From 20593006d22000c05e309baa54fe73cf2fbecb6f Mon Sep 17 00:00:00 2001
From: Garrett Edmonds <edmondsgarrett@gmail.com>
Date: Fri, 30 Aug 2024 16:32:59 -0500
Subject: [PATCH 1/4] SimCenter DesignSafe VM v0.0.1

---
 .../simcenter-designsafe-vm/Dockerfile        |  33 ++++++
 applications/simcenter-designsafe-vm/app.json | 100 ++++++++++++++++++
 .../get_folder_mount_path.py                  |  44 ++++++++
 .../simcenter-designsafe-vm/tapisjob_app.sh   |  67 ++++++++++++
 4 files changed, 244 insertions(+)
 create mode 100644 applications/simcenter-designsafe-vm/Dockerfile
 create mode 100644 applications/simcenter-designsafe-vm/app.json
 create mode 100644 applications/simcenter-designsafe-vm/get_folder_mount_path.py
 create mode 100644 applications/simcenter-designsafe-vm/tapisjob_app.sh

diff --git a/applications/simcenter-designsafe-vm/Dockerfile b/applications/simcenter-designsafe-vm/Dockerfile
new file mode 100644
index 0000000..6500525
--- /dev/null
+++ b/applications/simcenter-designsafe-vm/Dockerfile
@@ -0,0 +1,33 @@
+## taccaci/designsafe-simcenter-vm:0.0.1 ##
+
+FROM ubuntu:20.04
+
+LABEL maintainer="TACC-ACI-WMA <wma_prtl@tacc.utexas.edu>"
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ENV TZ=Etc/UTC
+
+RUN apt-get update && apt-get install -y \
+    python3-pip 
+
+RUN pip install --upgrade \
+    pip \
+    setuptools \
+    wheel
+
+RUN pip install \
+    h5py \
+    numpy \
+    pandas \
+    xarray \
+    tables \
+    netcdf4 \
+    h5netcdf \
+    scipy
+
+RUN useradd --create-home ubuntu
+
+USER ubuntu
+
+SHELL ["/bin/bash", "-c"]
\ No newline at end of file
diff --git a/applications/simcenter-designsafe-vm/app.json b/applications/simcenter-designsafe-vm/app.json
new file mode 100644
index 0000000..9613950
--- /dev/null
+++ b/applications/simcenter-designsafe-vm/app.json
@@ -0,0 +1,100 @@
+{
+    "id": "SimCenter-DesignSafeVM",
+    "version": "0.0.1",
+    "description": "An app for extracting the physics-based motion from OpenSees results.",
+    "owner": "${apiUserId}",
+    "enabled": true,
+    "runtime": "ZIP",
+    "runtimeVersion": null,
+    "runtimeOptions": null,
+    "containerImage": "tapis://cloud.data/corral/tacc/aci/CEP/applications/v3/simcenter-designsafe-vm/simcenter-designsafe-vm.zip",
+    "jobType": "FORK",
+    "maxJobs": -1,
+    "maxJobsPerUser": -1,
+    "strictFileInputs": true,
+    "jobAttributes": {
+        "description": "Extract the physics-based motion of your OpenSees results on a virtual machine.",
+        "dynamicExecSystem": false,
+        "execSystemConstraints": null,
+        "execSystemId": "wma-exec-01",
+        "execSystemExecDir": "${JobWorkingDir}",
+        "execSystemInputDir": "${JobWorkingDir}",
+        "execSystemOutputDir": "${JobWorkingDir}",
+        "execSystemLogicalQueue": "development",
+        "archiveSystemId": "cloud.data",
+        "archiveSystemDir": "HOST_EVAL($HOME)/tapis-jobs-archive/${JobCreateDate}/${JobName}-${JobUUID}",
+        "archiveOnAppError": true,
+        "isMpi": false,
+        "mpiCmd": null,
+        "cmdPrefix": null,
+        "parameterSet": {
+            "appArgs": [],
+            "schedulerOptions": [],
+            "envVariables": [
+                {
+                    "key": "inputScript",
+                    "value": "",
+                    "description": "The filename of the main OpenSees input script.",
+                    "inputMode": "REQUIRED",
+                    "notes": {
+                        "label": "Main Script"
+                    }
+                },
+                {
+                    "key": "dataDirectory",
+                    "value": "",
+                    "description": "The path directory containing your data to be processed. Defaults to My Projects if not provided.",
+                    "inputMode": "INCLUDE_ON_DEMAND",
+                    "notes": {
+                        "label": "Data Directory",
+                        "selectionMode": "directory"
+                    }
+                },
+                {
+                    "key": "_UserProjects",
+                    "value": "",
+                    "description": "User Project UUIDs and Project IDs",
+                    "inputMode": "INCLUDE_ON_DEMAND",
+                    "notes": {
+                        "isHidden": true
+                    }
+                }
+            ],
+            "archiveFilter": {
+                "includes": [],
+                "excludes": [],
+                "includeLaunchFiles": true
+            }
+        },
+        "fileInputs": [
+            {
+                "name": "Input Directory",
+                "description": "The directory containing your main OpenSees script and all necessary files. Defaults to My Data if not provided.",
+                "inputMode": "OPTIONAL",
+                "autoMountLocal": true,
+                "sourceUrl": null,
+                "targetPath": "*",
+                "envKey": "inputDirectory"
+            }
+          ],
+        "fileInputArrays": [],
+        "nodeCount": 1,
+        "coresPerNode": 1,
+        "memoryMB": 256000,
+        "maxMinutes": 1440,
+        "subscriptions": [],
+        "tags": []
+    },
+    "tags": [
+        "portalName: CEP",
+        "portalName: DesignSafe"
+    ],
+    "notes": {
+        "label": "SimCenter DesignSafe (VM)",
+        "helpUrl": "https://www.designsafe-ci.org/user-guide/tools/simulation/opensees/opensees/",
+        "hideNodeCountAndCoresPerNode": true,
+        "icon": null,
+        "category": "Analysis",
+        "isInteractive": false
+    }
+}
diff --git a/applications/simcenter-designsafe-vm/get_folder_mount_path.py b/applications/simcenter-designsafe-vm/get_folder_mount_path.py
new file mode 100644
index 0000000..d7cc0bf
--- /dev/null
+++ b/applications/simcenter-designsafe-vm/get_folder_mount_path.py
@@ -0,0 +1,44 @@
+import sys
+
+
+def set_mount_path(inputFolder, corralPrefix, tapisPrefix):
+    inputDir = inputFolder.replace(tapisPrefix,'')
+    mountPath = corralPrefix + inputDir             # /corral/projects/NHERI/shared/gedmonds/LAS/LAS_converted/"
+    return mountPath
+
+
+def main():
+    folderToMount = sys.argv[1]
+
+    prefixArr = [
+        [
+            "/corral/main/projects/NHERI/shared/", # "SHARED_PREFIX"
+            "tapis://designsafe.storage.default/" #"SHARED_TAPISPREFIX"
+        ],
+        [
+            "/corral/main/projects/NHERI/projects/", # "PROJECT_PREFIX"
+            "tapis://project-" # "PROJECT_TAPISPREFIX"
+        ],
+        [
+            "/corral/main/projects/NHERI/published/", # "PUBLISHED_PREFIX"
+            "tapis://designsafe.storage.published" # "PUBLISHED_TAPISPREFIX" 
+        ],
+        [
+            "/corral/main/projects/NHERI/community/", # "COMMUNITY_PREFIX"
+            "tapis://designsafe.storage.community" # "COMMUNITY_TAPISPREFIX": 
+        ]
+    ]
+
+    mountPath = None
+
+    for prefixGroup in prefixArr:
+        corralPrefix = prefixGroup[0]
+        tapisPrefix = prefixGroup[1]
+        if tapisPrefix in folderToMount:
+                mountPath = set_mount_path(folderToMount, corralPrefix, tapisPrefix)
+                break
+
+    print(mountPath)
+
+if __name__ == "__main__":
+    main()
diff --git a/applications/simcenter-designsafe-vm/tapisjob_app.sh b/applications/simcenter-designsafe-vm/tapisjob_app.sh
new file mode 100644
index 0000000..1097957
--- /dev/null
+++ b/applications/simcenter-designsafe-vm/tapisjob_app.sh
@@ -0,0 +1,67 @@
+#!/bin/bash
+
+handle_error() {
+  local EXITCODE=$1
+  echo "Phyiscs-based extractor job exited with an error status. $EXITCODE" >&2
+  echo "$EXITCODE" > "${_tapisExecSystemOutputDir}/tapisjob.exitcode"
+  exit $EXITCODE
+}
+
+set -x
+
+PBESCRIPT="${inputScript##*/}"
+echo "PBESCRIPT is $PBESCRIPT"
+
+inputPath="`pwd`/${inputDirectory}"
+INPUTDIR=${inputPath}
+if [ -z ${inputDirectory} ]; then
+    INPUTDIR="/corral/projects/NHERI/shared/${_tapisJobOwner}"
+fi
+
+#dataPath="`pwd`/${dataDirectory}"
+DATADIR_NAME="${dataDirectory##*/}"
+DATADIR=`python3 get_folder_mount_path.py $dataDirectory`
+
+DATADIR_MOUNT="--bind ${DATADIR}:/home/jovyan/work/projects/$DATADIR_NAME"
+if [ -z ${dataDirectory} ]; then
+    projects_dir="$HOME/MyProjects"
+
+    mkdir -p "$projects_dir"
+    IFS=' ' read -r -a projects <<< "${_UserProjects}"
+    for project in "${projects[@]}"; do
+        IFS=',' read -r uuid projectId <<< "$project"
+        target_path="/corral/main/projects/NHERI/projects/$uuid"
+        symlink_path="$projects_dir/$projectId"
+
+        if [ -e "$target_path" ]; then
+            if [ ! -e "$symlink_path" ]; then
+                ln -s "$target_path" "$symlink_path"
+                echo "TACC: Project Links: Created symlink: $symlink_path -> $target_path"
+            else
+                echo "TACC: Project Links: Symlink already exists: $symlink_path"
+            fi
+        else
+            echo "TACC: Project Links: Target path does not exist: $target_path"
+        fi
+    done
+    DATADIR_MOUNT="--bind ${projects_dir}:/home/jovyan/work/projects"
+fi
+
+echo "Running $PBESCRIPT"
+
+apptainer run \
+    --writable-tmpfs \
+    --memory 10G \
+    --bind $INPUTDIR:"/data/" \
+    --bind "/corral/main/projects/NHERI/shared/${_tapisJobOwner}":"/home/jovyan/work/MyData" \
+    --bind /corral/main/projects/NHERI/public/projects:/home/jovyan/work/NEES:ro \
+    --bind /corral/main/projects/NHERI/community:/home/jovyan/work/CommunityData:ro \
+    --bind /corral/main/projects/NHERI/published:/home/jovyan/work/NHERI-Published:ro \
+    --bind /corral/main/projects/NHERI/projects \
+    $DATADIR_MOUNT \
+    docker://taccaci/designsafe-simcenter-vm:0.0.1 /bin/sh -c "cd /data; python3 /data/$PBESCRIPT"
+
+if [ ! $? ]; then
+    handle_error 1
+    exit
+fi

From 03159b3a8bc25f1db3867ee48449655c86557d5c Mon Sep 17 00:00:00 2001
From: Garrett Edmonds <edmondsgarrett@gmail.com>
Date: Thu, 5 Sep 2024 10:45:31 -0500
Subject: [PATCH 2/4] Change container mount paths to remove  user

---
 applications/simcenter-designsafe-vm/tapisjob_app.sh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/applications/simcenter-designsafe-vm/tapisjob_app.sh b/applications/simcenter-designsafe-vm/tapisjob_app.sh
index 1097957..ea92402 100644
--- a/applications/simcenter-designsafe-vm/tapisjob_app.sh
+++ b/applications/simcenter-designsafe-vm/tapisjob_app.sh
@@ -22,7 +22,7 @@ fi
 DATADIR_NAME="${dataDirectory##*/}"
 DATADIR=`python3 get_folder_mount_path.py $dataDirectory`
 
-DATADIR_MOUNT="--bind ${DATADIR}:/home/jovyan/work/projects/$DATADIR_NAME"
+DATADIR_MOUNT="--bind ${DATADIR}:/home/${_tapisJobOwner}/work/projects/$DATADIR_NAME"
 if [ -z ${dataDirectory} ]; then
     projects_dir="$HOME/MyProjects"
 
@@ -44,7 +44,7 @@ if [ -z ${dataDirectory} ]; then
             echo "TACC: Project Links: Target path does not exist: $target_path"
         fi
     done
-    DATADIR_MOUNT="--bind ${projects_dir}:/home/jovyan/work/projects"
+    DATADIR_MOUNT="--bind ${projects_dir}:/home/${_tapisJobOwner}/work/projects"
 fi
 
 echo "Running $PBESCRIPT"
@@ -53,10 +53,10 @@ apptainer run \
     --writable-tmpfs \
     --memory 10G \
     --bind $INPUTDIR:"/data/" \
-    --bind "/corral/main/projects/NHERI/shared/${_tapisJobOwner}":"/home/jovyan/work/MyData" \
-    --bind /corral/main/projects/NHERI/public/projects:/home/jovyan/work/NEES:ro \
-    --bind /corral/main/projects/NHERI/community:/home/jovyan/work/CommunityData:ro \
-    --bind /corral/main/projects/NHERI/published:/home/jovyan/work/NHERI-Published:ro \
+    --bind "/corral/main/projects/NHERI/shared/${_tapisJobOwner}":"/home/${_tapisJobOwner}/work/MyData" \
+    --bind /corral/main/projects/NHERI/public/projects:/home/NEES:ro \
+    --bind /corral/main/projects/NHERI/community:/home/CommunityData:ro \
+    --bind /corral/main/projects/NHERI/published:/home/NHERI-Published:ro \
     --bind /corral/main/projects/NHERI/projects \
     $DATADIR_MOUNT \
     docker://taccaci/designsafe-simcenter-vm:0.0.1 /bin/sh -c "cd /data; python3 /data/$PBESCRIPT"

From 06e8572b2ae71b0745909b4b432ceacb42a08c51 Mon Sep 17 00:00:00 2001
From: Garrett Edmonds <edmondsgarrett@gmail.com>
Date: Thu, 7 Nov 2024 14:45:45 -0600
Subject: [PATCH 3/4] Handle case of DATADIR mount not being found + removing
 'work' from some container mount paths

---
 applications/simcenter-designsafe-vm/tapisjob_app.sh | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/applications/simcenter-designsafe-vm/tapisjob_app.sh b/applications/simcenter-designsafe-vm/tapisjob_app.sh
index ea92402..c99e41b 100644
--- a/applications/simcenter-designsafe-vm/tapisjob_app.sh
+++ b/applications/simcenter-designsafe-vm/tapisjob_app.sh
@@ -22,8 +22,12 @@ fi
 DATADIR_NAME="${dataDirectory##*/}"
 DATADIR=`python3 get_folder_mount_path.py $dataDirectory`
 
-DATADIR_MOUNT="--bind ${DATADIR}:/home/${_tapisJobOwner}/work/projects/$DATADIR_NAME"
-if [ -z ${dataDirectory} ]; then
+DATADIR_MOUNT="--bind ${DATADIR}:/home/${_tapisJobOwner}/projects/$DATADIR_NAME"
+if [ -z ${dataDirectory} || -z ${DATADIR} ]; then
+    
+    if [ -z ${DATADIR} ]; then
+        echo "No valid mount found for Data Directory specified in job request; defaulting to mounting your projects."
+    fi
     projects_dir="$HOME/MyProjects"
 
     mkdir -p "$projects_dir"
@@ -44,7 +48,7 @@ if [ -z ${dataDirectory} ]; then
             echo "TACC: Project Links: Target path does not exist: $target_path"
         fi
     done
-    DATADIR_MOUNT="--bind ${projects_dir}:/home/${_tapisJobOwner}/work/projects"
+    DATADIR_MOUNT="--bind ${projects_dir}:/home/${_tapisJobOwner}/projects"
 fi
 
 echo "Running $PBESCRIPT"
@@ -53,7 +57,7 @@ apptainer run \
     --writable-tmpfs \
     --memory 10G \
     --bind $INPUTDIR:"/data/" \
-    --bind "/corral/main/projects/NHERI/shared/${_tapisJobOwner}":"/home/${_tapisJobOwner}/work/MyData" \
+    --bind "/corral/main/projects/NHERI/shared/${_tapisJobOwner}":"/home/${_tapisJobOwner}/MyData" \
     --bind /corral/main/projects/NHERI/public/projects:/home/NEES:ro \
     --bind /corral/main/projects/NHERI/community:/home/CommunityData:ro \
     --bind /corral/main/projects/NHERI/published:/home/NHERI-Published:ro \

From 01aa442548cdaee9332f44af289bc51606ee657c Mon Sep 17 00:00:00 2001
From: Garrett Edmonds <edmondsgarrett@gmail.com>
Date: Thu, 7 Nov 2024 14:51:23 -0600
Subject: [PATCH 4/4] Decrease amount of memory dedicated for container by half

---
 applications/simcenter-designsafe-vm/tapisjob_app.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/applications/simcenter-designsafe-vm/tapisjob_app.sh b/applications/simcenter-designsafe-vm/tapisjob_app.sh
index c99e41b..a84d00e 100644
--- a/applications/simcenter-designsafe-vm/tapisjob_app.sh
+++ b/applications/simcenter-designsafe-vm/tapisjob_app.sh
@@ -55,7 +55,7 @@ echo "Running $PBESCRIPT"
 
 apptainer run \
     --writable-tmpfs \
-    --memory 10G \
+    --memory 5G \
     --bind $INPUTDIR:"/data/" \
     --bind "/corral/main/projects/NHERI/shared/${_tapisJobOwner}":"/home/${_tapisJobOwner}/MyData" \
     --bind /corral/main/projects/NHERI/public/projects:/home/NEES:ro \