From 5d618886570e98e6745593701246b877998a5367 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 23 Nov 2015 16:51:16 -0500
Subject: Correct Spack cc script

---
 lib/spack/env/cc | 34 +++++++++++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 75a63f6fac..f3fadfcf45 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -126,6 +126,11 @@ if [ -z "$mode" ]; then
         elif [ "$arg" = -c ]; then
             mode=cc
             break
+        elif [ "$arg" = -S ]; then
+            mode=as
+	    echo "spac cc mode as" "$@"
+	    exit 1
+            break
         fi
     done
 fi
@@ -155,6 +160,7 @@ libraries=()
 libs=()
 rpaths=()
 other_args=()
+all_args=("$@")
 
 while [ -n "$1" ]; do
     case "$1" in
@@ -178,6 +184,8 @@ while [ -n "$1" ]; do
             if [ -z "$arg" ]; then shift; arg="$1"; fi
             if [[ "$arg" = -rpath=* ]]; then
                 rpaths+=("${arg#-rpath=}")
+            elif [[ "$arg" = -rpath,* ]]; then
+                rpaths+=("${arg#-rpath,}")
             elif [[ "$arg" = -rpath ]]; then
                 shift; arg="$1"
                 if [[ "$arg" != -Wl,* ]]; then
@@ -193,6 +201,8 @@ while [ -n "$1" ]; do
             if [ -z "$arg" ]; then shift; arg="$1"; fi
             if [[ "$arg" = -rpath=* ]]; then
                 rpaths+=("${arg#-rpath=}")
+            elif [[ "$arg" = -rpath,* ]]; then
+                rpaths+=("${arg#-rpath,}")
             elif [[ "$arg" = -rpath ]]; then
                 shift; arg="$1"
                 if [[ "$arg" != -Xlinker,* ]]; then
@@ -247,25 +257,46 @@ IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
     if [ -d "$dep/include" ]; then
         includes+=("$dep/include")
+	all_args=("-I$dep/include" ${all_args[@]})
     fi
 
     if [ -d "$dep/lib" ]; then
         libraries+=("$dep/lib")
         rpaths+=("$dep/lib")
+	if [ "$mode" = ccld ]; then
+	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
+	elif [ "$mode" = ld ]; then
+	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
+	fi
     fi
 
     if [ -d "$dep/lib64" ]; then
         libraries+=("$dep/lib64")
         rpaths+=("$dep/lib64")
+        if [ "$mode" = ccld ]; then
+	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
+        elif [ "$mode" = ld ]; then
+	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
+	fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
 for dir in "${libraries[@]}"; do
     [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
+    if [ "$mode" = ccld ]; then
+	[[ dir = $SPACK_INSTALL* ]] && all_args=("-Wl,-rpath,$dir" ${all_args[@]})
+    elif [ "$mode" = ld ]; then
+	[[ dir = $SPACK_INSTALL* ]] && all_args=("-rpath" "$dir" ${all_args[@]})
+    fi
 done
 rpaths+=("$SPACK_PREFIX/lib")
 rpaths+=("$SPACK_PREFIX/lib64")
+if [ "$mode" = ccld ]; then
+    all_args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${all_args[@]})
+elif [ "$mode" = ld ]; then
+    all_args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${all_args[@]})
+fi
 
 # Put the arguments together
 args=()
@@ -317,7 +348,8 @@ done
 export PATH
 
 full_command=("$command")
-full_command+=("${args[@]}")
+# full_command+=("${args[@]}")
+full_command+=("${all_args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
-- 
cgit v1.2.3-70-g09d2


From ba22fc8b78841728500966d471db7b5bfd26cf56 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 21 Dec 2015 10:21:33 -0500
Subject: Simplify Spack cc script

---
 lib/spack/env/cc | 283 +++++++++++++++++++++++++------------------------------
 1 file changed, 130 insertions(+), 153 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index f3fadfcf45..053295f42d 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [ -z "${!param}" ]; then
+    if [[ -z ${!param} ]]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -114,114 +114,118 @@ case "$command" in
 esac
 
 # Finish setting up the mode.
-if [ -z "$mode" ]; then
+if [[ -z $mode ]]; then
     mode=ccld
     for arg in "$@"; do
-        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
-            mode=vcheck
-            break
-        elif [ "$arg" = -E ]; then
-            mode=cpp
-            break
-        elif [ "$arg" = -c ]; then
-            mode=cc
-            break
-        elif [ "$arg" = -S ]; then
-            mode=as
-	    echo "spac cc mode as" "$@"
-	    exit 1
-            break
-        fi
+        case "$arg" in
+            -v|-V|--version|-dumpversion)
+                mode=vcheck
+                break
+                ;;
+            -E)
+                mode=cpp
+                break
+                ;;
+            -c)
+                mode=cc
+                break
+                ;;
+            -S)
+                mode=as
+                break
+                ;;
+        esac
     done
 fi
 
 # Dump the version and exist if we're in testing mode.
-if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
+if [[ $SPACK_TEST_COMMAND = dump-mode ]]; then
     echo "$mode"
     exit
 fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [ -z "$command" ]; then
+if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
 # Save original command for debug logging
 input_command="$@"
+args=("$@")
 
-#
-# Now do real parsing of the command line args, trying hard to keep
-# non-rpath linker arguments in the proper order w.r.t. other command
-# line arguments.  This is important for things like groups.
-#
-includes=()
-libraries=()
-libs=()
-rpaths=()
-other_args=()
-all_args=("$@")
+# Dump parsed values for unit testing if asked for
+if [[ -n $SPACK_TEST_COMMAND ]]; then
 
-while [ -n "$1" ]; do
-    case "$1" in
-        -I*)
-            arg="${1#-I}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            includes+=("$arg")
-            ;;
-        -L*)
-            arg="${1#-L}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libraries+=("$arg")
-            ;;
-        -l*)
-            arg="${1#-l}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libs+=("$arg")
-            ;;
-        -Wl,*)
-            arg="${1#-Wl,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath,* ]]; then
-                rpaths+=("${arg#-rpath,}")
-            elif [[ "$arg" = -rpath ]]; then
-                shift; arg="$1"
-                if [[ "$arg" != -Wl,* ]]; then
-                    die "-Wl,-rpath was not followed by -Wl,*"
+    #
+    # Now do real parsing of the command line args, trying hard to keep
+    # non-rpath linker arguments in the proper order w.r.t. other command line
+    # arguments.  This is important for things like groups.
+    #
+    includes=()
+    libraries=()
+    libs=()
+    rpaths=()
+    other_args=()
+
+    while [[ -n $1 ]]; do
+        case "$1" in
+            -I*)
+                arg="${1#-I}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                includes+=("$arg")
+                ;;
+            -L*)
+                arg="${1#-L}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                libraries+=("$arg")
+                ;;
+            -l*)
+                arg="${1#-l}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                libs+=("$arg")
+                ;;
+            -Wl,*)
+                arg="${1#-Wl,}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [[ $arg = -rpath=* ]]; then
+                    rpaths+=("${arg#-rpath=}")
+                elif [[ $arg = -rpath,* ]]; then
+                    rpaths+=("${arg#-rpath,}")
+                elif [[ $arg = -rpath ]]; then
+                    shift; arg="$1"
+                    if [[ $arg != -Wl,* ]]; then
+                        die "-Wl,-rpath was not followed by -Wl,*"
+                    fi
+                    rpaths+=("${arg#-Wl,}")
+                else
+                    other_args+=("-Wl,$arg")
                 fi
-                rpaths+=("${arg#-Wl,}")
-            else
-                other_args+=("-Wl,$arg")
-            fi
-            ;;
-        -Xlinker,*)
-            arg="${1#-Xlinker,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath,* ]]; then
-                rpaths+=("${arg#-rpath,}")
-            elif [[ "$arg" = -rpath ]]; then
-                shift; arg="$1"
-                if [[ "$arg" != -Xlinker,* ]]; then
-                    die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                ;;
+            -Xlinker,*)
+                arg="${1#-Xlinker,}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [[ $arg = -rpath=* ]]; then
+                    rpaths+=("${arg#-rpath=}")
+                elif [[ $arg = -rpath,* ]]; then
+                    rpaths+=("${arg#-rpath,}")
+                elif [[ $arg = -rpath ]]; then
+                    shift; arg="$1"
+                    if [[ $arg != -Xlinker,* ]]; then
+                        die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                    fi
+                    rpaths+=("${arg#-Xlinker,}")
+                else
+                    other_args+=("-Xlinker,$arg")
                 fi
-                rpaths+=("${arg#-Xlinker,}")
-            else
-                other_args+=("-Xlinker,$arg")
-            fi
-            ;;
-        *)
-            other_args+=("$1")
-            ;;
-    esac
-    shift
-done
+                ;;
+            *)
+                other_args+=("$1")
+                ;;
+        esac
+        shift
+    done
 
-# Dump parsed values for unit testing if asked for
-if [ -n "$SPACK_TEST_COMMAND" ]; then
     IFS=$'\n'
     case "$SPACK_TEST_COMMAND" in
         dump-includes)   echo "${includes[*]}";;
@@ -246,8 +250,8 @@ if [ -n "$SPACK_TEST_COMMAND" ]; then
             echo "${other_args[*]}"
             ;;
         *)
-            echo "ERROR: Unknown test command"
-            exit 1 ;;
+            die "ERROR: Unknown test command"
+            ;;
     esac
     exit
 fi
@@ -255,66 +259,44 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [ -d "$dep/include" ]; then
-        includes+=("$dep/include")
-	all_args=("-I$dep/include" ${all_args[@]})
+    if [[ -d $dep/include ]]; then
+        args=("-I$dep/include" "${args[@]}")
     fi
 
-    if [ -d "$dep/lib" ]; then
-        libraries+=("$dep/lib")
-        rpaths+=("$dep/lib")
-	if [ "$mode" = ccld ]; then
-	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
-	elif [ "$mode" = ld ]; then
-	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
-	fi
+    if [[ -d $dep/lib ]]; then
+        # libraries+=("$dep/lib")
+	    if [[ $mode = ccld ]]; then
+            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+        elif [[ $mode = ld ]]; then
+            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib64" ]; then
-        libraries+=("$dep/lib64")
-        rpaths+=("$dep/lib64")
-        if [ "$mode" = ccld ]; then
-	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
-        elif [ "$mode" = ld ]; then
-	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
-	fi
+    if [[ -d $dep/lib64 ]]; then
+        # libraries+=("$dep/lib64")
+        if [[ $mode = ccld ]]; then
+            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+        elif [[ $mode = ld ]]; then
+            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+        fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
-for dir in "${libraries[@]}"; do
-    [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
-    if [ "$mode" = ccld ]; then
-	[[ dir = $SPACK_INSTALL* ]] && all_args=("-Wl,-rpath,$dir" ${all_args[@]})
-    elif [ "$mode" = ld ]; then
-	[[ dir = $SPACK_INSTALL* ]] && all_args=("-rpath" "$dir" ${all_args[@]})
-    fi
-done
-rpaths+=("$SPACK_PREFIX/lib")
-rpaths+=("$SPACK_PREFIX/lib64")
-if [ "$mode" = ccld ]; then
-    all_args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${all_args[@]})
-elif [ "$mode" = ld ]; then
-    all_args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${all_args[@]})
-fi
-
-# Put the arguments together
-args=()
-for dir in "${includes[@]}";  do args+=("-I$dir"); done
-args+=("${other_args[@]}")
-for dir in "${libraries[@]}"; do args+=("-L$dir"); done
-for lib in "${libs[@]}";      do args+=("-l$lib"); done
-
-if [ "$mode" = ccld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-Wl,-rpath")
-        args+=("-Wl,$dir");
-    done
-elif [ "$mode" = ld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-rpath")
-        args+=("$dir");
-    done
+if [[ $mode = ccld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-Wl,-rpath,$dir" "${args[@]}")
+    #     fi
+    # done
+    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${args[@]})
+elif [[ $mode = ld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-rpath" "$dir" "${args[@]}")
+    #     fi
+    # done
+    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${args[@]})
 fi
 
 #
@@ -330,34 +312,29 @@ unset DYLD_LIBRARY_PATH
 #
 IFS=':' read -ra env_path <<< "$PATH"
 IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
-spack_env_dirs+=(".")
+spack_env_dirs+=("" ".")
 PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
+        if [[ $dir = $rm_dir ]]; then remove=True; fi
     done
-    if [ -z "$remove" ]; then
-        if [ -z "$PATH" ]; then
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
-        fi
+    if [[ -z $remove ]]; then
+        PATH="${PATH:+$PATH:}$dir"
     fi
 done
 export PATH
 
 full_command=("$command")
-# full_command+=("${args[@]}")
-full_command+=("${all_args[@]}")
+full_command+=("${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [ "$SPACK_DEBUG" = "TRUE" ]; then
+if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command"     >> $input_log
+    echo "$input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 
-- 
cgit v1.2.3-70-g09d2


From 3427174eb065a6e74fc279076423c2c5c5e8e737 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 22 Dec 2015 15:49:14 -0500
Subject: Correct quoting

---
 lib/spack/env/cc | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 565f959ca4..4ac8f2e7f4 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -265,7 +265,7 @@ for dep in "${deps[@]}"; do
 
     if [[ -d $dep/lib ]]; then
         # libraries+=("$dep/lib")
-	    if [[ $mode = ccld ]]; then
+        if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
             args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
@@ -289,14 +289,14 @@ if [[ $mode = ccld ]]; then
     #         args=("-Wl,-rpath,$dir" "${args[@]}")
     #     fi
     # done
-    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${args[@]})
+    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
     # for dir in "${libraries[@]}"; do
     #     if [[ dir = $SPACK_INSTALL* ]]; then
     #         args=("-rpath" "$dir" "${args[@]}")
     #     fi
     # done
-    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${args[@]})
+    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
 #
@@ -325,8 +325,7 @@ for dir in "${env_path[@]}"; do
 done
 export PATH
 
-full_command=("$command")
-full_command+=("${args[@]}")
+full_command=("$command" "${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
-- 
cgit v1.2.3-70-g09d2


From ff81aff2540f9eadd8d0ce123ae3143ebcb68789 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 12 Feb 2016 13:05:42 -0500
Subject: Remove source-code optimization and cleanup

---
 lib/spack/env/cc | 106 +++++++++++++++++++++++--------------------------------
 1 file changed, 44 insertions(+), 62 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index b83731404b..ac8f717cc7 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [[ -z ${!param} ]]; then
+    if [ -z "${!param}" ]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -114,39 +114,31 @@ case "$command" in
 esac
 
 # Finish setting up the mode.
-if [[ -z $mode ]]; then
+if [ -z "$mode" ]; then
     mode=ccld
     for arg in "$@"; do
-        case "$arg" in
-            -v|-V|--version|-dumpversion)
-                mode=vcheck
-                break
-                ;;
-            -E)
-                mode=cpp
-                break
-                ;;
-            -c)
-                mode=cc
-                break
-                ;;
-            -S)
-                mode=as
-                break
-                ;;
-        esac
+        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
+            mode=vcheck
+            break
+        elif [ "$arg" = -E ]; then
+            mode=cpp
+            break
+        elif [ "$arg" = -c ]; then
+            mode=cc
+            break
+        fi
     done
 fi
 
 # Dump the version and exist if we're in testing mode.
-if [[ $SPACK_TEST_COMMAND = dump-mode ]]; then
+if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
     echo "$mode"
     exit
 fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [[ -z $command ]]; then
+if [ -z "$command" ]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
@@ -159,8 +151,8 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
 
     #
     # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command line
-    # arguments.  This is important for things like groups.
+    # non-rpath linker arguments in the proper order w.r.t. other command
+    # line arguments.  This is important for things like groups.
     #
     includes=()
     libraries=()
@@ -168,33 +160,31 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
     rpaths=()
     other_args=()
 
-    while [[ -n $1 ]]; do
+    while [ -n "$1" ]; do
         case "$1" in
             -I*)
                 arg="${1#-I}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 includes+=("$arg")
                 ;;
             -L*)
                 arg="${1#-L}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 libraries+=("$arg")
                 ;;
             -l*)
                 arg="${1#-l}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 libs+=("$arg")
                 ;;
             -Wl,*)
                 arg="${1#-Wl,}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
-                if [[ $arg = -rpath=* ]]; then
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
+                if [[ "$arg" = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath,* ]]; then
-                    rpaths+=("${arg#-rpath,}")
-                elif [[ $arg = -rpath ]]; then
+                elif [[ "$arg" = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ $arg != -Wl,* ]]; then
+                    if [[ "$arg" != -Wl,* ]]; then
                         die "-Wl,-rpath was not followed by -Wl,*"
                     fi
                     rpaths+=("${arg#-Wl,}")
@@ -204,14 +194,12 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
                 ;;
             -Xlinker,*)
                 arg="${1#-Xlinker,}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
-                if [[ $arg = -rpath=* ]]; then
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
+                if [[ "$arg" = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath,* ]]; then
-                    rpaths+=("${arg#-rpath,}")
-                elif [[ $arg = -rpath ]]; then
+                elif [[ "$arg" = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ $arg != -Xlinker,* ]]; then
+                    if [[ "$arg" != -Xlinker,* ]]; then
                         die "-Xlinker,-rpath was not followed by -Xlinker,*"
                     fi
                     rpaths+=("${arg#-Xlinker,}")
@@ -250,8 +238,8 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
             echo "${other_args[*]}"
             ;;
         *)
-            die "ERROR: Unknown test command"
-            ;;
+            echo "ERROR: Unknown test command"
+            exit 1 ;;
     esac
     exit
 fi
@@ -259,12 +247,11 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [[ -d $dep/include ]]; then
+    if [ -d "$dep/include" ]; then
         args=("-I$dep/include" "${args[@]}")
     fi
 
-    if [[ -d $dep/lib ]]; then
-        # libraries+=("$dep/lib")
+    if [ -d "$dep/lib" ]; then
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -272,7 +259,7 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
-    if [[ -d $dep/lib64 ]]; then
+    if [ -d "$dep/lib64" ]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
@@ -284,18 +271,8 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-Wl,-rpath,$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-rpath" "$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -317,23 +294,28 @@ PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [[ $dir = $rm_dir ]]; then remove=True; fi
+        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
     done
-    if [[ -z $remove ]]; then
-        PATH="${PATH:+$PATH:}$dir"
+    if [ -z "$remove" ]; then
+        if [ -z "$PATH" ]; then
+            PATH="$dir"
+        else
+            PATH="$PATH:$dir"
+        fi
     fi
 done
 export PATH
 
-full_command=("$command" "${args[@]}")
+full_command=("$command")
+full_command+=("${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [[ $SPACK_DEBUG = TRUE ]]; then
+if [ "$SPACK_DEBUG" = "TRUE" ]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command" >> $input_log
+    echo "$input_command"     >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 
-- 
cgit v1.2.3-70-g09d2


From f3ea0420f80f418a0f3e628479c782f197e6a43e Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Thu, 17 Mar 2016 21:53:13 -0400
Subject: Import recent changes

---
 lib/spack/env/cc | 185 +++++++++++++++++++------------------------------------
 1 file changed, 65 insertions(+), 120 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index df6795c264..c6a09724e9 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [ -z "${!param}" ]; then
+    if [[ -z ${!param} ]]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -78,10 +78,11 @@ done
 # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
 #
 # 'mode' is set to one of:
+#    cpp     preprocess
 #    cc      compile
+#    as      assemble
 #    ld      link
 #    ccld    compile & link
-#    cpp     preprocessor
 #    vcheck  version check
 #
 command=$(basename "$0")
@@ -131,6 +132,9 @@ if [ -z "$mode" ]; then
         if [ "$arg" = -E ]; then
             mode=cpp
             break
+        elif [ "$arg" = -S ]; then
+            mode=as
+            break
         elif [ "$arg" = -c ]; then
             mode=cc
             break
@@ -146,22 +150,25 @@ fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [ -z "$command" ]; then
+if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
+if [ "$mode" == vcheck ] ; then
+    exec ${command} "$@"
+fi
+
 # Save original command for debug logging
 input_command="$@"
 args=("$@")
 
-<<<<<<< HEAD
 # Dump parsed values for unit testing if asked for
 if [[ -n $SPACK_TEST_COMMAND ]]; then
 
     #
     # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command
-    # line arguments.  This is important for things like groups.
+    # non-rpath linker arguments in the proper order w.r.t. other command line
+    # arguments.  This is important for things like groups.
     #
     includes=()
     libraries=()
@@ -188,32 +195,44 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
                 ;;
             -Wl,*)
                 arg="${1#-Wl,}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                if [[ "$arg" = -rpath=* ]]; then
-                    rpaths+=("${arg#-rpath=}")
-                elif [[ "$arg" = -rpath ]]; then
+                # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
+                if [[ $arg == -rpath=* ]]; then
+                    arg="${arg#-rpath=}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
+                elif [[ $arg == -rpath,* ]]; then
+                    arg="${arg#-rpath,}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
+                elif [[ $arg == -rpath ]]; then
                     shift; arg="$1"
-                    if [[ "$arg" != -Wl,* ]]; then
+                    if [[ $arg != '-Wl,'* ]]; then
                         die "-Wl,-rpath was not followed by -Wl,*"
                     fi
-                    rpaths+=("${arg#-Wl,}")
+                    arg="${arg#-Wl,}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
                 else
                     other_args+=("-Wl,$arg")
                 fi
                 ;;
-            -Xlinker,*)
-                arg="${1#-Xlinker,}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                if [[ "$arg" = -rpath=* ]]; then
+            -Xlinker)
+                shift; arg="$1";
+                if [[ $arg = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ "$arg" = -rpath ]]; then
+                elif [[ $arg = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ "$arg" != -Xlinker,* ]]; then
-                        die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                    if [[ $arg != -Xlinker ]]; then
+                        die "-Xlinker -rpath was not followed by -Xlinker <arg>"
                     fi
-                    rpaths+=("${arg#-Xlinker,}")
+                    shift; arg="$1"
+                    rpaths+=("$arg")
                 else
-                    other_args+=("-Xlinker,$arg")
+                    other_args+=("-Xlinker")
+                    other_args+=("$arg")
                 fi
                 ;;
             *)
@@ -222,88 +241,6 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
         esac
         shift
     done
-=======
-if [ "$mode" == vcheck ] ; then
-    exec ${command} "$@"
-fi
-
-#
-# Now do real parsing of the command line args, trying hard to keep
-# non-rpath linker arguments in the proper order w.r.t. other command
-# line arguments.  This is important for things like groups.
-#
-includes=()
-libraries=()
-libs=()
-rpaths=()
-other_args=()
-
-while [ -n "$1" ]; do
-    case "$1" in
-        -I*)
-            arg="${1#-I}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            includes+=("$arg")
-            ;;
-        -L*)
-            arg="${1#-L}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libraries+=("$arg")
-            ;;
-        -l*)
-            arg="${1#-l}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libs+=("$arg")
-            ;;
-        -Wl,*)
-            arg="${1#-Wl,}"
-            # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
-            if [[ $arg == -rpath=* ]]; then
-                arg="${arg#-rpath=}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            elif [[ $arg == -rpath,* ]]; then
-                arg="${arg#-rpath,}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            elif [[ $arg == -rpath ]]; then
-                shift; arg="$1"
-                if [[ $arg != '-Wl,'* ]]; then
-                    die "-Wl,-rpath was not followed by -Wl,*"
-                fi
-                arg="${arg#-Wl,}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            else
-                other_args+=("-Wl,$arg")
-            fi
-            ;;
-        -Xlinker)
-            shift; arg="$1";
-            if [[ $arg = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ $arg = -rpath ]]; then
-                shift; arg="$1"
-                if [[ $arg != -Xlinker ]]; then
-                    die "-Xlinker -rpath was not followed by -Xlinker <arg>"
-                fi
-                shift; arg="$1"
-                rpaths+=("$arg")
-            else
-                other_args+=("-Xlinker")
-                other_args+=("$arg")
-            fi
-            ;;
-        *)
-            other_args+=("$1")
-            ;;
-    esac
-    shift
-done
->>>>>>> develop
 
     IFS=$'\n'
     case "$SPACK_TEST_COMMAND" in
@@ -329,8 +266,8 @@ done
             echo "${other_args[*]}"
             ;;
         *)
-            echo "ERROR: Unknown test command"
-            exit 1 ;;
+            die "ERROR: Unknown test command"
+            ;;
     esac
     exit
 fi
@@ -338,11 +275,14 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [ -d "$dep/include" ]; then
-        args=("-I$dep/include" "${args[@]}")
+    if [[ -d $dep/include ]]; then
+        if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then
+            args=("-I$dep/include" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib" ]; then
+    if [[ -d $dep/lib ]]; then
+        # libraries+=("$dep/lib")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -350,7 +290,7 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
-    if [ -d "$dep/lib64" ]; then
+    if [[ -d $dep/lib64 ]]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
@@ -362,8 +302,18 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-Wl,-rpath,$dir" "${args[@]}")
+    #     fi
+    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-rpath" "$dir" "${args[@]}")
+    #     fi
+    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -385,28 +335,23 @@ PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
+        if [[ $dir = $rm_dir ]]; then remove=True; fi
     done
-    if [ -z "$remove" ]; then
-        if [ -z "$PATH" ]; then
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
-        fi
+    if [[ -z $remove ]]; then
+        PATH="${PATH:+$PATH:}$dir"
     fi
 done
 export PATH
 
-full_command=("$command")
-full_command+=("${args[@]}")
+full_command=("$command" "${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [ "$SPACK_DEBUG" = "TRUE" ]; then
+if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command"     >> $input_log
+    echo "$input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 
-- 
cgit v1.2.3-70-g09d2


From a26992ef55fed958c15b45b989fc0a4d57f02251 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 22 Mar 2016 01:56:16 -0700
Subject: Change from PR #552: rename setup_dependent_python_module ->
 setup_dependent_package

- Fixed in package.py
- Fixed wrong prototypes in packages that use it.
- Fixed build_environment to set module variables properly
  - added hacky fix to ensure spec/package consistency in build processes.
  - Need to think about defensive spec copy done by `Repo.get`.  May be
    time to think about an immutable spec implementation.
---
 lib/spack/spack/build_environment.py               | 52 ++++++++++++++++------
 lib/spack/spack/package.py                         |  2 +-
 var/spack/repos/builtin/packages/mpich/package.py  |  2 +-
 .../builtin/packages/netlib-scalapack/package.py   | 22 ++++-----
 4 files changed, 52 insertions(+), 26 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index fc5b7d6207..119a255a34 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -225,7 +225,7 @@ def set_module_variables_for_package(pkg, module):
     m.spack_cc  = join_path(link_dir, pkg.compiler.link_paths['cc'])
     m.spack_cxx = join_path(link_dir, pkg.compiler.link_paths['cxx'])
     m.spack_f77 = join_path(link_dir, pkg.compiler.link_paths['f77'])
-    m.spack_f90 = join_path(link_dir, pkg.compiler.link_paths['fc'])
+    m.spack_fc  = join_path(link_dir, pkg.compiler.link_paths['fc'])
 
     # Emulate some shell commands for convenience
     m.pwd          = os.getcwd
@@ -270,32 +270,56 @@ def parent_class_modules(cls):
     return result
 
 
+def setup_module_variables_for_dag(pkg):
+    """Set module-scope variables for all packages in the DAG."""
+    for spec in pkg.spec.traverse(order='post'):
+        # If a user makes their own package repo, e.g.
+        # spack.repos.mystuff.libelf.Libelf, and they inherit from
+        # an existing class like spack.repos.original.libelf.Libelf,
+        # then set the module variables for both classes so the
+        # parent class can still use them if it gets called.
+        spkg = spec.package
+        modules = parent_class_modules(spkg.__class__)
+        for mod in modules:
+            set_module_variables_for_package(spkg, mod)
+        set_module_variables_for_package(spkg, spkg.module)
+
+
 def setup_package(pkg):
     """Execute all environment setup routines."""
     spack_env = EnvironmentModifications()
     run_env   = EnvironmentModifications()
 
+    # Before proceeding, ensure that specs and packages are consistent
+    #
+    # This is a confusing behavior due to how packages are
+    # constructed.  `setup_dependent_package` may set attributes on
+    # specs in the DAG for use by other packages' install
+    # method. However, spec.package will look up a package via
+    # spack.repo, which defensively copies specs into packages.  This
+    # code ensures that all packages in the DAG have pieces of the
+    # same spec object at build time.
+    #
+    # This is safe for the build process, b/c the build process is a
+    # throwaway environment, but it is kind of dirty.
+    #
+    # TODO: Think about how to avoid this fix and do something cleaner.
+    for s in pkg.spec.traverse(): s.package.spec = s
+
     set_compiler_environment_variables(pkg, spack_env)
     set_build_environment_variables(pkg, spack_env)
-
-    # If a user makes their own package repo, e.g.
-    # spack.repos.mystuff.libelf.Libelf, and they inherit from
-    # an existing class like spack.repos.original.libelf.Libelf,
-    # then set the module variables for both classes so the
-    # parent class can still use them if it gets called.
-    modules = parent_class_modules(pkg.__class__)
-    for mod in modules:
-        set_module_variables_for_package(pkg, mod)
+    setup_module_variables_for_dag(pkg)
 
     # Allow dependencies to modify the module
-    for dependency_spec in pkg.spec.traverse(root=False):
+    spec = pkg.spec
+    for dependency_spec in spec.traverse(root=False):
         dpkg = dependency_spec.package
-        dpkg.setup_dependent_python_module(pkg.module, pkg.spec)
+        dpkg.setup_dependent_package(pkg.module, spec)
 
     # Allow dependencies to set up environment as well
-    for dependency_spec in pkg.spec.traverse(root=False):
+    for dependency_spec in spec.traverse(root=False):
         dpkg = dependency_spec.package
-        dpkg.setup_dependent_environment(spack_env, run_env, pkg.spec)
+        dpkg.setup_dependent_environment(spack_env, run_env, spec)
 
     # Allow the package to apply some settings.
     pkg.setup_environment(spack_env, run_env)
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 9d8ac87bd7..9af3221837 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -1075,7 +1075,7 @@ class Package(object):
         self.setup_environment(spack_env, run_env)
 
 
-    def setup_dependent_python_module(self, module, dependent_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         """Set up Python module-scope variables for dependent packages.
 
         Called before the install() method of dependents.
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index c4d9940bb7..b20dc8dd60 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -54,7 +54,7 @@ class Mpich(Package):
         env.set('MPICH_F90', spack_f90)
         env.set('MPICH_FC', spack_fc)
 
-    def setup_dependent_python_module(self, module, spec, dep_spec):
+    def setup_dependent_package(self, module, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
         # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
         module.mpicc = join_path(self.prefix.bin, 'mpicc')
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 62abfcc48e..c3e6822cdf 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import sys
 
 class NetlibScalapack(Package):
     """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines"""
@@ -11,16 +12,16 @@ class NetlibScalapack(Package):
     version('2.0.0', '9e76ae7b291be27faaad47cfc256cbfe')
     # versions before 2.0.0 are not using cmake and requires blacs as
     # a separated package
-    
+
     variant('shared', default=True, description='Build the shared library version')
     variant('fpic', default=False, description="Build with -fpic compiler option")
-    
+
     provides('scalapack')
-    
+
     depends_on('mpi')
     depends_on('lapack')
-    
-    def install(self, spec, prefix):       
+
+    def install(self, spec, prefix):
         options = [
             "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'),
             "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'),
@@ -40,10 +41,11 @@ class NetlibScalapack(Package):
             make()
             make("install")
 
-    def setup_dependent_python_module(self, module, spec, dependent_spec):
+    def setup_dependent_package(self, module, dependent_spec):
+        spec = self.spec
         lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
-        lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a'
+        lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
 
-        spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib
-        spec['scalapack'].cc_link = spec['scalapack'].fc_link
-        spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, 'libscalapack%s' % lib_suffix)]
+        spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib
+        spec.cc_link = spec.fc_link
+        spec.libraries = [join_path(spec.prefix.lib, 'libscalapack%s' % lib_suffix)]
-- 
cgit v1.2.3-70-g09d2


From c4134ee71e43a6a2a38822e25cc72ca73efdcfea Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 23 Mar 2016 00:36:32 -0700
Subject: Fix #608: broken numpy build.

- Failed to catch all instances of modify_module when it was renamed
  to setup_dependent_package.

- Refactored remaining modify_module calls.

- Also modified Python's setup_dependent_package slightly: only
  creates empty site-packages directory for Python extensions now, not
  for all dependents.
---
 lib/spack/spack/modules.py                         |  4 ++--
 lib/spack/spack/preferred_packages.py              |  4 +++-
 var/spack/repos/builtin/packages/python/package.py | 11 ++++++-----
 var/spack/repos/builtin/packages/ruby/package.py   |  6 +++---
 4 files changed, 14 insertions(+), 11 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 05c93cd3e6..8ed98e5d38 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -160,8 +160,8 @@ class EnvModule(object):
         # package-specific modifications
         for extendee in self.pkg.extendees:
             extendee_spec = self.spec[extendee]
-            extendee_spec.package.modify_module(
-                self.pkg.module, extendee_spec, self.spec)
+            extendee_spec.package.setup_dependent_package(
+                self.pkg.module, self.spec)
 
         # Package-specific environment modifications
         spack_env = EnvironmentModifications()
diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index 4d8526c75f..f0a5382dc9 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -150,7 +150,9 @@ class PreferredPackages(object):
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is
            respecively less-than, equal-to, or greater-than version b of pkgname.
-           One version is less-than another if it is preferred over the other."""
+           Versions marked 'preferred=True' in package.py take precedence over any
+           versions not marked preferred.
+        """
         return self._spec_compare(pkgname, 'version', a, b, True, None)
 
 
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 4f55bc803e..6d9030805b 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -108,7 +108,7 @@ class Python(Package):
         run_env.set('PYTHONPATH', pythonpath)
 
 
-    def modify_module(self, module, spec, ext_spec):
+    def setup_dependent_package(self, module, ext_spec):
         """
         Called before python modules' install() methods.
 
@@ -118,17 +118,18 @@ class Python(Package):
         """
         # Python extension builds can have a global python executable function
         if self.version >= Version("3.0.0") and self.version < Version("4.0.0"):
-            module.python = Executable(join_path(spec.prefix.bin, 'python3'))
+            module.python = Executable(join_path(self.spec.prefix.bin, 'python3'))
         else:
-            module.python = Executable(join_path(spec.prefix.bin, 'python'))
+            module.python = Executable(join_path(self.spec.prefix.bin, 'python'))
 
         # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
         module.python_lib_dir     = os.path.join(ext_spec.prefix, self.python_lib_dir)
         module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)
         module.site_packages_dir  = os.path.join(ext_spec.prefix, self.site_packages_dir)
 
-        # Make the site packages directory if it does not exist already.
-        mkdirp(module.site_packages_dir)
+        # Make the site packages directory for extensions, if it does not exist already.
+        if ext_spec.package.is_extension:
+            mkdirp(module.site_packages_dir)
 
     # ========================================================================
     # Handle specifics of activating and deactivating python modules.
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 7ff1898ce9..e13677e4d2 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -30,7 +30,7 @@ class Ruby(Package):
         # The actual installation path for this gem
         spack_env.set('GEM_HOME', extension_spec.prefix)
 
-    def modify_module(self, module, spec, ext_spec):
+    def setup_dependent_package(self, module, ext_spec):
         """Called before ruby modules' install() methods.  Sets GEM_HOME
         and GEM_PATH to values appropriate for the package being built.
 
@@ -39,5 +39,5 @@ class Ruby(Package):
             gem('install', '<gem-name>.gem')
         """
         # Ruby extension builds have global ruby and gem functions
-        module.ruby = Executable(join_path(spec.prefix.bin, 'ruby'))
-        module.gem = Executable(join_path(spec.prefix.bin, 'gem'))
+        module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby'))
+        module.gem = Executable(join_path(self.spec.prefix.bin, 'gem'))
-- 
cgit v1.2.3-70-g09d2


From 38350ae33d29e108803cebdf13b90b6898947328 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 23 Mar 2016 01:32:54 -0700
Subject: resurrect preferred=True option for packages lost in merge of
 externals support.

- Pyton 2.7.11 is preferred again.
---
 lib/spack/spack/concretize.py         | 4 ++++
 lib/spack/spack/preferred_packages.py | 4 +---
 lib/spack/spack/test/concretize.py    | 9 +++++++++
 3 files changed, 14 insertions(+), 3 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index 2e576743ec..ed9bf79868 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -159,6 +159,10 @@ class DefaultConcretizer(object):
              if any(v.satisfies(sv) for sv in spec.versions)],
             cmp=cmp_versions)
 
+        def prefer_key(v):
+            return pkg.versions.get(Version(v)).get('preferred', False)
+        valid_versions.sort(key=prefer_key, reverse=True)
+
         if valid_versions:
             spec.versions = ver([valid_versions[0]])
         else:
diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index f0a5382dc9..4d8526c75f 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -150,9 +150,7 @@ class PreferredPackages(object):
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is
            respecively less-than, equal-to, or greater-than version b of pkgname.
-           Versions marked 'preferred=True' in package.py take precedence over any
-           versions not marked preferred.
-        """
+           One version is less-than another if it is preferred over the other."""
         return self._spec_compare(pkgname, 'version', a, b, True, None)
 
 
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index 08cce09674..9cd8c969ae 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -24,6 +24,7 @@
 ##############################################################################
 import spack
 from spack.spec import Spec, CompilerSpec
+from spack.version import ver
 from spack.concretize import find_spec
 from spack.test.mock_packages_test import *
 
@@ -77,6 +78,14 @@ class ConcretizeTest(MockPackagesTest):
         self.check_concretize('mpich')
 
 
+    def test_concretize_preferred_version(self):
+        spec = self.check_concretize('python')
+        self.assertEqual(spec.versions, ver('2.7.11'))
+
+        spec = self.check_concretize('python@3.5.1')
+        self.assertEqual(spec.versions, ver('3.5.1'))
+
+
     def test_concretize_with_virtual(self):
         self.check_concretize('mpileaks ^mpi')
         self.check_concretize('mpileaks ^mpi@:1.1')
-- 
cgit v1.2.3-70-g09d2


From 0fbdb3f65d234d6ed8f77d3732c134962ad47b35 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 15:43:16 +0100
Subject: modules : added configuration file with disable keyword

---
 lib/spack/spack/config.py  | 28 +++++++++++++++++++++++++---
 lib/spack/spack/modules.py | 12 ++++++++++--
 2 files changed, 35 insertions(+), 5 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 6afd69b3ac..6ef79c70b1 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -237,7 +237,29 @@ section_schemas = {
                                 'type' : 'object',
                                 'default' : {},
                             }
-                        },},},},},}
+                        },},},},},},
+    'modules': {
+        '$schema': 'http://json-schema.org/schema#',
+        'title': 'Spack module file configuration file schema',
+        'type': 'object',
+        'additionalProperties': False,
+        'patternProperties': {
+            r'modules:?': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'disable': {
+                        'type': 'array',
+                        'default': [],
+                        'items': {
+                            'type': 'string'
+                        }
+                    }
+                }
+            },
+        },
+    },
 }
 
 """OrderedDict of config scopes keyed by name.
@@ -405,11 +427,11 @@ def _read_config_file(filename, schema):
             validate_section(data, schema)
         return data
 
-    except MarkedYAMLError, e:
+    except MarkedYAMLError as e:
         raise ConfigFileError(
             "Error parsing yaml%s: %s" % (str(e.context_mark), e.problem))
 
-    except IOError, e:
+    except IOError as e:
         raise ConfigFileError(
             "Error reading configuration file %s: %s" % (filename, str(e)))
 
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 8ed98e5d38..639f1101b8 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -48,6 +48,7 @@ import textwrap
 
 import llnl.util.tty as tty
 import spack
+import spack.config
 from llnl.util.filesystem import join_path, mkdirp
 from spack.environment import *
 
@@ -57,6 +58,13 @@ __all__ = ['EnvModule', 'Dotkit', 'TclModule']
 module_types = {}
 
 
+def read_configuration_file():
+    f = spack.config.get_config('modules')
+    f.setdefault('disable', [])  # Default : disable nothing
+    return f
+
+CONFIGURATION = read_configuration_file()
+
 def print_help():
     """For use by commands to tell user how to activate shell support."""
 
@@ -115,8 +123,8 @@ class EnvModule(object):
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.name != 'env_module':
-                module_types[cls.name] = cls
+            if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
+                    module_types[cls.name] = cls
 
     def __init__(self, spec=None):
         self.spec = spec
-- 
cgit v1.2.3-70-g09d2


From d93f2b335d5a5198b943cc6293a1d24d614c979b Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 16:04:36 +0100
Subject: modules : fixed annoying indent

---
 lib/spack/spack/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 639f1101b8..d354c8bb71 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -124,7 +124,7 @@ class EnvModule(object):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
             if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
-                    module_types[cls.name] = cls
+                module_types[cls.name] = cls
 
     def __init__(self, spec=None):
         self.spec = spec
-- 
cgit v1.2.3-70-g09d2


From f095e619b985a9271ff96cd469086d4654edf489 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 24 Mar 2016 09:31:28 +0100
Subject: module files configuration : enable/disable logic is now positive

---
 lib/spack/spack/config.py  | 2 +-
 lib/spack/spack/modules.py | 9 ++-------
 2 files changed, 3 insertions(+), 8 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 6ef79c70b1..14e5aaf4fb 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -249,7 +249,7 @@ section_schemas = {
                 'default': {},
                 'additionalProperties': False,
                 'properties': {
-                    'disable': {
+                    'enable': {
                         'type': 'array',
                         'default': [],
                         'items': {
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index d354c8bb71..6c32937c3c 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -57,13 +57,8 @@ __all__ = ['EnvModule', 'Dotkit', 'TclModule']
 # Registry of all types of modules.  Entries created by EnvModule's metaclass
 module_types = {}
 
+CONFIGURATION = spack.config.get_config('modules')
 
-def read_configuration_file():
-    f = spack.config.get_config('modules')
-    f.setdefault('disable', [])  # Default : disable nothing
-    return f
-
-CONFIGURATION = read_configuration_file()
 
 def print_help():
     """For use by commands to tell user how to activate shell support."""
@@ -123,7 +118,7 @@ class EnvModule(object):
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
+            if cls.name != 'env_module' and cls.name in CONFIGURATION['enable']:
                 module_types[cls.name] = cls
 
     def __init__(self, spec=None):
-- 
cgit v1.2.3-70-g09d2


From 758a9c9096bd6c306f2dba0e40b46544dcec1992 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 11:18:11 +0100
Subject: python extensions : create PYTHONPATH in module files

---
 lib/spack/spack/modules.py                         | 10 +++++-----
 var/spack/repos/builtin/packages/python/package.py |  5 ++++-
 2 files changed, 9 insertions(+), 6 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 6c32937c3c..d45fdde703 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -161,13 +161,13 @@ class EnvModule(object):
 
         # Let the extendee modify their extensions before asking for
         # package-specific modifications
-        for extendee in self.pkg.extendees:
-            extendee_spec = self.spec[extendee]
-            extendee_spec.package.setup_dependent_package(
-                self.pkg.module, self.spec)
+        spack_env = EnvironmentModifications()
+        for item in self.pkg.extendees:
+            package = self.spec[item].package
+            package.setup_dependent_package(self.pkg.module, self.spec)
+            package.setup_dependent_environment(spack_env, env, self.spec)
 
         # Package-specific environment modifications
-        spack_env = EnvironmentModifications()
         self.spec.package.setup_environment(spack_env, env)
 
         # TODO : implement site-specific modifications and filters
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 6d9030805b..f5237c3b57 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -105,7 +105,10 @@ class Python(Package):
 
         pythonpath = ':'.join(python_paths)
         spack_env.set('PYTHONPATH', pythonpath)
-        run_env.set('PYTHONPATH', pythonpath)
+
+        # For run time environment set only the path for extension_spec and prepend it to PYTHONPATH
+        if extension_spec.package.extends(self.spec):
+            run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
 
 
     def setup_dependent_package(self, module, ext_spec):
-- 
cgit v1.2.3-70-g09d2


From 9985816642bad10008f45583a7d715761a6ae03d Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 24 Mar 2016 14:49:41 -0500
Subject: Fix spack info indentation

---
 lib/spack/spack/cmd/info.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py
index e7abe7f4a5..c93db55c63 100644
--- a/lib/spack/spack/cmd/info.py
+++ b/lib/spack/spack/cmd/info.py
@@ -52,7 +52,7 @@ def print_text_info(pkg):
     print "Safe versions:  "
 
     if not pkg.versions:
-        print("None")
+        print("    None")
     else:
         pad = padder(pkg.versions, 4)
         for v in reversed(sorted(pkg.versions)):
@@ -62,7 +62,7 @@ def print_text_info(pkg):
     print
     print "Variants:"
     if not pkg.variants:
-        print "None"
+        print "    None"
     else:
         pad = padder(pkg.variants, 4)
 
-- 
cgit v1.2.3-70-g09d2


From b0b882cbb3d903a85413acb0439a02d6ac9e26fc Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 26 Mar 2016 00:56:19 -0700
Subject: Speed up directives  by skipping debug info in stack traversal.

- `caller_locals()` doesn't need debug info, only frame locals.
- `get_calling_module()` doesn't either.

- Changed calls to `inspect.stack()` -> `inspect.stack(0)`
---
 lib/spack/llnl/util/lang.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py
index 13d301f84e..3b4e2c8352 100644
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -117,7 +117,8 @@ def caller_locals():
        scope.  Yes, this is some black magic, and yes it's useful
        for implementing things like depends_on and provides.
     """
-    stack = inspect.stack()
+    # Passing zero here skips line context for speed.
+    stack = inspect.stack(0)
     try:
         return stack[2][0].f_locals
     finally:
@@ -128,7 +129,8 @@ def get_calling_module_name():
     """Make sure that the caller is a class definition, and return the
        enclosing module's name.
     """
-    stack = inspect.stack()
+    # Passing zero here skips line context for speed.
+    stack = inspect.stack(0)
     try:
         # Make sure locals contain __module__
         caller_locals = stack[2][0].f_locals
-- 
cgit v1.2.3-70-g09d2


From 5695e4c03d6c98fc187ec405923cd1dcf2fbdff6 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sun, 27 Mar 2016 15:37:52 -0500
Subject: Wrap the long description of an environment module so it is more
 readable.

---
 lib/spack/spack/modules.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index d45fdde703..f6a11c92e3 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -278,6 +278,6 @@ class TclModule(EnvModule):
         # Long description
         if self.long_description:
             module_file.write('proc ModulesHelp { } {\n')
-            doc = re.sub(r'"', '\"', self.long_description)
-            module_file.write("puts stderr \"%s\"\n" % doc)
+            for line in textwrap.wrap(self.long_description, 72):
+                module_file.write("puts stderr \"%s\"\n" % line)
             module_file.write('}\n\n')
-- 
cgit v1.2.3-70-g09d2


From 7eca1284c81c3efc5a87b8a174a0974811656b3e Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 08:59:25 +0200
Subject: metis/parmetis/boost/oce/scalapack: correct install_name on Darwin
 via a global function.

---
 lib/spack/llnl/util/filesystem.py                  | 30 ++++++++++++-
 var/spack/repos/builtin/packages/boost/package.py  | 50 ++++++++++++----------
 var/spack/repos/builtin/packages/metis/package.py  |  6 ++-
 .../builtin/packages/netlib-scalapack/package.py   |  5 +++
 var/spack/repos/builtin/packages/oce/package.py    |  6 ++-
 .../repos/builtin/packages/parmetis/package.py     |  6 ++-
 6 files changed, 76 insertions(+), 27 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index c4665c284c..46ca03bec4 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -27,9 +27,10 @@ __all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree'
            'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
            'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
            'set_executable', 'copy_mode', 'unset_executable_mode',
-           'remove_dead_links', 'remove_linked_tree']
+           'remove_dead_links', 'remove_linked_tree', 'fix_darwin_install_name']
 
 import os
+import glob
 import sys
 import re
 import shutil
@@ -38,6 +39,7 @@ import errno
 import getpass
 from contextlib import contextmanager, closing
 from tempfile import NamedTemporaryFile
+import subprocess
 
 import llnl.util.tty as tty
 from spack.util.compression import ALLOWED_ARCHIVE_TYPES
@@ -392,3 +394,29 @@ def remove_linked_tree(path):
             os.unlink(path)
         else:
             shutil.rmtree(path, True)
+
+def fix_darwin_install_name(path):
+    """
+    Fix install name of dynamic libraries on Darwin to have full path.
+    There are two parts of this task:
+    (i) use install_name('-id',...) to change install name of a single lib;
+    (ii) use install_name('-change',...) to change the cross linking between libs.
+    The function assumes that all libraries are in one folder and currently won't
+    follow subfolders.
+
+    Args:
+        path: directory in which .dylib files are alocated
+
+    """
+    libs = glob.glob(join_path(path,"*.dylib"))
+    for lib in libs:
+        # fix install name first:
+        subprocess.Popen(["install_name_tool", "-id",lib,lib], stdout=subprocess.PIPE).communicate()[0]
+        long_deps = subprocess.Popen(["otool", "-L",lib], stdout=subprocess.PIPE).communicate()[0].split('\n')
+        deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]]
+        # fix all dependencies:
+        for dep in deps:
+            for loc in libs:
+                if dep == os.path.basename(loc):
+                    subprocess.Popen(["install_name_tool", "-change",dep,loc,lib], stdout=subprocess.PIPE).communicate()[0]
+                    break
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index fb1f5daee7..82ce6fbb74 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -1,5 +1,6 @@
 from spack import *
 import spack
+import sys
 
 class Boost(Package):
     """Boost provides free peer-reviewed portable C++ source
@@ -45,34 +46,34 @@ class Boost(Package):
     version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5')
     version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0')
 
-    default_install_libs = set(['atomic', 
-        'chrono', 
-        'date_time', 
-        'filesystem', 
+    default_install_libs = set(['atomic',
+        'chrono',
+        'date_time',
+        'filesystem',
         'graph',
         'iostreams',
         'locale',
         'log',
-        'math', 
+        'math',
         'program_options',
-        'random', 
-        'regex', 
-        'serialization', 
-        'signals', 
-        'system', 
-        'test', 
-        'thread', 
+        'random',
+        'regex',
+        'serialization',
+        'signals',
+        'system',
+        'test',
+        'thread',
         'wave'])
 
-    # mpi/python are not installed by default because they pull in many 
-    # dependencies and/or because there is a great deal of customization 
+    # mpi/python are not installed by default because they pull in many
+    # dependencies and/or because there is a great deal of customization
     # possible (and it would be difficult to choose sensible defaults)
     default_noinstall_libs = set(['mpi', 'python'])
 
     all_libs = default_install_libs | default_noinstall_libs
 
     for lib in all_libs:
-        variant(lib, default=(lib not in default_noinstall_libs), 
+        variant(lib, default=(lib not in default_noinstall_libs),
             description="Compile with {0} library".format(lib))
 
     variant('debug', default=False, description='Switch to the debug version of Boost')
@@ -124,9 +125,9 @@ class Boost(Package):
 
         with open('user-config.jam', 'w') as f:
             compiler_wrapper = join_path(spack.build_env_path, 'c++')
-            f.write("using {0} : : {1} ;\n".format(boostToolsetId, 
+            f.write("using {0} : : {1} ;\n".format(boostToolsetId,
                 compiler_wrapper))
-            
+
             if '+mpi' in spec:
                 f.write('using mpi : %s ;\n' %
                     join_path(spec['mpi'].prefix.bin, 'mpicxx'))
@@ -155,7 +156,7 @@ class Boost(Package):
         linkTypes = ['static']
         if '+shared' in spec:
             linkTypes.append('shared')
-        
+
         threadingOpts = []
         if '+multithreaded' in spec:
             threadingOpts.append('multi')
@@ -163,12 +164,12 @@ class Boost(Package):
             threadingOpts.append('single')
         if not threadingOpts:
             raise RuntimeError("At least one of {singlethreaded, multithreaded} must be enabled")
-        
+
         options.extend([
             'toolset=%s' % self.determine_toolset(spec),
             'link=%s' % ','.join(linkTypes),
             '--layout=tagged'])
-        
+
         return threadingOpts
 
     def install(self, spec, prefix):
@@ -177,14 +178,14 @@ class Boost(Package):
             if "+{0}".format(lib) in spec:
                 withLibs.append(lib)
         if not withLibs:
-            # if no libraries are specified for compilation, then you dont have 
+            # if no libraries are specified for compilation, then you dont have
             # to configure/build anything, just copy over to the prefix directory.
             src = join_path(self.stage.source_path, 'boost')
             mkdirp(join_path(prefix, 'include'))
             dst = join_path(prefix, 'include', 'boost')
             install_tree(src, dst)
             return
-    
+
         # to make Boost find the user-config.jam
         env['BOOST_BUILD_PATH'] = './'
 
@@ -207,4 +208,7 @@ class Boost(Package):
         # Boost.MPI if the threading options are not separated.
         for threadingOpt in threadingOpts:
             b2('install', 'threading=%s' % threadingOpt, *b2_options)
-        
+
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin') and ('+shared' in spec):
+            fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 68b9f6fd30..9301135f9f 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-import glob
+import glob,sys
 
 class Metis(Package):
     """
@@ -90,3 +90,7 @@ class Metis(Package):
             fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
             for f in fs:
                 install(f, GKlib_dist)
+
+            # The shared library is not installed correctly on Darwin; correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index c3e6822cdf..d59f8e41fe 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -41,6 +41,11 @@ class NetlibScalapack(Package):
             make()
             make("install")
 
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin') and ('+shared' in spec):
+            fix_darwin_install_name(prefix.lib)
+
+
     def setup_dependent_package(self, module, dependent_spec):
         spec = self.spec
         lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
index 06acb96736..4d5081ac9d 100644
--- a/var/spack/repos/builtin/packages/oce/package.py
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -1,5 +1,5 @@
 from spack import *
-import platform
+import platform, sys
 
 class Oce(Package):
     """
@@ -45,3 +45,7 @@ class Oce(Package):
         cmake('.', *options)
 
         make("install/strip")
+
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin'):
+            fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index f5b8b6de91..ff4370aa4b 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-
+import sys
 
 class Parmetis(Package):
     """
@@ -83,3 +83,7 @@ class Parmetis(Package):
             cmake(source_directory, *options)
             make()
             make("install")
+
+            # The shared library is not installed correctly on Darwin; correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fix_darwin_install_name(prefix.lib)
-- 
cgit v1.2.3-70-g09d2


From f3dd889d4462d14c9f0233540bccbf6a9720bcf0 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 03:51:05 -0700
Subject: Fix bug with lib64 RPATH setting in cc.

---
 lib/spack/env/cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index c6a09724e9..17740250d1 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -293,9 +293,9 @@ for dep in "${deps[@]}"; do
     if [[ -d $dep/lib64 ]]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+            args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+            args=("-L$dep/lib64" "-rpath" "$dep/lib64" "${args[@]}")
         fi
     fi
 done
-- 
cgit v1.2.3-70-g09d2


From d8579a5b80efd8b09e5332a922dee533f2a0a55e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 03:51:41 -0700
Subject: Simplify cc: Remove old logic and add better tests.

- removed a lot of old logic that was only still needed for tests.

- Added better unit tests for dependency RPATH, -L, and -I args

- tests now check whether the compiler omits -I args in link mode.
---
 lib/spack/env/cc           | 138 +++++----------------------------------------
 lib/spack/spack/test/cc.py | 127 +++++++++++++++++++++++++++++++++++------
 2 files changed, 123 insertions(+), 142 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 17740250d1..4217159a25 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -114,7 +114,9 @@ case "$command" in
         ;;
 esac
 
-# If any of the arguments below is present then the mode is vcheck. In vcheck mode nothing is added in terms of extra search paths or libraries
+# If any of the arguments below is present then the mode is vcheck. In
+# vcheck mode nothing is added in terms of extra search paths or
+# libraries
 if [ -z "$mode" ]; then
     for arg in "$@"; do
         if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
@@ -125,7 +127,6 @@ if [ -z "$mode" ]; then
 fi
 
 # Finish setting up the mode.
-
 if [ -z "$mode" ]; then
     mode=ccld
     for arg in "$@"; do
@@ -162,127 +163,18 @@ fi
 input_command="$@"
 args=("$@")
 
-# Dump parsed values for unit testing if asked for
-if [[ -n $SPACK_TEST_COMMAND ]]; then
-
-    #
-    # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command line
-    # arguments.  This is important for things like groups.
-    #
-    includes=()
-    libraries=()
-    libs=()
-    rpaths=()
-    other_args=()
-
-    while [ -n "$1" ]; do
-        case "$1" in
-            -I*)
-                arg="${1#-I}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                includes+=("$arg")
-                ;;
-            -L*)
-                arg="${1#-L}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                libraries+=("$arg")
-                ;;
-            -l*)
-                arg="${1#-l}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                libs+=("$arg")
-                ;;
-            -Wl,*)
-                arg="${1#-Wl,}"
-                # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
-                if [[ $arg == -rpath=* ]]; then
-                    arg="${arg#-rpath=}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                elif [[ $arg == -rpath,* ]]; then
-                    arg="${arg#-rpath,}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                elif [[ $arg == -rpath ]]; then
-                    shift; arg="$1"
-                    if [[ $arg != '-Wl,'* ]]; then
-                        die "-Wl,-rpath was not followed by -Wl,*"
-                    fi
-                    arg="${arg#-Wl,}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                else
-                    other_args+=("-Wl,$arg")
-                fi
-                ;;
-            -Xlinker)
-                shift; arg="$1";
-                if [[ $arg = -rpath=* ]]; then
-                    rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath ]]; then
-                    shift; arg="$1"
-                    if [[ $arg != -Xlinker ]]; then
-                        die "-Xlinker -rpath was not followed by -Xlinker <arg>"
-                    fi
-                    shift; arg="$1"
-                    rpaths+=("$arg")
-                else
-                    other_args+=("-Xlinker")
-                    other_args+=("$arg")
-                fi
-                ;;
-            *)
-                other_args+=("$1")
-                ;;
-        esac
-        shift
-    done
-
-    IFS=$'\n'
-    case "$SPACK_TEST_COMMAND" in
-        dump-includes)   echo "${includes[*]}";;
-        dump-libraries)  echo "${libraries[*]}";;
-        dump-libs)       echo "${libs[*]}";;
-        dump-rpaths)     echo "${rpaths[*]}";;
-        dump-other-args) echo "${other_args[*]}";;
-        dump-all)
-            echo "INCLUDES:"
-            echo "${includes[*]}"
-            echo
-            echo "LIBRARIES:"
-            echo "${libraries[*]}"
-            echo
-            echo "LIBS:"
-            echo "${libs[*]}"
-            echo
-            echo "RPATHS:"
-            echo "${rpaths[*]}"
-            echo
-            echo "ARGS:"
-            echo "${other_args[*]}"
-            ;;
-        *)
-            die "ERROR: Unknown test command"
-            ;;
-    esac
-    exit
-fi
-
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
+    # Prepend include directories
     if [[ -d $dep/include ]]; then
         if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then
             args=("-I$dep/include" "${args[@]}")
         fi
     fi
 
+    # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
-        # libraries+=("$dep/lib")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -290,8 +182,8 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
+    # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
-        # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -302,18 +194,8 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-Wl,-rpath,$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-rpath" "$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -345,6 +227,14 @@ export PATH
 
 full_command=("$command" "${args[@]}")
 
+# In test command mode, write out full command for Spack tests.
+if [[ $SPACK_TEST_COMMAND = dump-args ]]; then
+    echo "${full_command[@]}"
+    exit
+elif [[ -n $SPACK_TEST_COMMAND ]]; then
+    die "ERROR: Unknown test command"
+fi
+
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index f3f6d4a22e..0b1aeb2a8f 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -28,6 +28,8 @@ arguments correctly.
 """
 import os
 import unittest
+import tempfile
+import shutil
 
 from llnl.util.filesystem import *
 import spack
@@ -55,13 +57,40 @@ class CompilerTest(unittest.TestCase):
         self.ld = Executable(join_path(spack.build_env_path, "ld"))
         self.cpp = Executable(join_path(spack.build_env_path, "cpp"))
 
-        os.environ['SPACK_CC'] = "/bin/mycc"
-        os.environ['SPACK_PREFIX'] = "/usr"
+        self.realcc = "/bin/mycc"
+        self.prefix = "/spack-test-prefix"
+
+        os.environ['SPACK_CC'] = self.realcc
+        os.environ['SPACK_PREFIX'] = self.prefix
         os.environ['SPACK_ENV_PATH']="test"
         os.environ['SPACK_DEBUG_LOG_DIR'] = "."
         os.environ['SPACK_COMPILER_SPEC'] = "gcc@4.4.7"
         os.environ['SPACK_SHORT_SPEC'] = "foo@1.2"
 
+        # Make some fake dependencies
+        self.tmp_deps = tempfile.mkdtemp()
+        self.dep1 = join_path(self.tmp_deps, 'dep1')
+        self.dep2 = join_path(self.tmp_deps, 'dep2')
+        self.dep3 = join_path(self.tmp_deps, 'dep3')
+        self.dep4 = join_path(self.tmp_deps, 'dep4')
+
+        mkdirp(join_path(self.dep1, 'include'))
+        mkdirp(join_path(self.dep1, 'lib'))
+
+        mkdirp(join_path(self.dep2, 'lib64'))
+
+        mkdirp(join_path(self.dep3, 'include'))
+        mkdirp(join_path(self.dep3, 'lib64'))
+
+        mkdirp(join_path(self.dep4, 'include'))
+
+        if 'SPACK_DEPENDENCIES' in os.environ:
+            del os.environ['SPACK_DEPENDENCIES']
+
+
+    def tearDown(self):
+        shutil.rmtree(self.tmp_deps, True)
+
 
     def check_cc(self, command, args, expected):
         os.environ['SPACK_TEST_COMMAND'] = command
@@ -92,6 +121,10 @@ class CompilerTest(unittest.TestCase):
         self.check_cpp('dump-mode', [], "cpp")
 
 
+    def test_as_mode(self):
+        self.check_cc('dump-mode', ['-S'], "as")
+
+
     def test_ccld_mode(self):
         self.check_cc('dump-mode', [], "ccld")
         self.check_cc('dump-mode', ['foo.c', '-o', 'foo'], "ccld")
@@ -104,27 +137,85 @@ class CompilerTest(unittest.TestCase):
         self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ld")
 
 
-    def test_includes(self):
-        self.check_cc('dump-includes', test_command,
-                      "\n".join(["/test/include", "/other/include"]))
+    def test_dep_rpath(self):
+        """Ensure RPATHs for root package are added."""
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      ' '.join(test_command))
+
+
+    def test_dep_include(self):
+        """Ensure a single dependency include directory is added."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep4
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-I' + self.dep4 + '/include ' +
+                      ' '.join(test_command))
+
+
+    def test_dep_lib(self):
+        """Ensure a single dependency RPATH is added."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep2
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+                      ' '.join(test_command))
+
+
+    def test_all_deps(self):
+        """Ensure includes and RPATHs for all deps are added. """
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+
+        # This is probably more constrained than it needs to be; it
+        # checks order within prepended args and doesn't strictly have
+        # to.  We could loosen that if it becomes necessary
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+
+                      '-I' + self.dep4 + '/include ' +
+
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep3 + '/lib64 ' +
+                      '-I' + self.dep3 + '/include ' +
+
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+
+                      '-L' + self.dep1 + '/lib ' +
+                      '-Wl,-rpath,' + self.dep1 + '/lib ' +
+                      '-I' + self.dep1 + '/include ' +
+
+                      ' '.join(test_command))
 
 
-    def test_libraries(self):
-        self.check_cc('dump-libraries', test_command,
-                      "\n".join(["/test/lib", "/other/lib"]))
+    def test_ld_deps(self):
+        """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
 
+        self.check_ld('dump-args', test_command,
+                      'ld ' +
+                      '-rpath ' + self.prefix + '/lib ' +
+                      '-rpath ' + self.prefix + '/lib64 ' +
 
-    def test_libs(self):
-        self.check_cc('dump-libs', test_command,
-                      "\n".join(["lib1", "lib2", "lib3", "lib4"]))
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-rpath ' + self.dep3 + '/lib64 ' +
 
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-rpath ' + self.dep2 + '/lib64 ' +
 
-    def test_rpaths(self):
-        self.check_cc('dump-rpaths', test_command,
-                      "\n".join(["/first/rpath", "/second/rpath", "/third/rpath", "/fourth/rpath"]))
+                      '-L' + self.dep1 + '/lib ' +
+                      '-rpath ' + self.dep1 + '/lib ' +
 
+                      ' '.join(test_command))
 
-    def test_other_args(self):
-        self.check_cc('dump-other-args', test_command,
-                      "\n".join(["arg1", "-Wl,--start-group", "arg2", "arg3", "arg4",
-                                 "-Wl,--end-group", "arg5", "arg6"]))
-- 
cgit v1.2.3-70-g09d2


From a14527ec0619151d6defc909a46aefd2a9378cb7 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 15:34:25 -0700
Subject: Add command to compiler input log.

---
 lib/spack/env/cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 4217159a25..68cd8514f4 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -241,7 +241,7 @@ fi
 if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command" >> $input_log
+    echo "$command $input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 
-- 
cgit v1.2.3-70-g09d2


From f80e839ff48809a5ba8b7343d2378133a3fbce82 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 29 Mar 2016 02:58:05 -0700
Subject: Handle Darwin's ld -r option properly

- ld -r doesn't work with RPATH on OS X.

- for GNU ld, the -r option only means 'relocatable',
  and doesn't affect RPATH.

- This adds special handling to omit RPATHs for ld -r on OS X
---
 lib/spack/env/cc | 35 +++++++++++++++++++++++++++--------
 1 file changed, 27 insertions(+), 8 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 68cd8514f4..2eb6f46afe 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -85,6 +85,10 @@ done
 #    ccld    compile & link
 #    vcheck  version check
 #
+# Depending on the mode, we may or may not add extra rpaths.
+# This variable controls whether they are added.
+add_rpaths=true
+
 command=$(basename "$0")
 case "$command" in
     cc|c89|c99|gcc|clang|icc|pgcc|xlc)
@@ -108,6 +112,17 @@ case "$command" in
         ;;
     ld)
         mode=ld
+
+        # Darwin's linker has a -r argument that merges object files
+        # together. It doesn't work with -rpath.
+        if [[ $OSTYPE = darwin* ]]; then
+            for arg in "$@"; do
+                if [ "$arg" = -r ]; then
+                    add_rpaths=false
+                    break
+	            fi
+            done
+        fi
         ;;
     *)
         die "Unkown compiler: $command"
@@ -176,27 +191,31 @@ for dep in "${deps[@]}"; do
     # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+            $add_rpaths && args=("-Wl,-rpath,$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+            $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
         fi
     fi
 
     # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
+            $add_rpaths && args=("-Wl,-rpath,$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib64" "-rpath" "$dep/lib64" "${args[@]}")
+            $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
         fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
 #
@@ -241,8 +260,8 @@ fi
 if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$command $input_command" >> $input_log
-    echo "$mode       ${full_command[@]}" >> $output_log
+    echo "[$mode] $command $input_command" >> $input_log
+    echo "[$mode] ${full_command[@]}" >> $output_log
 fi
 
 exec "${full_command[@]}"
-- 
cgit v1.2.3-70-g09d2


From dfc5cf288c1017ef62390489cb534848aef5a9a6 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 29 Mar 2016 04:35:41 -0700
Subject: Fix bug in restage

- Restage previously only removed the source directory from the stage.
- Now removes any other directories in stage as well.
---
 lib/spack/spack/fetch_strategy.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 0d0a7db8a9..4ea87bea7e 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -289,8 +289,14 @@ class URLFetchStrategy(FetchStrategy):
         if not self.archive_file:
             raise NoArchiveFileError("Tried to reset URLFetchStrategy before fetching",
                                      "Failed on reset() for URL %s" % self.url)
-        if self.stage.source_path:
-            shutil.rmtree(self.stage.source_path, ignore_errors=True)
+
+        # Remove everythigng but the archive from the stage
+        for filename in os.listdir(self.stage.path):
+            abspath = os.path.join(self.stage.path, filename)
+            if abspath != self.archive_file:
+                shutil.rmtree(abspath, ignore_errors=True)
+
+        # Expand the archive again
         self.expand()
 
     def __repr__(self):
-- 
cgit v1.2.3-70-g09d2