-$V"
+	MODULE_FAMILY='Tools'
+	MODULE_NAME="Pmodules/${PMODULES_VERSION}"
+	# set PREFIX of module
+	PREFIX="${PSI_PREFIX}/${MODULE_FAMILY}/${MODULE_NAME}"
+	
+	MODULE_RELEASE='unstable'
+	info "${MODULE_NAME}: will be released as \"${MODULE_RELEASE}\""
 
-	    # directory for README's, license files etc
-	    DOCDIR="${PREFIX}/share/doc/$P"
+	# directory for README's, license files etc
+	DOCDIR="${PREFIX}/share/doc/$P"
 
-	    # set tar-ball and flags for tar
-	    TARBALL="${BUILD_DOWNLOADSDIR}/${P/_serial}"
-	    if [[ -r "${TARBALL}-${V}.tar.gz" ]]; then
-		    TARBALL+="-${V}.tar.gz"
-	    elif [[ -r "${TARBALL}-${OS}-${V}.tar.gz" ]]; then
-		    TARBALL+="-${OS}-${V}.tar.gz"
-	    elif [[ -r "${TARBALL}-${V}.tar.bz2" ]]; then
-		    TARBALL+="-${V}.tar.bz2"
-	    elif [[ -r "${TARBALL}-${OS}-${V}.tar.bz2" ]]; then
-		    TARBALL+="-${OS}-${V}.tar.bz2"
-	    else
-		    error "tar-ball for $P/$V not found."
-		    exit 43
-	    fi
-	    C_INCLUDE_PATH="${PREFIX}/include"
-	    CPLUS_INCLUDE_PATH="${PREFIX}/include"
-	    CPP_INCLUDE_PATH="${PREFIX}/include"
-	    LIBRARY_PATH="${PREFIX}/lib"
-	    LD_LIBRARY_PATH="${PREFIX}/lib"
-	    DYLD_LIBRARY_PATH="${PREFIX}/lib"
+	# set tar-ball and flags for tar
+	TARBALL="${BUILD_DOWNLOADSDIR}/${P/_serial}"
+	if [[ -r "${TARBALL}-${V}.tar.gz" ]]; then
+	        TARBALL+="-${V}.tar.gz"
+	elif [[ -r "${TARBALL}-${OS}-${V}.tar.gz" ]]; then
+	        TARBALL+="-${OS}-${V}.tar.gz"
+	elif [[ -r "${TARBALL}-${V}.tar.bz2" ]]; then
+	        TARBALL+="-${V}.tar.bz2"
+	elif [[ -r "${TARBALL}-${OS}-${V}.tar.bz2" ]]; then
+	        TARBALL+="-${OS}-${V}.tar.bz2"
+	else
+	        error "tar-ball for $P/$V not found."
+	        exit 43
+	fi
+	C_INCLUDE_PATH="${PREFIX}/include"
+	CPLUS_INCLUDE_PATH="${PREFIX}/include"
+	CPP_INCLUDE_PATH="${PREFIX}/include"
+	LIBRARY_PATH="${PREFIX}/lib"
+	LD_LIBRARY_PATH="${PREFIX}/lib"
+	DYLD_LIBRARY_PATH="${PREFIX}/lib"
 
-	    PATH+=":${PREFIX}/bin"
-    }
-fi
+	PATH+=":${PREFIX}/bin"
+}
 
 function _prep() {
 
@@ -600,7 +601,11 @@ function em.make_all() {
 	_setup_env1
 	_load_build_dependencies
 	# setup module specific environment
-	_setup_env2
+	if [[ ${bootstrap} == no ]]; then
+		_setup_env2
+	else
+		_setup_env2_bootstrap
+	fi
 
 	if [[ ! -d "${PREFIX}" ]] || [[ ${force_rebuild} == 'yes' ]]; then
  		echo "Building $P/$V ..."

From 406536df533609b6c8c8f159f98c235c8832f16b Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 17:44:57 +0100
Subject: [PATCH 16/50] scripts/Bootstrap/Pmodules/modmanage.in: unset CDPATH
 added

---
 scripts/Bootstrap/Pmodules/modmanage.in | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scripts/Bootstrap/Pmodules/modmanage.in b/scripts/Bootstrap/Pmodules/modmanage.in
index dfec8d1..4579575 100755
--- a/scripts/Bootstrap/Pmodules/modmanage.in
+++ b/scripts/Bootstrap/Pmodules/modmanage.in
@@ -1,5 +1,7 @@
 #!@PMODULES_HOME@/bin/bash
 
+unset CDPATH
+
 shopt -s expand_aliases
 
 declare -r bindir=$(cd $(dirname "$0") && pwd)

From a777b1240c6c3be5ff65e902df308c469fb9ba44 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 17:46:18 +0100
Subject: [PATCH 17/50] scripts/Bootstrap/Pmodules/modulecmd.in: unset CDPATH
 added; print message in sub-command 'load' if no module specified

---
 scripts/Bootstrap/Pmodules/modulecmd.in | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/scripts/Bootstrap/Pmodules/modulecmd.in b/scripts/Bootstrap/Pmodules/modulecmd.in
index bc47ba7..bb67e02 100755
--- a/scripts/Bootstrap/Pmodules/modulecmd.in
+++ b/scripts/Bootstrap/Pmodules/modulecmd.in
@@ -1,4 +1,8 @@
 #!@PMODULES_HOME@/bin/bash
+#
+
+# we have to unset CDPATH, otherwise 'cd' prints the directoy!
+unset CDPATH
 
 declare -r  PMODULES_DIR=$( cd "$(dirname $0)/.." && pwd )
 declare -r  version='@PMODULES_VERSION@'
@@ -464,6 +468,11 @@ subcommand_generic1plus() {
 	"${modulecmd}" "${shell}" "${subcommand}" "$@"
 }
 
+#
+# load module
+# 
+# $1: module to load
+#
 subcommand_load() {
 	output_load_hints() {
 		local -ra rels=( ${available_releases//:/ } )
@@ -509,7 +518,9 @@ subcommand_load() {
 	}
 	
 	local -r m=$1
-	if module_is_available "${m}"; then
+	if [[ "${m}" == "" ]]; then
+		echo "No module specified." 1>&2
+	elif module_is_available "${m}"; then
 		"${modulecmd}" "${shell}" load "${m}"
 	else
 		if [[ ${userlvl} = 'novice' ]]; then

From 8a800c602fe905589dbc18d5726b4050df3b28d9 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 17:47:20 +0100
Subject: [PATCH 18/50] scripts/Bootstrap/compile_pmodules.sh: print message
 and exit, if something failed to compile

---
 scripts/Bootstrap/compile_pmodules.sh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/scripts/Bootstrap/compile_pmodules.sh b/scripts/Bootstrap/compile_pmodules.sh
index 5c38325..9d60e93 100755
--- a/scripts/Bootstrap/compile_pmodules.sh
+++ b/scripts/Bootstrap/compile_pmodules.sh
@@ -8,13 +8,13 @@ source "${BASE_DIR}/config/Pmodules.conf"
 unset PMODULES_HOME
 source "/opt/psi/config/environment.bash"
 
-${BOOTSTRAP_DIR}/gettext/build --bootstrap
-${BOOTSTRAP_DIR}/getopt/build --bootstrap
-${BOOTSTRAP_DIR}/dialog/build --bootstrap
-${BOOTSTRAP_DIR}/bash/build --bootstrap
-${BOOTSTRAP_DIR}/Tcl/build --bootstrap
+${BOOTSTRAP_DIR}/gettext/build --bootstrap || { echo "compiling 'gettext' failed!"; exit 1; }
+${BOOTSTRAP_DIR}/getopt/build --bootstrap  || { echo "compiling 'getopt' failed!"; exit 1; }
+${BOOTSTRAP_DIR}/dialog/build --bootstrap  || { echo "compiling 'dialog' failed!"; exit 1; }
+${BOOTSTRAP_DIR}/bash/build --bootstrap    || { echo "compiling 'bash' failed!"; exit 1; }
+${BOOTSTRAP_DIR}/Tcl/build --bootstrap     || { echo "compiling 'Tcl' failed!"; exit 1; }
 
 # we have to remove the init directory - otherwise the next build will fail...
 rm -rf "${PMODULES_HOME}/init"
-${BOOTSTRAP_DIR}/Modules/build --bootstrap
+${BOOTSTRAP_DIR}/Modules/build --bootstrap || { echo "compiling 'Modules' failed!"; exit 1; }
 mv -v "${PMODULES_HOME}/bin/modulecmd" "${PMODULES_HOME}/bin/modulecmd.tcl"

From 907ab0d0505f651c9d8ffa485b03a78732363f31 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 17:49:04 +0100
Subject: [PATCH 19/50] scripts/Bootstrap: all build dependencies removed

---
 scripts/Bootstrap/Tcl/build     | 3 +--
 scripts/Bootstrap/bash/build    | 3 +--
 scripts/Bootstrap/dialog/build  | 1 -
 scripts/Bootstrap/gettext/build | 1 -
 4 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/scripts/Bootstrap/Tcl/build b/scripts/Bootstrap/Tcl/build
index 402004d..78de767 100755
--- a/scripts/Bootstrap/Tcl/build
+++ b/scripts/Bootstrap/Tcl/build
@@ -21,7 +21,6 @@ function em.post_install() {
 	{ cd "${PREFIX}"/bin && rm -f tclsh && ln -fs tclsh${V%.*} tclsh; };
 }
 
-em.add_to_family 'Programming'
+em.add_to_family 'Tools'
 em.set_docfiles 'license.terms' 'README'
-em.set_build_dependencies "${COMPILER}"
 em.make_all
diff --git a/scripts/Bootstrap/bash/build b/scripts/Bootstrap/bash/build
index 19ef03f..edc9d5b 100755
--- a/scripts/Bootstrap/bash/build
+++ b/scripts/Bootstrap/bash/build
@@ -8,6 +8,5 @@ function em.configure() {
 		|| exit 1
 }
 
-em.add_to_family 'System'
-em.set_build_dependencies "${COMPILER}"
+em.add_to_family 'Tools'
 em.make_all
diff --git a/scripts/Bootstrap/dialog/build b/scripts/Bootstrap/dialog/build
index ae80ddd..edc9d5b 100755
--- a/scripts/Bootstrap/dialog/build
+++ b/scripts/Bootstrap/dialog/build
@@ -9,5 +9,4 @@ function em.configure() {
 }
 
 em.add_to_family 'Tools'
-em.set_build_dependencies "${COMPILER}"
 em.make_all
diff --git a/scripts/Bootstrap/gettext/build b/scripts/Bootstrap/gettext/build
index 68d8744..9409c14 100755
--- a/scripts/Bootstrap/gettext/build
+++ b/scripts/Bootstrap/gettext/build
@@ -20,5 +20,4 @@ function em.configure() {
 }
 
 em.add_to_family 'Tools'
-em.set_build_dependencies "${COMPILER}"
 em.make_all

From 247d9431b51ebcec50494b3cae9ad9fb9b693ec8 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 18:08:05 +0100
Subject: [PATCH 20/50] scripts/Bootstrap/Pmodules/modmanage.in: in sub-command
 'init': option '--version=' added, with this option you specify the version
 of Pmodules to be sync'ed

---
 scripts/Bootstrap/Pmodules/modmanage.in | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/scripts/Bootstrap/Pmodules/modmanage.in b/scripts/Bootstrap/Pmodules/modmanage.in
index 4579575..5168a50 100755
--- a/scripts/Bootstrap/Pmodules/modmanage.in
+++ b/scripts/Bootstrap/Pmodules/modmanage.in
@@ -142,7 +142,7 @@ subcommand_init() {
 	local target_prefixes=()
 	local user=''
 	local opts=''
-	opts=$(get_options -o h -l src: -l user: -l help -- "$@")
+	opts=$(get_options -o h -l src: -l user: -l help -l version: -- "$@")
 	if [[ $? != 0 ]]; then
 		subcommand_help_init
 		exit 1
@@ -158,6 +158,10 @@ subcommand_init() {
 				user=$2
 				shift
 				;;
+			--version )
+				PMODULES_VERSION=$2
+				shift
+				;;
 			-- )
 				:
 				;;

From 1b6781702dc7b6aecca6a260dbb6fd4f75d18c37 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 18:17:30 +0100
Subject: [PATCH 21/50] config/versions.conf: default version of ippl changed

---
 config/versions.conf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/versions.conf b/config/versions.conf
index 9dacd8a..55f2324 100644
--- a/config/versions.conf
+++ b/config/versions.conf
@@ -19,7 +19,7 @@ H5hut		1.99.13
 H5root		1.2.0
 hdf5_serial	1.8.14
 hdf5		1.8.14
-ippl		1.1.3
+ippl		1.1.4
 libtool		2.4.2
 libungif	4.1.4
 lua		5.1.4.5

From 4fc10233c6e6d3e12cafad4feca920eea8e35d99 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 18:20:01 +0100
Subject: [PATCH 22/50] scripts/Bootstrap/Modules/build: bugfix: use
 PMODULES_VERSION to set TCL_DIR

---
 scripts/Bootstrap/Modules/build | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/Bootstrap/Modules/build b/scripts/Bootstrap/Modules/build
index 115b214..a22a7e1 100755
--- a/scripts/Bootstrap/Modules/build
+++ b/scripts/Bootstrap/Modules/build
@@ -2,7 +2,7 @@
 #set -o functrace
 source "$(dirname $0)/../../../lib/libem.bash"
 
-TCL_DIR="${PSI_PREFIX}/Tools/Pmodules/0.99.0"
+TCL_DIR="${PSI_PREFIX}/Tools/Pmodules/${PMODULES_VERSION}"
 
 PATH="${TCL_DIR}/bin:${PATH}"
 

From a85c5070ca01a7767e9bb51e809c08bfbf6addbf Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 18:25:39 +0100
Subject: [PATCH 23/50] scripts/Bootstrap/Pmodules/modmanage.in: in sub-command
 'install': options '--dry-run' and '--force' added; do not re-sync existing
 moules if not forced

---
 scripts/Bootstrap/Pmodules/modmanage.in | 27 +++++++++++++++++--------
 1 file changed, 19 insertions(+), 8 deletions(-)

diff --git a/scripts/Bootstrap/Pmodules/modmanage.in b/scripts/Bootstrap/Pmodules/modmanage.in
index dfec8d1..361fe3e 100755
--- a/scripts/Bootstrap/Pmodules/modmanage.in
+++ b/scripts/Bootstrap/Pmodules/modmanage.in
@@ -51,7 +51,7 @@ init [--src=<src>] [--user=<user>] <dst>
 
 subcommand_help_install() {
 	echo "
-install <module> [--with=<dep>...]
+install <module>... [--with=<dep>...] [--release=<release>...] [--src=<src>]
                 Install matching modules
 " 1>&2
 }
@@ -111,11 +111,12 @@ sync_module() {
 	local -r rel_module_prefix=$( get_module_prefix "${rel_modulefile}" )
 	local -r rel_releasefile=$( get_releasefile_name "${rel_modulefile}" )
 
-	$DRY mkdir -p "${target_prefix}/${rel_module_prefix}" || return $?
-	$DRY rsync --links --perms --recursive --delete \
-	      "${src_prefix}/${rel_module_prefix}/" \
-	      "${target_prefix}/${rel_module_prefix}/" || return $?
-
+	if [[ ! -d "${target_prefix}/${rel_module_prefix}" ]] || [[ "${force}" == 'yes' ]]; then
+		$DRY mkdir -p "${target_prefix}/${rel_module_prefix}" || return $?
+		$DRY rsync --links --perms --recursive --delete \
+		      "${src_prefix}/${rel_module_prefix}/" \
+		      "${target_prefix}/${rel_module_prefix}/" || return $?
+	fi
 	local -r src_modulefile="${src_prefix}/${PSI_MODULES_ROOT}/${rel_modulefile}"
 	local -r src_releasefile="${src_prefix}/${PSI_MODULES_ROOT}/${rel_releasefile}"
 	local -r target_modulefile="${target_prefix}/${PSI_MODULES_ROOT}/${rel_modulefile}"
@@ -270,7 +271,7 @@ subcommand_install() {
 	local -r src_prefix="${PMODULES_INSTALL_SOURCE}"
 	local -r target_prefix="${PSI_PREFIX}"
 
-	opts=$(get_options -o h -l with: -l release: -l help -l src: -- "$@")
+	opts=$(get_options -o hf -l dry-run -l force -l with: -l release: -l help -l src: -- "$@")
 	if [[ $? != 0 ]]; then
 		subcommand_help_install
 		exit 1
@@ -278,6 +279,12 @@ subcommand_install() {
 	eval set --  "${opts}"
 	while (($# > 0)); do
 		case $1 in
+			--dry-run )
+				DRY='echo'
+				;;
+			--force | -f )
+				force='yes'
+				;;
 			--release )
 				releases+=( "$2" )
 				shift
@@ -293,7 +300,11 @@ subcommand_install() {
 			-- )
 				:
 				;;
-			-* | -h | --help )
+			-h | --help )
+				subcommand_help_install
+				exit 1
+				;;
+			-* )
 				echo "$1: illegal option" 1>&2
 				subcommand_help_init
 				exit 1

From d722a60c895710cae1cdf4ce541694150f23cf0a Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 18 Mar 2015 18:37:57 +0100
Subject: [PATCH 24/50] scripts/Bootstrap/Pmodules/modmanage.in: bugfix in
 sub-command 'install'

---
 scripts/Bootstrap/Pmodules/modmanage.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/Bootstrap/Pmodules/modmanage.in b/scripts/Bootstrap/Pmodules/modmanage.in
index abf6a45..ba3dd3e 100755
--- a/scripts/Bootstrap/Pmodules/modmanage.in
+++ b/scripts/Bootstrap/Pmodules/modmanage.in
@@ -328,7 +328,7 @@ subcommand_install() {
 		let n+=1
 	done < <(${PMODULES_HOME}/bin/modulecmd bash search \
 				 "${module_pattern[@]}" \
-				 "${with[@]/#/--with}" \
+				 "${with[@]/#/--with=}" \
 				 "${releases[@]/#/--release=}" \
 				 --no-header --print-modulefiles \
 				 --src="${src_prefix}" 2>&1)

From 0ad320508bb176a5002b4c23e9a79ed9ea7dfcfd Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 19 Mar 2015 16:51:29 +0100
Subject: [PATCH 25/50] lib/libem.bash: do not overwrite versions set with
 '--with=' with default versions defined in 'config/versions.conf'

---
 lib/libem.bash | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/lib/libem.bash b/lib/libem.bash
index 5dcb5cb..34f6029 100644
--- a/lib/libem.bash
+++ b/lib/libem.bash
@@ -28,15 +28,6 @@ declare -xr BUILD_TMPDIR="${BUILD_BASEDIR}/tmp"
 declare -xr BUILD_DOWNLOADSDIR="${BUILD_BASEDIR}/Downloads"
 declare -xr BUILD_VERSIONSFILE="${BUILD_CONFIGDIR}/versions.conf"
 
-#declare -xr PSI_TEMPLATES_DIR='templates'
-
-if [[ -z "${BUILD_CONFIGDIR}/families.d/"*.conf ]]; then
-	die 1 "Default family configuration not set in ${BUILD_CONFIGDIR}/families.d"
-fi
-
-#for f in "${BUILD_CONFIGDIR}/families.d/"*.conf; do
-#	source "${f}"
-#done
 source "${BUILD_CONFIGDIR}/Pmodules.conf"
 
 declare -x  PREFIX=''
@@ -62,7 +53,8 @@ declare -x  LIBRARY_PATH
 declare -x  LD_LIBRARY_PATH
 declare -x  DYLD_LIBRARY_PATH
 
-
+##############################################################################
+#
 function usage() {
 	error "
 Usage: $0 [OPTIONS..] [VERSION] [ENV=VALUE...]
@@ -260,6 +252,8 @@ function _write_build_dependencies() {
 
 # setup general environment
 function _setup_env1() {
+	local varname=''
+
 	C_INCLUDE_PATH=''
 	CPLUS_INCLUDE_PATH=''
 	CPP_INCLUDE_PATH=''
@@ -277,8 +271,11 @@ function _setup_env1() {
 		[[ -z ${_name} ]] && continue
 		[[ -z ${_version} ]] && continue
 		[[ "${_name:0:1}" == '#' ]] && continue
-		_NAME=$(echo ${_name} | tr [:lower:] [:upper:])
-		eval ${_NAME}_VERSION=$_version 
+		var_name=$(echo ${_name} | tr [:lower:] [:upper:])_VERSION
+		# don't set version, if already set
+		if [[ -z ${!var_name} ]]; then
+			eval ${var_name}="${_version}"
+		fi
 	done < "${BUILD_VERSIONSFILE}"
 
 }

From bde7be36df59427f5f57fa6e3df7b9818a04703e Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 19 Mar 2015 18:10:13 +0100
Subject: [PATCH 26/50] scripts/Tools/git/build: added

---
 scripts/Tools/git/build | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100755 scripts/Tools/git/build

diff --git a/scripts/Tools/git/build b/scripts/Tools/git/build
new file mode 100755
index 0000000..ed9c700
--- /dev/null
+++ b/scripts/Tools/git/build
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+source "$(dirname $0)/../../../lib/libem.bash"
+
+function em.configure() {
+	cd "${MODULE_SRCDIR}"
+	"${MODULE_SRCDIR}"/configure \
+		--prefix="${PREFIX}" \
+		--with-tcltk="${PMODULES_HOME}" \
+		|| exit 1
+}
+
+function em.build() {
+        cd "${MODULE_SRCDIR}"
+        make
+}
+
+em.add_to_family 'Tools'
+em.set_docfiles 'COPYING' 'README'
+em.make_all
+
+# Local Variables:
+# mode: sh
+# sh-basic-offset: 8
+# tab-width: 8
+# End:

From ad664353cd677e538e844bcef00b09a38605e188 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 19 Mar 2015 18:10:37 +0100
Subject: [PATCH 27/50] scripts/MPI/OPAL/with: added

---
 scripts/MPI/OPAL/with | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 scripts/MPI/OPAL/with

diff --git a/scripts/MPI/OPAL/with b/scripts/MPI/OPAL/with
new file mode 100644
index 0000000..4463df4
--- /dev/null
+++ b/scripts/MPI/OPAL/with
@@ -0,0 +1,9 @@
+gcc/4.8.3
+openmpi/1.8.2
+ippl/1.1.4
+hdf5/1.8.12
+H5hut/1.99.13
+trilinos/11.10.2
+boost/1.55.0
+gsl/1.15
+root/5.34.19

From d148fbbdf72e8b4f9c4fd31f2f5ac48f241da292 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 20 Mar 2015 12:43:39 +0100
Subject: [PATCH 28/50] lib/libem.bash: do not load modules twice while loading
 build dependencies

---
 lib/libem.bash | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/lib/libem.bash b/lib/libem.bash
index 34f6029..b92df28 100644
--- a/lib/libem.bash
+++ b/lib/libem.bash
@@ -28,7 +28,7 @@ declare -xr BUILD_TMPDIR="${BUILD_BASEDIR}/tmp"
 declare -xr BUILD_DOWNLOADSDIR="${BUILD_BASEDIR}/Downloads"
 declare -xr BUILD_VERSIONSFILE="${BUILD_CONFIGDIR}/versions.conf"
 
-source "${BUILD_CONFIGDIR}/Pmodules.conf"
+#source "${BUILD_CONFIGDIR}/Pmodules.conf"
 
 declare -x  PREFIX=''
 declare -x  DOCDIR=''
@@ -91,10 +91,26 @@ ENV=VALUE
 	exit 1
 }
 
+##############################################################################
+#
+# test whether a the string passed in $1 is a valid release name
+#
+# $1: string to be tested
+#
 is_release () {
 	[[ ${releases} =~ :$1: ]]
 }
 
+##############################################################################
+#
+# test whether a module is loaded or not
+#
+# $1: module name
+#
+em.is_loaded() {
+        [[ :${LOADEDMODULES}: =~ :$1: ]]
+}
+
 function em.set_release() {
 	is_release "$1" || die 1 "$P: unknown release type: $1"
 	[[ "$1" == "deprecated" ]] && die 0 "$P: is deprecated, we don't rebuild it."
@@ -149,6 +165,7 @@ function _load_build_dependencies() {
 				echo "$m: warning: No version set, loading default ..."
 			fi
 		fi
+		em.is_loaded "$m" && continue
 		if ! module_is_available "$m"; then
 		        debug "${m}: module not available"
 			local rels=( ${releases//:/ } )

From f42d8c41a44a7ab1522e97844a3d3b92a73ba75d Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 20 Mar 2015 16:27:55 +0100
Subject: [PATCH 29/50] lib/libem.bash: family 'OPAL' added; load modules
 listed in file 'with_modules', if exist

---
 lib/libem.bash | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/lib/libem.bash b/lib/libem.bash
index b92df28..88a08f6 100644
--- a/lib/libem.bash
+++ b/lib/libem.bash
@@ -8,7 +8,8 @@ unset CDPATH
 shopt -s expand_aliases
 
 
-declare -r  BUILDSCRIPT=$( cd $(dirname "$0") && pwd )/$(basename "$0")
+declare -r  BUILDSCRIPT_DIR=$( cd $(dirname "$0") && pwd )
+declare -r  BUILDSCRIPT="${BUILDSCRIPT_DIR}"/$(basename "$0")
 declare -rx ARGS="$@"
 declare -rx SHLIBDIR=$( cd $(dirname "$BASH_SOURCE") && pwd )
 declare -r OS=$(uname -s)
@@ -366,6 +367,17 @@ function _setup_env2() {
 			MODULE_NAME+="${HDF5}/${HDF5_VERSION}/"
 			MODULE_NAME+="${P}/${V}"
 			;;
+		OPAL )
+			MODULE_RPREFIX="${P}/${V}"
+			MODULE_RPREFIX+="/${OPAL}/${OPAL_VERSION}"
+			MODULE_RPREFIX+="/${MPI}/${MPI_VERSION}"
+			MODULE_RPREFIX+="/${COMPILER}/${COMPILER_VERSION}"
+			
+			MODULE_NAME="${COMPILER}/${COMPILER_VERSION}/"
+			MODULE_NAME+="${MPI}/${MPI_VERSION}/"
+			MODULE_NAME+="${OPAL}/${OPAL_VERSION}/"
+			MODULE_NAME+="${P}/${V}"
+			;;
 		HDF5_serial )
 			MODULE_RPREFIX="${P}/${V}"
 			MODULE_RPREFIX+="/hdf5_serial/${HDF5_SERIAL_VERSION}"
@@ -660,6 +672,10 @@ bootstrap='no'
 # array collecting all modules specified on the command line via '--with=module'
 with_modules=()
 
+if [[ -r "${BUILDSCRIPT_DIR}/with_modules" ]]; then
+	with_modules+=( $(cat "${BUILDSCRIPT_DIR}/with_modules") )
+fi
+
 while (( $# > 0 )); do
 	case $1 in
 	-j )

From e928d9984b2d237863a894c82c3cf1fc30beb1c6 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 20 Mar 2015 16:30:47 +0100
Subject: [PATCH 30/50] optPilot moved to family 'OPAL' and renamed to
 'opt-pilot'

---
 scripts/{MPI/optPilot => OPAL/opt-pilot}/build |  4 ++--
 scripts/OPAL/opt-pilot/with_modules            | 10 ++++++++++
 2 files changed, 12 insertions(+), 2 deletions(-)
 rename scripts/{MPI/optPilot => OPAL/opt-pilot}/build (86%)
 create mode 100644 scripts/OPAL/opt-pilot/with_modules

diff --git a/scripts/MPI/optPilot/build b/scripts/OPAL/opt-pilot/build
similarity index 86%
rename from scripts/MPI/optPilot/build
rename to scripts/OPAL/opt-pilot/build
index f6e5e83..eee8d88 100755
--- a/scripts/MPI/optPilot/build
+++ b/scripts/OPAL/opt-pilot/build
@@ -12,9 +12,9 @@ function em.configure() {
 		"${MODULE_SRCDIR}"
 }
 
-em.add_to_family 'MPI'
+em.add_to_family 'OPAL'
 em.set_runtime_dependencies "${COMPILER}" "${MPI}"
 em.set_build_dependencies 'cmake' "${COMPILER}" "${MPI}" 'boost' 'hdf5' 'H5hut' 'trilinos' 'ippl' 'gsl' 'boost' 'OPAL'
-em.set_supported_compilers 'gcc/4.7' 'gcc/4.8'
+em.set_supported_compilers 'gcc/4.8'
 em.make_all
 
diff --git a/scripts/OPAL/opt-pilot/with_modules b/scripts/OPAL/opt-pilot/with_modules
new file mode 100644
index 0000000..bbad858
--- /dev/null
+++ b/scripts/OPAL/opt-pilot/with_modules
@@ -0,0 +1,10 @@
+gcc/4.8.3
+openmpi/1.8.2
+ippl/1.1.4
+hdf5/1.8.12
+H5hut/1.99.13
+trilinos/11.10.2
+boost/1.55.0
+gsl/1.15
+root/5.34.19
+OPAL/1.3.2

From 99bc0f1e67dd486ce7504966bcbea222548f8c6e Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 20 Mar 2015 17:25:49 +0100
Subject: [PATCH 31/50] scripts/MPI/OPAL/with_modules: renamed

---
 scripts/MPI/OPAL/{with => with_modules} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename scripts/MPI/OPAL/{with => with_modules} (100%)

diff --git a/scripts/MPI/OPAL/with b/scripts/MPI/OPAL/with_modules
similarity index 100%
rename from scripts/MPI/OPAL/with
rename to scripts/MPI/OPAL/with_modules

From 9523996b8a1d6f7a1aee8a1d905ec44331fa2436 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 20 Mar 2015 17:27:55 +0100
Subject: [PATCH 32/50] lib/libem.bash: bugfix in environment cleanup

---
 lib/libem.bash | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/lib/libem.bash b/lib/libem.bash
index 88a08f6..35ac0e2 100644
--- a/lib/libem.bash
+++ b/lib/libem.bash
@@ -268,9 +268,11 @@ function _write_build_dependencies() {
 	done
 }
 
-# setup general environment
-function _setup_env1() {
-	local varname=''
+##############################################################################
+# 
+# cleanup environment
+#
+em.cleanup_env() {
 
 	C_INCLUDE_PATH=''
 	CPLUS_INCLUDE_PATH=''
@@ -284,7 +286,14 @@ function _setup_env1() {
 	CXXFLAGS=''
 	LIBS=''
 	LDFLAGS=''
-	
+}
+
+##############################################################################
+#
+# load default versions
+#
+ _setup_env1() {
+	local varname=''
 	while read _name _version; do
 		[[ -z ${_name} ]] && continue
 		[[ -z ${_version} ]] && continue
@@ -669,6 +678,8 @@ ENVIRONMENT_ARGS=''
 dry_run='no'
 bootstrap='no'
 
+em.cleanup_env
+
 # array collecting all modules specified on the command line via '--with=module'
 with_modules=()
 

From 40e0143b9f773779540ec5a76ee135891561f3a1 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 23 Mar 2015 17:01:24 +0100
Subject: [PATCH 33/50] scripts/Bootstrap/Pmodules/libmodules.tcl: add debug
 output if PREFIX does not exist

---
 scripts/Bootstrap/Pmodules/libmodules.tcl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scripts/Bootstrap/Pmodules/libmodules.tcl b/scripts/Bootstrap/Pmodules/libmodules.tcl
index 7ad721c..f1a355e 100644
--- a/scripts/Bootstrap/Pmodules/libmodules.tcl
+++ b/scripts/Bootstrap/Pmodules/libmodules.tcl
@@ -181,6 +181,8 @@ proc set_std_environment { PREFIX name version } {
 		if { [lsearch ${::dont-setenv} "${NAME}_HOME"] == -1 } {
 			setenv		${NAME}_HOME		$PREFIX
 		}
+	} else {
+		debug "$PREFIX is not a directory"
 	}
 
 	if { [file isdirectory "$PREFIX/bin"] } {

From c2ffa54b9100f0291b5fa1c830dc64e40e2f33e5 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 23 Mar 2015 17:29:15 +0100
Subject: [PATCH 34/50] scripts/HDF5/build_all_variants: exit if a build failed

---
 scripts/HDF5/build_all_variants | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/HDF5/build_all_variants b/scripts/HDF5/build_all_variants
index 262f179..88d48a6 100755
--- a/scripts/HDF5/build_all_variants
+++ b/scripts/HDF5/build_all_variants
@@ -19,6 +19,7 @@ for cc in "${COMPILER_VERSIONS[@]}"; do
 				echo "        compile: $cc"
 				echo "        mpi:     $mpi"
 				echo "        hdf5:    $hdf5"
+				exit 1
 			}
 		done
 	done

From 8d8925c9035abbe338f31100e1602b00358085c3 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 23 Mar 2015 17:30:10 +0100
Subject: [PATCH 35/50] scripts/HDF5/H5hut/build: disable vtkconvert

---
 scripts/HDF5/H5hut/build | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/HDF5/H5hut/build b/scripts/HDF5/H5hut/build
index eb9097a..a689248 100755
--- a/scripts/HDF5/H5hut/build
+++ b/scripts/HDF5/H5hut/build
@@ -18,7 +18,6 @@ function em.configure() {
 		--prefix="${PREFIX}" \
 		--enable-parallel \
 		--enable-debug \
-		--enable-vtkconverter \
 		--with-hdf5=$HDF5_PREFIX \
 		--with-pic \
 		|| exit 1

From 3b75bd4d75e624e3c9eb203f1d0d665170323509 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 23 Mar 2015 17:36:25 +0100
Subject: [PATCH 36/50] scripts/HDF5_serial/build_all_variants: added

---
 scripts/HDF5_serial/build_all_variants | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100755 scripts/HDF5_serial/build_all_variants

diff --git a/scripts/HDF5_serial/build_all_variants b/scripts/HDF5_serial/build_all_variants
new file mode 100755
index 0000000..6854f9e
--- /dev/null
+++ b/scripts/HDF5_serial/build_all_variants
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+declare -r basedir=$(dirname $0)
+source '../../config/Pmodules.conf'
+
+declare -r recipe="${basedir}/$1/build"
+shift
+
+if [[ ! -x "${recipe}" ]]; then
+	echo "Error: no recipe to build '$1'!"
+	exit 1
+fi
+
+for cc in "${COMPILER_VERSIONS[@]}"; do
+	for hdf in "${HDF5_SERIAL_VERSIONS[@]}"; do
+		"${recipe}" "$@" --with=$cc --with=$hdf || {
+			echo "Oops: build failed for:"
+			echo "        compiler:      $cc"
+			echo "        HDF5 (serial): $hdf"
+			}
+	done
+done

From 9cb136ccc4e6b59346407dddf468545cab862768 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 23 Mar 2015 18:36:40 +0100
Subject: [PATCH 37/50] config/Pmodules.conf: (P)MODULES_VERSION removed

---
 config/Pmodules.conf | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/config/Pmodules.conf b/config/Pmodules.conf
index 956049e..22d1961 100644
--- a/config/Pmodules.conf
+++ b/config/Pmodules.conf
@@ -1,6 +1,4 @@
-declare -x PMODULES_VERSION=0.99.2
-declare -x MODULES_VERSION=3.2.10
-
 declare -a COMPILER_VERSIONS=( 'gcc/4.7.4' 'gcc/4.8.3' 'gcc/4.8.4' 'gcc/4.9.2' )
 declare -a MPI_VERSIONS=( 'openmpi/1.6.5' 'openmpi/1.8.2' 'openmpi/1.8.4' )
 declare -a HDF5_VERSIONS=( 'hdf5/1.8.12' 'hdf5/1.8.14' )
+declare -a HDF5_SERIAL_VERSIONS=( 'hdf5_serial/1.8.12' 'hdf5_serial/1.8.14' )

From 9e3f159bfcb1b9be947d4dba0151334c99c4ac0b Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 23 Mar 2015 18:40:03 +0100
Subject: [PATCH 38/50] scripts/Bootstrap: read (P)MODULES_VERSION from
 Pmodules_version.conf

---
 scripts/Bootstrap/Pmodules_version.conf | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 scripts/Bootstrap/Pmodules_version.conf

diff --git a/scripts/Bootstrap/Pmodules_version.conf b/scripts/Bootstrap/Pmodules_version.conf
new file mode 100644
index 0000000..6057d13
--- /dev/null
+++ b/scripts/Bootstrap/Pmodules_version.conf
@@ -0,0 +1,7 @@
+declare -x PMODULES_VERSION=0.99.1
+declare -x MODULES_VERSION=3.2.10
+
+declare -a COMPILER_VERSIONS=( 'gcc/4.7.4' 'gcc/4.8.3' 'gcc/4.8.4' 'gcc/4.9.2' )
+declare -a MPI_VERSIONS=( 'openmpi/1.6.5' 'openmpi/1.8.2' 'openmpi/1.8.4' )
+declare -a HDF5_VERSIONS=( 'hdf5/1.8.12' 'hdf5/1.8.14' )
+declare -a HDF5_SERIAL_VERSIONS=( 'hdf5_serial/1.8.12' 'hdf5_serial/1.8.14' )

From 15815f6e6a505aeb57eed204cfe3a1f3cb96cfce Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 23 Mar 2015 18:40:21 +0100
Subject: [PATCH 39/50] scripts/Bootstrap: read (P)MODULES_VERSION from
 Pmodules_version.conf

---
 scripts/Bootstrap/compile_pmodules.sh | 2 +-
 scripts/Bootstrap/install_pmodules.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/Bootstrap/compile_pmodules.sh b/scripts/Bootstrap/compile_pmodules.sh
index 9d60e93..5de1ca8 100755
--- a/scripts/Bootstrap/compile_pmodules.sh
+++ b/scripts/Bootstrap/compile_pmodules.sh
@@ -3,7 +3,7 @@
 declare -r BASE_DIR=$(cd "$(dirname $0)/../.." && pwd)
 declare -r BOOTSTRAP_DIR="${BASE_DIR}/scripts/Bootstrap"
 
-source "${BASE_DIR}/config/Pmodules.conf"
+source "${BOOTSTRAP_DIR}/Pmodules_version.conf"
 
 unset PMODULES_HOME
 source "/opt/psi/config/environment.bash"
diff --git a/scripts/Bootstrap/install_pmodules.sh b/scripts/Bootstrap/install_pmodules.sh
index 13d301d..a6fb606 100755
--- a/scripts/Bootstrap/install_pmodules.sh
+++ b/scripts/Bootstrap/install_pmodules.sh
@@ -4,7 +4,7 @@ declare -r BASE_DIR=$(cd "$(dirname $0)/../.." && pwd)
 declare -r BOOTSTRAP_DIR="${BASE_DIR}/scripts/Bootstrap"
 declare -r SRC_DIR="${BOOTSTRAP_DIR}/Pmodules"
 
-source "${BASE_DIR}/config/Pmodules.conf"
+source "${BOOTSTRAP_DIR}/Pmodules_version.conf"
 
 unset PMODULES_HOME
 source "/opt/psi/config/environment.bash"

From 12d6f2f5329bb2c316c388258f486040b3ea502a Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 24 Mar 2015 13:28:34 +0100
Subject: [PATCH 40/50] scripts/Programming/Tcl/build: compile with system
 compiler

---
 scripts/Programming/Tcl/build | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/Programming/Tcl/build b/scripts/Programming/Tcl/build
index 402004d..6aa8add 100755
--- a/scripts/Programming/Tcl/build
+++ b/scripts/Programming/Tcl/build
@@ -21,7 +21,9 @@ function em.post_install() {
 	{ cd "${PREFIX}"/bin && rm -f tclsh && ln -fs tclsh${V%.*} tclsh; };
 }
 
+# use system's cc
+declare CC=cc
+
 em.add_to_family 'Programming'
 em.set_docfiles 'license.terms' 'README'
-em.set_build_dependencies "${COMPILER}"
 em.make_all

From 87ffe565a1587260d50c4d6b73123d5e8ab613fb Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 24 Mar 2015 13:29:20 +0100
Subject: [PATCH 41/50] scripts/Programming/Tk/build: added

---
 scripts/Programming/Tk/build | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100755 scripts/Programming/Tk/build

diff --git a/scripts/Programming/Tk/build b/scripts/Programming/Tk/build
new file mode 100755
index 0000000..9ca58c4
--- /dev/null
+++ b/scripts/Programming/Tk/build
@@ -0,0 +1,32 @@
+#!/bin/bash
+
+source "$(dirname $0)/../../../lib/libem.bash"
+
+function em.configure() {
+	case ${OS} in
+	Linux )
+		srcdir="${MODULE_SRCDIR}/unix"
+		;;
+	Darwin )
+		srcdir="${MODULE_SRCDIR}/macosx"
+		;;
+	esac
+	"${srcdir}"/configure \
+		--prefix="${PREFIX}" \
+		--with-tcl=${TCL_PREFIX}/lib \
+		--enable-shared=no \
+		|| exit 1
+}
+
+function em.post_install() {
+	:
+	#{ cd "${PREFIX}"/bin && rm -f tclsh && ln -fs tclsh${V%.*} tclsh; };
+}
+
+# use system's cc
+declare CC=cc
+
+em.add_to_family 'Programming'
+em.set_build_dependencies 'Tcl'
+em.set_docfiles 'license.terms' 'README'
+em.make_all

From 38f3a237f2278194fe96205f953689fb6718e26b Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 24 Mar 2015 13:30:01 +0100
Subject: [PATCH 42/50] scripts/Tools/git/build: run-time dependencies 'Tcl'
 and 'Tk' added

---
 scripts/Tools/git/build | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/Tools/git/build b/scripts/Tools/git/build
index ed9c700..52423c3 100755
--- a/scripts/Tools/git/build
+++ b/scripts/Tools/git/build
@@ -16,6 +16,7 @@ function em.build() {
 }
 
 em.add_to_family 'Tools'
+em.set_runtime_dependencies 'Tcl' 'Tk'
 em.set_docfiles 'COPYING' 'README'
 em.make_all
 

From 4f9229e8f13674313839cf771bbf4b948a68bd9d Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 24 Mar 2015 13:30:59 +0100
Subject: [PATCH 43/50] scripts/Tools/git/with_modules: added

---
 scripts/Tools/git/with_modules | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 scripts/Tools/git/with_modules

diff --git a/scripts/Tools/git/with_modules b/scripts/Tools/git/with_modules
new file mode 100644
index 0000000..70974ad
--- /dev/null
+++ b/scripts/Tools/git/with_modules
@@ -0,0 +1,2 @@
+Tcl/8.6.4
+Tk/8.6.4

From ebc2a121c51b2d9dcbf4aee3cc4f47cddcf4d30a Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 24 Mar 2015 13:36:47 +0100
Subject: [PATCH 44/50] scripts/HDF5/H5hut/build: 'vtk' removed as build
 dependency

---
 scripts/HDF5/H5hut/build | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/HDF5/H5hut/build b/scripts/HDF5/H5hut/build
index a689248..4420013 100755
--- a/scripts/HDF5/H5hut/build
+++ b/scripts/HDF5/H5hut/build
@@ -36,7 +36,7 @@ function em.install() {
 
 em.add_to_family 'HDF5'
 em.set_runtime_dependencies "${COMPILER}" "${MPI}" 'hdf5'
-em.set_build_dependencies   "autoconf" "automake" "libtool" "${COMPILER}" "${MPI}" "vtk" "hdf5"
+em.set_build_dependencies   "autoconf" "automake" "libtool" "${COMPILER}" "${MPI}" "hdf5"
 em.set_docfiles 'AUTHORS' 'COPYING'
 em.make_all
 

From b4652a6d76e55a06f7f948a9b7aa909a49b98e4f Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 24 Mar 2015 13:37:41 +0100
Subject: [PATCH 45/50] scripts/System/nmap/build: setting release removed

---
 scripts/System/nmap/build | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/System/nmap/build b/scripts/System/nmap/build
index aaf593f..f71397c 100755
--- a/scripts/System/nmap/build
+++ b/scripts/System/nmap/build
@@ -23,7 +23,6 @@ function em.install() {
 	make install
 }
 
-em.release 'unstable'
 em.add_to_family 'System'
 em.set_build_dependencies "${COMPILER}"
 em.make_all

From b6021f80a4bebf780ca15fd0579b1d82b9ba9b17 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 24 Mar 2015 14:43:06 +0100
Subject: [PATCH 46/50] lib/libem.bash: bugfix in 'em.cleanup_build()'

---
 lib/libem.bash | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/lib/libem.bash b/lib/libem.bash
index 35ac0e2..4ec90e1 100644
--- a/lib/libem.bash
+++ b/lib/libem.bash
@@ -584,14 +584,14 @@ function _set_link() {
 }
 
 function em.cleanup_build() {
-    (
-	[[ -d /${MODULE_BUILDDIR} ]] || return 0
-	cd "/${MODULE_BUILDDIR}/..";
-	if [[ $(pwd) != / ]]; then
-		echo "Cleaning up $(pwd)/${COMPILER_VERSION}"
-		rm -rf *
-	fi
-    );
+	[[ -n "${MODULE_BUILDDIR}" ]]     \
+		|| die 1 "Oops: internal error: MODULE_BUILDDIR is set to empty string..."
+	[[ "${MODULE_BUILDDIR}" == "/" ]] \
+		&& die 1 "Oops: internal error: MODULE_BUILDDIR is set to '/'..."
+	[[ -d "/${MODULE_BUILDDIR}" ]]    \
+		|| die 1 "Oops: internal error: MODULE_BUILDDIR=${MODULE_BUILDDIR} is not a directory..."
+	echo "Cleaning up '/${MODULE_BUILDDIR}'..."
+	rm -rf  "/${MODULE_BUILDDIR}"
 }
 
 function em.cleanup_src() {

From 3aae40abcd27f5aa361b39da415ed95657c33045 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 24 Mar 2015 14:43:41 +0100
Subject: [PATCH 47/50] scripts/MPI/build_all_variants: exit on error

---
 scripts/MPI/build_all_variants | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/MPI/build_all_variants b/scripts/MPI/build_all_variants
index e626c5a..5aa47d3 100755
--- a/scripts/MPI/build_all_variants
+++ b/scripts/MPI/build_all_variants
@@ -17,6 +17,7 @@ for cc in "${COMPILER_VERSIONS[@]}"; do
 			echo "Oops: build failed for:"
 			echo "        compiler: $cc"
 			echo "        mpi:      $mpi"
+			exit 1
 			}
 	done
 done

From 2e45aa799d39e07e6b07a0bbb498ac7b7b79b763 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 24 Mar 2015 14:44:26 +0100
Subject: [PATCH 48/50] scripts/Tools/git/build: use bar '--with-tcltk'

---
 scripts/Tools/git/build | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/Tools/git/build b/scripts/Tools/git/build
index 52423c3..0f72c23 100755
--- a/scripts/Tools/git/build
+++ b/scripts/Tools/git/build
@@ -6,7 +6,7 @@ function em.configure() {
 	cd "${MODULE_SRCDIR}"
 	"${MODULE_SRCDIR}"/configure \
 		--prefix="${PREFIX}" \
-		--with-tcltk="${PMODULES_HOME}" \
+		--with-tcltk \
 		|| exit 1
 }
 

From 0ba06aa74b71952599cc7fa96cbd2352e91bb27e Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 24 Mar 2015 18:54:12 +0100
Subject: [PATCH 49/50] lib/libem.bash: - bugfixes in setting up family
 HDF5_serial - skip call of em.cleanup_build() if nothing was build

---
 lib/libem.bash | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/lib/libem.bash b/lib/libem.bash
index 4ec90e1..f1949c9 100644
--- a/lib/libem.bash
+++ b/lib/libem.bash
@@ -393,7 +393,7 @@ function _setup_env2() {
 			MODULE_RPREFIX+="/${COMPILER}/${COMPILER_VERSION}"
 			
 			MODULE_NAME="${COMPILER}/${COMPILER_VERSION}/"
-			MODULE_NAME+="hdf5_serial/${HDF5_VERSION}/"
+			MODULE_NAME+="hdf5_serial/${HDF5_SERIAL_VERSION}/"
 			MODULE_NAME+="${P}/${V}"
 			;;
 		* )
@@ -632,6 +632,7 @@ function _post_install() {
 }
 
 function em.make_all() {
+	local building='no'
 	echo "${P}:"
 	_setup_env1
 	_load_build_dependencies
@@ -643,6 +644,7 @@ function em.make_all() {
 	fi
 
 	if [[ ! -d "${PREFIX}" ]] || [[ ${force_rebuild} == 'yes' ]]; then
+		building='yes'
  		echo "Building $P/$V ..."
 		[[ ${dry_run} == yes ]] && die 0 ""
 		_check_compiler
@@ -667,7 +669,8 @@ function em.make_all() {
 	if [[ ${bootstrap} == 'no' ]]; then
 		_set_link
 	fi
-	em.cleanup_build
+	[[ ${building} == yes ]] && em.cleanup_build
+	return 0
 }
 
 ##############################################################################

From 308079c18d194e112207802b65d7c2706404665f Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 24 Mar 2015 18:54:48 +0100
Subject: [PATCH 50/50] scripts/HDF5_serial/build_all_variants: - exit if a
 build failed

---
 scripts/HDF5_serial/build_all_variants | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/HDF5_serial/build_all_variants b/scripts/HDF5_serial/build_all_variants
index 6854f9e..65d7c65 100755
--- a/scripts/HDF5_serial/build_all_variants
+++ b/scripts/HDF5_serial/build_all_variants
@@ -17,6 +17,7 @@ for cc in "${COMPILER_VERSIONS[@]}"; do
 			echo "Oops: build failed for:"
 			echo "        compiler:      $cc"
 			echo "        HDF5 (serial): $hdf"
+			exit 1
 			}
 	done
 done