Update App.json

Author: wmobley

app-s3.json

@@ -0,0 +1,106 @@
+{
+  "id": "ODM-CLI-S3",
+  "version": "0.1.1-s3",
+  "description": "Run an non-interactive script on TACC using docker.",
+  "owner": "${apiUserId}",
+  "enabled": true,
+  "runtime": "SINGULARITY",
+  "runtimeVersion": null,
+  "runtimeOptions": ["SINGULARITY_RUN"],
+  "containerImage": "docker://opendronemap/odm",
+  "jobType": "BATCH",
+  "maxJobs": -1,
+  "maxJobsPerUser": -1,
+  "strictFileInputs": true,
+  "jobAttributes": {
+    "description": null,
+    "dynamicExecSystem": false,
+    "execSystemConstraints": null,
+    "execSystemId": "stampede3",
+    "execSystemExecDir": "${JobWorkingDir}",
+    "execSystemInputDir": "${JobWorkingDir}",
+    "execSystemOutputDir": "${JobWorkingDir}/output",
+    "execSystemLogicalQueue": "skx-dev",
+    "archiveSystemId": "cloud.data",
+    "archiveSystemDir": "HOST_EVAL($HOME)/tapis-jobs-archive/${JobCreateDate}/${JobName}-${JobUUID}",
+    "archiveOnAppError": true,
+    "isMpi": false,
+    "mpiCmd": null,
+    "cmdPrefix": "mkdir $PWD/work $PWD/home $PWD/scratch;",
+    "parameterSet": {
+      "appArgs": [
+                {
+                    "name": "Rstudio apptainer runscript",
+                    "inputMode": "FIXED",
+                    "arg": "--orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm --smrf-threshold 0.4   --smrf-window 24 --dsm --pc-csv --pc-las  --rerun-all --orthophoto-kmz --force-gps  --ignore-gsd  --matcher-type flann --feature-quality ultra --max-concurrency 128  --cog --pc-classify --sky-removal  --pc-quality high --rerun-all  --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000   --project-path images_dir/",
+                    "notes": {
+                        "isHidden": true
+                    }
+                }
+            ],
+      "containerArgs": [
+        {
+          "name": "Jupyter Mounts",
+          "description": "Mount for TAP functions and user dirs",
+          "inputMode": "FIXED",
+          "arg": "--bind /share,$WORK:$PWD/work,$HOME:$PWD/home,$SCRATCH:$PWD/scratch",
+          "notes": {
+            "isHidden": true
+          }
+        }
+      ],
+      "schedulerOptions": [
+        {
+          "name": "TACC Scheduler Profile",
+          "description": "Scheduler profile for HPC clusters at TACC",
+          "inputMode": "FIXED",
+          "arg": "--tapis-profile tacc-apptainer",
+          "notes": {
+            "isHidden": true
+          }
+        },
+        {
+          "name": "TAP Session Substring",
+          "description": "TAP Functions require the substring 'tap_' and in the slurm job name in order to function.",
+          "inputMode": "FIXED",
+          "arg": "--job-name ${JobName}-tap_",
+          "notes": {
+            "isHidden": true
+          }
+        }
+      ],
+      "envVariables": [],
+      "archiveFilter": {
+        "includes": [],
+        "excludes": [],
+        "includeLaunchFiles": true
+      }
+    },
+    "fileInputs": [{
+        "name": "Image Directory",
+        "description": "Directory for the images",
+        "inputMode": "REQUIRED",
+        "autoMountLocal": true,
+        "sourceUrl": null,
+        "targetPath": "images_dir/"
+      }],
+    "fileInputArrays": [],
+    "nodeCount": 1,
+    "coresPerNode": 1,
+    "memoryMB": 1000,
+    "maxMinutes": 10,
+    "subscriptions": [],
+    "tags": []
+  },
+  "tags": ["portalName: ALL"],
+  "notes": {
+    "label": "Open Drone Map - Photogrammetry",
+    "helpUrl": "https://github.com/In-For-Disaster-Analytics/odm-cli",
+    "helpText": "This app for non-interactive run of ODM command line and will generate point clouds and orthophotos. ",
+    "hideNodeCountAndCoresPerNode": true,
+    "isInteractive": false,
+    "icon": "jupyter",
+    "category": "Data Processing",
+    "queueFilter": ["skx-dev"]
+  }
+}

app.json

@@ -1,19 +1,13 @@
 {
   "id": "ODM-CLI",
-  "version": "0.1.0:sha-45af82e",
+  "version": "0.1.4",
   "description": "Run an non-interactive script on TACC using docker.",
   "owner": "${apiUserId}",
-  "moduleLoads": [
-        {
-            "moduleLoadCommand": "module load",
-            "modulesToLoad": ["tacc-apptainer"]
-        }
-    ],
   "enabled": true,
   "runtime": "SINGULARITY",
   "runtimeVersion": null,
   "runtimeOptions": ["SINGULARITY_RUN"],
-  "containerImage": "docker://ghcr.io/in-for-disaster-analytics/odm-cli:sha-45af82e",
+  "containerImage": "docker://opendronemap/odm",
   "jobType": "BATCH",
   "maxJobs": -1,
   "maxJobsPerUser": -1,
@@ -25,7 +19,7 @@
     "execSystemId": "ls6",
     "execSystemExecDir": "${JobWorkingDir}",
     "execSystemInputDir": "${JobWorkingDir}",
-    "execSystemOutputDir": "${JobWorkingDir}/output",
+    "execSystemOutputDir": "${JobWorkingDir}/images_dir",
     "execSystemLogicalQueue": "development",
     "archiveSystemId": "cloud.data",
     "archiveSystemDir": "HOST_EVAL($HOME)/tapis-jobs-archive/${JobCreateDate}/${JobName}-${JobUUID}",
@@ -35,8 +29,15 @@
     "cmdPrefix": "mkdir $PWD/work $PWD/home $PWD/scratch;",
     "parameterSet": {
       "appArgs": [
-        
-      ],
+                {
+                    "name": "Rstudio apptainer runscript",
+                    "inputMode": "FIXED",
+                    "arg": "--mesh-octree-depth 12 --ignore-gsd --dtm --smrf-threshold 0.4 --orthophoto-resolution 1  --smrf-window 24 --dsm --pc-csv --pc-las  --rerun-all --orthophoto-kmz --force-gps  --ignore-gsd  --matcher-type flann --feature-quality ultra --max-concurrency 128  --cog --pc-classify   --pc-quality high --rerun-all  --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000   --project-path images_dir/",
+                    "notes": {
+                        "isHidden": true
+                    }
+                }
+            ],
       "containerArgs": [
         {
           "name": "Jupyter Mounts",