Merge pull request apptainer#1238 from vsoch/scif-revision

SCIF revision
ahkumar · Jan 20, 2018 · f4210ff · f4210ff
2 parents 8be8cb2 + e9b1ad3
commit f4210ff
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,6 +22,7 @@ and changes prior to that are (unfortunately) done retrospectively. Critical ite
  - [nvliblist.conf](https://github.com/singularityware/singularity/blob/master/etc/nvliblist.conf) now has a section for binaries
  - --nv can be made default with all action commands in singularity.conf
  - --nv can be controlled by env vars `$SINGULARITY_NV` and `$SINGULARITY_NV_OFF`
+ - Adjustments to SCIF (Scientific Filesystem) integration for broader use
 
 ### Security related fixes
  - Add capability support and secure build #934
@@ -31,6 +32,7 @@ and changes prior to that are (unfortunately) done retrospectively. Critical ite
 
 ### Bug Fixes
  - Put /usr/local/{bin,sbin} in front of the default PATH
+ - Fixed bug that did not export environment variables for apps with "-" in name
 
 ## [v2.4.2](https://github.com/singularityware/singularity/tree/release-2.4)
 

diff --git a/examples/apps/README.md b/examples/apps/README.md
@@ -1,15 +1,21 @@
 # Singularity SCI-F Apps
 
+The Scientific Filesystem is well suited for Singularity containers to allow you
+to build a container that has multiple entrypoints, along with modular environments,
+libraries, and executables. Here we will review the basic building and using of a
+Singularity container that implements SCIF. For more quick start tutorials, see
+the [official documentation for SCIF](https://vsoch.github.io/scif/).
+
 Build your image
 
 ```
-sudo singularity build cowsay.img Singularity.cowsay 
+sudo singularity build cowsay.simg Singularity.cowsay 
 ```
 
 What apps are installed?
 
 ```
-singularity apps cowsay.img
+singularity apps cowsay.simg
 cowsay
 fortune
 lolcat
@@ -18,23 +24,25 @@ lolcat
 Ask for help for a specific app!
 
 ```
-singularity help --app fortune cowsay.img
+singularity help --app fortune cowsay.simg
 fortune is the best app
 ```
 
 Run a particular app
 
 ```
-singularity run --app fortune cowsay.img
+singularity run --app fortune cowsay.simg
+When I reflect upon the number of disagreeable people who I know who have gone
+to a better world, I am moved to lead a different life.
+		-- Mark Twain, "Pudd'nhead Wilson's Calendar"
 ```
 
 Inspect an app
 
 ```
  singularity inspect --app fortune cowsay.img 
 {
-    "SINGULARITY_APP_NAME": "fortune",
-    "SINGULARITY_APP_SIZE": "1MB"
+    "SCIF_APPNAME": "fortune",
+    "SCIF_APPSIZE": "1MB"
 }
 ```
-
diff --git a/libexec/bootstrap-scripts/deffile-sections.sh b/libexec/bootstrap-scripts/deffile-sections.sh
@@ -302,8 +302,8 @@ if [ -z "${SINGULARITY_BUILDSECTION:-}" -o "${SINGULARITY_BUILDSECTION:-}" == "a
             # Make sure we have metadata
             APPBASE="$SINGULARITY_ROOTFS/scif/apps/${APPNAME}"
             APPFOLDER_SIZE=$(singularity_calculate_size "${APPBASE}")
-            $ADD_LABEL --key "SINGULARITY_APP_SIZE" --value "${APPFOLDER_SIZE}MB" --file "$APPBASE/scif/labels.json"
-            $ADD_LABEL --key "SINGULARITY_APP_NAME" --value "${APPNAME}" --file "${APPBASE}/scif/labels.json"
+            $ADD_LABEL --key "SCIF_APPSIZE" --value "${APPFOLDER_SIZE}MB" --file "$APPBASE/scif/labels.json"
+            $ADD_LABEL --key "SCIF_APPNAME" --value "${APPNAME}" --file "${APPBASE}/scif/labels.json"
 
         done
     fi
@@ -325,7 +325,7 @@ fi
 
 
 ### APPLABELS
-if [ -z "${SINGULARITY_BUILDSECTION:-}" -o "${SINGULARITY_BUILDSECTION:-}" == "appfiles" ]; then
+if [ -z "${SINGULARITY_BUILDSECTION:-}" -o "${SINGULARITY_BUILDSECTION:-}" == "applabels" ]; then
     if singularity_section_exists "applabels" "$SINGULARITY_BUILDDEF"; then
         APPNAMES=(`singularity_section_args "applabels" "$SINGULARITY_BUILDDEF"`)
 
@@ -349,15 +349,15 @@ if [ -z "${SINGULARITY_BUILDSECTION:-}" -o "${SINGULARITY_BUILDSECTION:-}" == "a
         for APPNAME in "${APPNAMES[@]}"; do
             message 1 "Installing ${APPNAME}\n"
             APPBASE="$SINGULARITY_ROOTFS/scif/apps/${APPNAME}"
-            SINGULARITY_APPROOT="/scif/apps/${APPNAME}"
-            export SINGULARITY_APPROOT
+            SCIF_APPROOT="/scif/apps/${APPNAME}"
+            export SCIF_APPROOT
             singularity_app_init "${APPNAME}" "${SINGULARITY_ROOTFS}"
             singularity_app_save "${APPNAME}" "$SINGULARITY_BUILDDEF" "${APPBASE}/scif/Singularity"
             singularity_app_install_get "${APPNAME}" "$SINGULARITY_BUILDDEF" | chroot "$SINGULARITY_ROOTFS" /bin/sh -xe || ABORT 255
 
             APPFOLDER_SIZE=$(singularity_calculate_size "${APPBASE}")
-            $ADD_LABEL --key "SINGULARITY_APP_SIZE" --value "${APPFOLDER_SIZE}MB" --file "$APPBASE/scif/labels.json" --quiet -f
-            $ADD_LABEL --key "SINGULARITY_APP_NAME" --value "${APPNAME}" --file "${APPBASE}/scif/labels.json" --quiet -f
+            $ADD_LABEL --key "SCIF_APPSIZE" --value "${APPFOLDER_SIZE}MB" --file "$APPBASE/scif/labels.json" --quiet -f
+            $ADD_LABEL --key "SCIF_APPNAME" --value "${APPNAME}" --file "${APPBASE}/scif/labels.json" --quiet -f
 
         done
     fi
@@ -373,34 +373,34 @@ for app in ${SINGULARITY_ROOTFS}/scif/apps/*; do
     if [ -d "$app" ]; then
 
         app="${app##*/}"
-        app=(`echo $app | sed -e "s/-/_/g"`)
+        appvar=(`echo $app | sed -e "s/-/_/g"`)
         appbase="${SINGULARITY_ROOTFS}/scif/apps/$app"
         appmeta="${appbase}/scif"
 
         # Export data, root, metadata, labels, environment
-        echo "APPDATA_$app=/scif/data/$app" >> "${APPGLOBAL}"
-        echo "APPMETA_$app=/scif/apps/$app/scif" >> "${APPGLOBAL}"
-        echo "APPROOT_$app=/scif/apps/$app" >> "${APPGLOBAL}"
-        echo "APPBIN_$app=/scif/apps/$app/bin" >> "${APPGLOBAL}"
-        echo "APPLIB_$app=/scif/apps/$app/lib" >> "${APPGLOBAL}"
-        echo "export APPDATA_$app APPROOT_$app APPMETA_$app APPBIN_$app APPLIB_$app"  >> "${APPGLOBAL}"
+        echo "SCIF_APPDATA_$appvar=/scif/data/$app" >> "${APPGLOBAL}"
+        echo "SCIF_APPMETA_$appvar=/scif/apps/$app/scif" >> "${APPGLOBAL}"
+        echo "SCIF_APPROOT_$appvar=/scif/apps/$app" >> "${APPGLOBAL}"
+        echo "SCIF_APPBIN_$appvar=/scif/apps/$app/bin" >> "${APPGLOBAL}"
+        echo "SCIF_APPLIB_$appvar=/scif/apps/$app/lib" >> "${APPGLOBAL}"
+        echo "export SCIF_APPDATA_$appvar SCIF_APPROOT_$appvar SCIF_APPMETA_$appvar SCIF_APPBIN_$appvar SCIF_APPLIB_$appvar"  >> "${APPGLOBAL}"
 
         # Environment
         if [ -e "${appmeta}/env/90-environment.sh" ]; then
-            echo  "APPENV_${app}=/scif/apps/$app/scif/env/90-environment.sh" >> "${APPGLOBAL}"
-            echo  "export APPENV_${app}" >> "${APPGLOBAL}"
+            echo  "SCIF_APPENV_${appvar}=/scif/apps/$app/scif/env/90-environment.sh" >> "${APPGLOBAL}"
+            echo  "export SCIF_APPENV_${appvar}" >> "${APPGLOBAL}"
         fi
 
         # Labels
         if [ -e "${appmeta}/labels.json" ]; then
-            echo  "APPLABELS_${app}=/scif/apps/$app/scif/labels.json" >> "${APPGLOBAL}"
-            echo  "export APPLABELS_${app}" >> "${APPGLOBAL}"
+            echo  "SCIF_APPLABELS_${appvar}=/scif/apps/$app/scif/labels.json" >> "${APPGLOBAL}"
+            echo  "export SCIF_APPLABELS_${appvar}" >> "${APPGLOBAL}"
         fi
 
         # Runscript
         if [ -e "${appmeta}/runscript" ]; then
-            echo  "APPRUN_${app}=/scif/apps/$app/scif/runscript" >> "${APPGLOBAL}"
-            echo  "export APPRUN_${app}" >> "${APPGLOBAL}"
+            echo  "SCIF_APPRUN_${appvar}=/scif/apps/$app/scif/runscript" >> "${APPGLOBAL}"
+            echo  "export SCIF_APPRUN_${appvar}" >> "${APPGLOBAL}"
         fi
     fi
 done

diff --git a/libexec/bootstrap-scripts/environment/95-apps.sh b/libexec/bootstrap-scripts/environment/95-apps.sh
@@ -18,9 +18,9 @@ if test -n "${SINGULARITY_APPNAME:-}"; then
     export SINGULARITY_APPNAME
 
     if test -d "/scif/apps/${SINGULARITY_APPNAME:-}/"; then
-        SINGULARITY_APPS="/scif/apps"
-        SINGULARITY_APPROOT="/scif/apps/${SINGULARITY_APPNAME:-}"
-        export SINGULARITY_APPROOT SINGULARITY_APPS
+        SCIF_APPS="/scif/apps"
+        SCIF_APPROOT="/scif/apps/${SINGULARITY_APPNAME:-}"
+        export SCIF_APPROOT SCIF_APPS
         PATH="/scif/apps/${SINGULARITY_APPNAME:-}:$PATH"
 
         # Automatically add application bin to path

diff --git a/libexec/bootstrap-scripts/functions b/libexec/bootstrap-scripts/functions
@@ -198,14 +198,14 @@ singularity_app_init() {
 
     # App specific variables should be exposed at run, shell, exec
     echo "
-    SINGULARITY_APPNAME=$APPNAME
-    SINGULARITY_APPROOT=\"/scif/apps/${APPNAME}\"
-    SINGULARITY_APPMETA=\"/scif/apps/${APPNAME}/scif\"
-    SINGULARITY_DATA=\"/scif/data\"
-    SINGULARITY_APPDATA=\"/scif/data/${APPNAME}\"
-    SINGULARITY_APPINPUT=\"/scif/data/${APPNAME}/input\"
-    SINGULARITY_APPOUTPUT=\"/scif/data/${APPNAME}/output\"
-    export SINGULARITY_APPDATA SINGULARITY_APPNAME SINGULARITY_APPROOT SINGULARITY_APPMETA SINGULARITY_APPINPUT SINGULARITY_APPOUTPUT SINGULARITY_DATA
+    SCIF_APPNAME=$APPNAME
+    SCIF_APPROOT=\"/scif/apps/${APPNAME}\"
+    SCIF_APPMETA=\"/scif/apps/${APPNAME}/scif\"
+    SCIF_DATA=\"/scif/data\"
+    SCIF_APPDATA=\"/scif/data/${APPNAME}\"
+    SCIF_APPINPUT=\"/scif/data/${APPNAME}/input\"
+    SCIF_APPOUTPUT=\"/scif/data/${APPNAME}/output\"
+    export SCIF_APPDATA SCIF_APPNAME SCIF_APPROOT SCIF_APPMETA SCIF_APPINPUT SCIF_APPOUTPUT SCIF_DATA
     " > "${APPMETA}/env/01-base.sh"
 
 }
diff --git a/libexec/cli/apps.info b/libexec/cli/apps.info
@@ -24,20 +24,20 @@ for all apps regardless of the active:
 
 ACTIVE APP ENVIRONMENT:
 
-    SINGULARITY_APPNAME     the name of the application
-    SINGULARITY_APPROOT     the application base (/scif/apps/<app>)
-    SINGULARITY_APPMETA     the application metadata folder
-    SINGULARITY_APPDATA     the data base folder for active app
-        SINGULARITY_APPINPUT    expected input folder within data base folder
-        SINGULARITY_APPOUTPUT   the output data folder within data base folder
+    SCIF_APPNAME     the name of the application
+    SCIF_APPROOT     the application base (/scif/apps/<app>)
+    SCIF_APPMETA     the application metadata folder
+    SCIF_APPDATA     the data base folder for active app
+        SCIF_APPINPUT    expected input folder within data base folder
+        SCIF_APPOUTPUT   the output data folder within data base folder
 
 
 GLOBAL APP ENVIRONMENT:
 
-    SINGULARITY_DATA        scif defined data base for all apps (/scif/data)
-    SINGULARITY_APPS        scif defined install bases for all apps (/scif/apps)
-    APPROOT_<app>           root for application <app>
-    APPDATA_<app>           data root for application <app>
+    SCIF_DATA        scif defined data base for all apps (/scif/data)
+    SCIF_APPS        scif defined install bases for all apps (/scif/apps)
+    SCIF_APPROOT_<app>    root for application <app>
+    SCIF_APPDATA_<app>    data root for application <app>
 
 
 For additional help, please visit our public documentation pages which are