Task/wa 177 dynamic exec system

.gitignore

@@ -1 +1,5 @@
 client_secrets.py
+__pycache__
+.python-version
+.DS_Store
+.vscode

README.md

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 # WMA-Tapis-Templates
+
+## Requirements
+- [Tapipy](https://github.com/tapis-project/tapipy/tree/main/tapipy)
+- (Optional) [pyenv](https://github.com/pyenv/pyenv)
+- (Optional) [pyenv-virtualenv](https://github.com/pyenv/pyenv-virtualenv)
+
+## Provisioning a Tenant
+1. Create a `client_secrets.py` file with a `CLIENT_USERNAME` and `CLIENT_PASSWORD` (see client_secrets.example.py)
+2. Adjust the tenants, systems, and apps you wish to create in `initialize_tenant.py`
+3. Run `python initialize_tenant.py` to create/update the apps and systems in the tenants listed in `TENANT_BASE_URLS`
+
+## Creating a client
+1. (Optional) Install Tapipy in a pyenv environemnt
+  a. `pyenv install 3.11`
+  b. `pyenv virtualenv 3.11 tapipy`
+  c. `pyenv local tapipy`
+  c. `pip install tapipy`
+2. Install ipython
+  a. `pip install ipython`
+3. Initiate an ipython session
+  a. `ipython`
+4. Create a client
+```
+from tapipy.tapis import Tapis
+client = Tapis(base_url='https://portals.tapis.io', username='$USER', password='******')
+client.get_tokens()
+```
+
+## Creating a credential
+1. Create a keypair locally
+  a. `ssh-keygen -m PEM -t rsa -b 2048 -f ~/.ssh/$USER.frontera`
+2. Copy the public key to your `~/.ssh/authorized_keys` file on the frontera host
+```
+ssh [email protected]
+PUBKEY="PASTE PUBLIC KEY HERE"
+echo $PUBKEY >> ~/.ssh/authorized_keys`
+```
+3. Copy the public and private key to the `USER_CREDENTIAL_PRIVATE_KEY` and `USER_CREDENTIAL_PUBLIC_KEY` values in `client_secrets.py`
+4. Adjust the `systemId` and `base_url` values for your desired tenant/system and run the `create_client_credential.py` script
+5. Test the keypair works by making a file listing on a system
+  a. `client.files.listFiles(systemId='frontera', path='/')`

applications/GiD-stampede3/app.json

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+{
+    "id": "GiD-stampede3",
+    "version": "16.1.0",
+    "description": "GiD is designed to cover all the common needs in the numerical simulation field from pre to post processing: geometrical modeling, effective definition of analysis data, meshing, data transfer to analysis software, as well as the analysis and visualization of numerical results.",
+    "owner": "${apiUserId}",
+    "enabled": true,
+    "runtime": "ZIP",
+    "runtimeVersion": null,
+    "runtimeOptions": null,
+    "containerImage": "tapis://cloud.data/corral/tacc/aci/CEP/applications/v3/interactive-template/interactive.zip",
+    "jobType": "BATCH",
+    "maxJobs": -1,
+    "maxJobsPerUser": -1,
+    "strictFileInputs": true,
+    "jobAttributes": {
+        "description": "",
+        "dynamicExecSystem": false,
+        "execSystemConstraints": null,
+        "execSystemId": "stampede3",
+        "execSystemExecDir": "${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": null,
+        "parameterSet": {
+            "appArgs": [],
+            "containerArgs": [],
+            "schedulerOptions": [
+                {
+                    "name": "TACC Scheduler Profile",
+                    "description": "Scheduler profile for HPC clusters at TACC",
+                    "inputMode": "FIXED",
+                    "arg": "--tapis-profile tacc-apptainer",
+                    "notes": {
+                        "isHidden": true
+                    }
+                },
+                {
+                    "name": "TACC Interactive Session Substrings",
+                    "description": "VNC and DCV sessions require the substrings 'tap_' and '-dcvserver' in the slurm job name in order to function.",
+                    "inputMode": "FIXED",
+                    "arg": "--job-name ${JobName}-dcvserver-tap_",
+                    "notes": {
+                        "isHidden": true
+                    }
+                }
+            ],
+            "envVariables": [
+                {
+                    "key": "_XTERM_CMD",
+                    "value": "/work/projects/wma_apps/stampede3/gid16.1.10/gid",
+                    "description": "Command passed to XTERM, launched within the interactive session.",
+                    "inputMode": "FIXED",
+                    "notes": {
+                        "isHidden": true
+                    }
+                },
+                {
+                    "key": "APPEND_PATH",
+                    "value": "$PATH",
+                    "description": "Append host $PATH to Singularity container default $PATH.",
+                    "inputMode": "FIXED",
+                    "notes": {
+                        "isHidden": true
+                    }
+                }
+            ],
+            "archiveFilter": {
+                "includes": [],
+                "excludes": [],
+                "includeLaunchFiles": true
+            }
+        },
+        "fileInputs": [
+            {
+                "name": "Input Directory",
+                "description": "The directory containing the files that you want to work on. This directory and its files will be copied to where your GiD session runs.",
+                "inputMode": "OPTIONAL",
+                "autoMountLocal": true,
+                "sourceUrl": null,
+                "targetPath": "inputDirectory"
+            }
+        ],
+        "fileInputArrays": [],
+        "nodeCount": 1,
+        "coresPerNode": 48,
+        "memoryMB": 192000,
+        "maxMinutes": 120,
+        "subscriptions": [],
+        "tags": []
+    },
+    "tags": [
+        "portalName: DesignSafe"
+    ],
+    "notes": {
+        "icon": "GiD",
+        "label": "GiD (Stampede3) - v16.1.0",
+        "helpUrl": "/use-designsafe/tools-applications/visualization/gid",
+        "hideNodeCountAndCoresPerNode": true,
+        "category": "Simulation",
+        "isInteractive": true
+    }
+}

applications/GiD/app.json

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+{
+    "id": "GiD",
+    "version": "15.0.1",
+    "description": "GiD is designed to cover all the common needs in the numerical simulation field from pre to post processing: geometrical modeling, effective definition of analysis data, meshing, data transfer to analysis software, as well as the analysis and visualization of numerical results.",
+    "owner": "${apiUserId}",
+    "enabled": true,
+    "runtime": "ZIP",
+    "runtimeVersion": null,
+    "runtimeOptions": null,
+    "containerImage": "tapis://cloud.data/corral/tacc/aci/CEP/applications/v3/interactive-template/interactive.zip",
+    "jobType": "BATCH",
+    "maxJobs": -1,
+    "maxJobsPerUser": -1,
+    "strictFileInputs": true,
+    "jobAttributes": {
+        "description": "",
+        "dynamicExecSystem": false,
+        "execSystemConstraints": null,
+        "execSystemId": "frontera",
+        "execSystemExecDir": "${JobWorkingDir}",
+        "execSystemInputDir": "${JobWorkingDir}",
+        "execSystemOutputDir": "${JobWorkingDir}/output",
+        "execSystemLogicalQueue": "small",
+        "archiveSystemId": "cloud.data",
+        "archiveSystemDir": "HOST_EVAL($HOME)/tapis-jobs-archive/${JobCreateDate}/${JobName}-${JobUUID}",
+        "archiveOnAppError": true,
+        "isMpi": false,
+        "mpiCmd": null,
+        "cmdPrefix": null,
+        "parameterSet": {
+            "appArgs": [],
+            "containerArgs": [],
+            "schedulerOptions": [
+                {
+                    "name": "TACC Scheduler Profile",
+                    "description": "Scheduler profile for HPC clusters at TACC",
+                    "inputMode": "FIXED",
+                    "arg": "--tapis-profile tacc-apptainer",
+                    "notes": {
+                        "isHidden": true
+                    }
+                },
+                {
+                    "name": "TACC Interactive Session Substrings",
+                    "description": "VNC and DCV sessions require the substrings 'tap_' and '-dcvserver' in the slurm job name in order to function.",
+                    "inputMode": "FIXED",
+                    "arg": "--job-name ${JobName}-dcvserver-tap_",
+                    "notes": {
+                        "isHidden": true
+                    }
+                }
+            ],
+            "envVariables": [
+                {
+                    "key": "_XTERM_CMD",
+                    "value": "/work/projects/wma_apps/frontera/gid/15.0.1/gid",
+                    "description": "Command passed to XTERM, launched within the interactive session.",
+                    "inputMode": "FIXED",
+                    "notes": {
+                        "isHidden": true
+                    }
+                },
+                {
+                    "key": "APPEND_PATH",
+                    "value": "$PATH",
+                    "description": "Append host $PATH to Singularity container default $PATH.",
+                    "inputMode": "FIXED",
+                    "notes": {
+                        "isHidden": true
+                    }
+                }
+            ],
+            "archiveFilter": {
+                "includes": [],
+                "excludes": [],
+                "includeLaunchFiles": true
+            }
+        },
+        "fileInputs": [
+            {
+                "name": "Input Directory",
+                "description": "The directory containing the files that you want to work on. This directory and its files will be copied to where your GiD session runs.",
+                "inputMode": "OPTIONAL",
+                "autoMountLocal": true,
+                "sourceUrl": null,
+                "targetPath": "inputDirectory"
+            }
+        ],
+        "fileInputArrays": [],
+        "nodeCount": 1,
+        "coresPerNode": 56,
+        "memoryMB": 192000,
+        "maxMinutes": 120,
+        "subscriptions": [],
+        "tags": []
+    },
+    "tags": [
+        "portalName: DesignSafe"
+    ],
+    "notes": {
+        "icon": "GiD",
+        "label": "GiD (Frontera) - v15.0.1",
+        "helpUrl": "https://www.gidhome.com/support/",
+        "hideNodeCountAndCoresPerNode": true,
+        "category": "Simulation",
+        "isInteractive": true
+    }
+}

applications/LS-Dyna-stampede3/app.json

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+{
+    "id": "ls-dyna-stampede3",
+    "version": "2024R1",
+    "description": "LS-DYNA is an advanced general-purpose multiphysics simulation software package.",
+    "owner": "${apiUserId}",
+    "enabled": true,
+    "runtime": "ZIP",
+    "runtimeVersion": null,
+    "runtimeOptions": null,
+    "containerImage": "tapis://cloud.data//corral/tacc/aci/CEP/applications/v3/ls-dyna-stampede3/ls-dyna-stampede3.zip",
+    "jobType": "BATCH",
+    "maxJobs": -1,
+    "maxJobsPerUser": -1,
+    "strictFileInputs": true,
+    "jobAttributes": {
+        "description": "",
+        "dynamicExecSystem": false,
+        "execSystemConstraints": null,
+        "execSystemId": "stampede3",
+        "execSystemExecDir": "${JobWorkingDir}",
+        "execSystemInputDir": "${JobWorkingDir}",
+        "execSystemOutputDir": "${JobWorkingDir}",
+        "execSystemLogicalQueue": "skx-dev",
+        "archiveSystemId": "cloud.data",
+        "archiveSystemDir": "HOST_EVAL($HOME)/tapis-jobs-archive/${JobCreateDate}/${JobName}-${JobUUID}",
+        "archiveOnAppError": true,
+        "isMpi": false,
+        "mpiCmd": null,
+        "cmdPrefix": null,
+        "parameterSet": {
+            "appArgs": [
+                {
+                    "name": "Input file",
+                    "description": "Please enter the input file in .txt format. Add one .k case file per line if there are multiple case files.",
+                    "arg": "myfilename.txt",
+                    "inputMode": "REQUIRED",
+                    "notes": {
+                        "validator": {
+                            "regex": "\\.txt$",
+                            "message": "The input file must be a .txt file."
+                        }
+                    }
+                }
+            ],
+            "containerArgs": [],
+            "schedulerOptions": [
+                {
+                    "name": "TACC Scheduler Profile",
+                    "description": "Scheduler profile for HPC clusters at TACC",
+                    "inputMode": "FIXED",
+                    "arg": "--tapis-profile ls-dyna-2024R1",
+                    "notes": {
+                        "isHidden": true
+                    }
+                },
+                {
+                    "name": "Slurm job name",
+                    "description": "Set the slurm job name to be identical to the Tapis job name.",
+                    "inputMode": "FIXED",
+                    "arg": "--job-name ${JobName}",
+                    "notes": {
+                        "isHidden": true
+                    }
+                }
+            ],
+            "envVariables": [
+                {
+                    "key": "pre",
+                    "value": "S",
+                    "description": "Please choose the precision for the solver. S = Single Precision and D = Double Precision. Default is Single Precision.",
+                    "inputMode": "REQUIRED",
+                    "notes": {
+                        "label": "Precision",
+                        "enum_values": [
+                            {
+                                "S": "S"
+                            },
+                            {
+                                "D": "D"
+                            }
+                        ]
+                    }
+                }
+            ],
+            "archiveFilter": {
+                "includes": [],
+                "excludes": [
+                    "tapisjob_app.sh",
+                    "ls-dyna-stampede3.zip",
+                    "tapisjob.env"
+                ],
+                "includeLaunchFiles": true
+            }
+        },
+        "fileInputs": [
+            {
+                "name": "Input Directory",
+                "description": "The directory containing the files that you want to work on. This directory and its files will be copied to where your GiD session runs. Copy and paste to try an example input: tapis://cloud.data/corral/tacc/aci/CEP/community/app_examples/ls-dyna",
+                "inputMode": "REQUIRED",
+                "autoMountLocal": true,
+                "sourceUrl": null,
+                "targetPath": "inputDirectory"
+            }
+        ],
+        "fileInputArrays": [],
+        "nodeCount": 1,
+        "coresPerNode": 48,
+        "memoryMB": 192000,
+        "maxMinutes": 120,
+        "subscriptions": [],
+        "tags": []
+    },
+    "tags": [
+        "portalName: DesignSafe"
+    ],
+    "notes": {
+        "licenseType": "LS-DYNA",
+        "icon": "LS-DYNA",
+        "label": "LS-Dyna (Stampede3)",
+        "helpUrl": "https://www.designsafe-ci.org/user-guide/tools/simulation/lsdyna/",
+        "hideNodeCountAndCoresPerNode": false,
+        "category": "Simulation",
+        "isInteractive": false
+    }
+}