Merge pull request #252 from SouthernMethodistUniversity/remove_personal_work

don't use personal work in apptainer binds

Author: jrlagrone

containers/classes/stat3341/build.sh

@@ -110,7 +110,7 @@ family("R")
 always_load('apptainer')
 local sif_file = '${IMAGE_LOCATION}/${CONTAINER_NAME}'
 
-local work_dir = os.getenv("WORK")
+local work_dir = '/work'
 local scratch_dir = os.getenv("SCRATCH")
 local home = os.getenv("HOME")
 local user_libs = pathJoin(home, 'R/rocker/${COURSE_NUMBER}_${YEAR}_${TERM}_${VERSION}')

containers/code-server/build_container.sh

@@ -35,7 +35,7 @@ sed 's/^ \{2\}//' > "$MODULE_FILE" << EOL
   always_load('singularity')
   local sif_file = '/hpc/${CLUSTER}/containers/code-server/code-server_${TAG}.sif'
 
-  local work_dir = os.getenv("WORK")
+  local work_dir = '/work'
   local scratch_dir = os.getenv("SCRATCH")
 
   function build_command(app)

containers/r/build_container.sh

@@ -83,7 +83,7 @@ family("R")
 always_load('apptainer')
 local sif_file = '/hpc/${CLUSTER}/containers/rocker/${CONTAINER_NAME}'
 
-local work_dir = os.getenv("WORK")
+local work_dir = '/work'
 local scratch_dir = os.getenv("SCRATCH")
 local home = os.getenv("HOME")
 local user_libs = pathJoin(home, 'R/rocker/${TAG}')

docs/examples/conda/container/ds.lua

@@ -1,7 +1,7 @@
 load("apptainer")
 
 local img_name      = 'ds_latest_2023_02_10_16_07_16.sif'
-local work          = os.getenv("WORK")
+local work          = '/work'
 local img_directory = 'images'
 local img_path      = pathJoin(work, img_directory, img_name)
 

modules/m3/applications/R/4.2.3.lua

@@ -22,7 +22,7 @@ family("R")
 always_load('apptainer')
 local sif_file = '/hpc/m3/containers/rocker/rocker_geospatial_4.2.3.sif'
 
-local work_dir = os.getenv("WORK")
+local work_dir = '/work'
 local scratch_dir = os.getenv("SCRATCH")
 local home = os.getenv("HOME")
 local user_libs = pathJoin(home, 'R/rocker/4.2.3')

modules/m3/applications/R/4.3.0.lua

@@ -21,7 +21,7 @@ family("R")
 always_load('apptainer')
 local sif_file = '/hpc/m3/containers/rocker/rocker_geospatial_4.3.0.sif'
 
-local work_dir = os.getenv("WORK")
+local work_dir = '/work'
 local scratch_dir = os.getenv("SCRATCH")
 local home = os.getenv("HOME")
 local user_libs = pathJoin(home, 'R/rocker/4.3.0')

modules/m3/applications/R/4.3.2.lua

@@ -22,7 +22,7 @@ family("R")
 always_load('apptainer')
 local sif_file = '/hpc/m3/containers/rocker/rocker_geospatial_4.3.2.sif'
 
-local work_dir = os.getenv("WORK")
+local work_dir = '/work'
 local scratch_dir = os.getenv("SCRATCH")
 local home = os.getenv("HOME")
 local user_libs = pathJoin(home, 'R/rocker/4.3.2')

modules/m3/applications/R/4.4.0.lua

@@ -22,7 +22,7 @@ family("R")
 always_load('apptainer')
 local sif_file = '/hpc/m3/containers/rocker/rocker_geospatial_4.4.0.sif'
 
-local work_dir = os.getenv("WORK")
+local work_dir = '/work'
 local scratch_dir = os.getenv("SCRATCH")
 local home = os.getenv("HOME")
 local user_libs = pathJoin(home, 'R/rocker/4.4.0')

modules/m3/applications/R/4.4.1.lua

@@ -22,7 +22,7 @@ family("R")
 always_load('apptainer')
 local sif_file = '/hpc/m3/containers/rocker/rocker_ml-verse_4.4.1.sif'
 
-local work_dir = os.getenv("WORK")
+local work_dir = '/work'
 local scratch_dir = os.getenv("SCRATCH")
 local home = os.getenv("HOME")
 local user_libs = pathJoin(home, 'R/rocker/4.4.1')