modules/agent-framework/deployments/jupyterhub/data/md_demo/molecular_dynamics.ipynb (1,706 lines of code) (raw):
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%pip install airavata-python-sdk-test==0.1.0"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Error in token refresh request: 400 - {\"error\":\"invalid_grant\",\"error_description\":\"Session not active\"}\n",
"Access token is invalid!\n",
"Please authenticate by visiting: https://auth.cybershuttle.org/realms/default/device?user_code=LEEP-VBBU\n",
"Waiting for authorization...\n",
"Authenticated via device auth!\n"
]
}
],
"source": [
"import airavata_experiments as ae\n",
"from airavata_experiments import md"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>cluster</th>\n",
" <th>category</th>\n",
" <th>queue_name</th>\n",
" <th>node_count</th>\n",
" <th>cpu_count</th>\n",
" <th>gpu_count</th>\n",
" <th>walltime</th>\n",
" <th>group</th>\n",
" </tr>\n",
" <tr>\n",
" <th>id</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>remote</th>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>30</td>\n",
" <td>Default</td>\n",
" </tr>\n",
" <tr>\n",
" <th>remote</th>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>30</td>\n",
" <td>Default</td>\n",
" </tr>\n",
" <tr>\n",
" <th>remote</th>\n",
" <td>anvil.rcac.purdue.edu</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>24</td>\n",
" <td>0</td>\n",
" <td>30</td>\n",
" <td>Default</td>\n",
" </tr>\n",
" <tr>\n",
" <th>remote</th>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>30</td>\n",
" <td>GaussianGroup</td>\n",
" </tr>\n",
" <tr>\n",
" <th>remote</th>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>30</td>\n",
" <td>GaussianGroup</td>\n",
" </tr>\n",
" <tr>\n",
" <th>remote</th>\n",
" <td>anvil.rcac.purdue.edu</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>24</td>\n",
" <td>0</td>\n",
" <td>30</td>\n",
" <td>GaussianGroup</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" cluster category queue_name node_count cpu_count \\\n",
"id \n",
"remote login.expanse.sdsc.edu gpu gpu-shared 1 10 \n",
"remote login.expanse.sdsc.edu cpu shared 1 10 \n",
"remote anvil.rcac.purdue.edu cpu shared 1 24 \n",
"remote login.expanse.sdsc.edu gpu gpu-shared 1 10 \n",
"remote login.expanse.sdsc.edu cpu shared 1 10 \n",
"remote anvil.rcac.purdue.edu cpu shared 1 24 \n",
"\n",
" gpu_count walltime group \n",
"id \n",
"remote 1 30 Default \n",
"remote 0 30 Default \n",
"remote 0 30 Default \n",
"remote 1 30 GaussianGroup \n",
"remote 0 30 GaussianGroup \n",
"remote 0 30 GaussianGroup "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"# ae.login(\"gateway.cybershuttle.org\", \"realm\")\n",
"\n",
"runtimes = ae.list_runtimes()\n",
"ae.display(runtimes)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## AlphaFold2"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"exp = md.AlphaFold2.initialize(\n",
" name=\"AlphaFold2_test\",\n",
" input_seq=\"data/alphafold2/Abeta42_Dimer.fasta\",\n",
" max_template_date=\"2023-09-18\",\n",
" model_preset=\"multimer\",\n",
" multimers_per_model=6,\n",
")\n",
"exp.create_task(*ae.list_runtimes(cluster=\"login.expanse.sdsc.edu\", category=\"gpu\", group=\"Default\", walltime=60))\n",
"ae.display(exp)\n",
"plan = exp.plan()\n",
"plan.launch()\n",
"plan.save_json(\"plan_alphafold2.json\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## AMBER"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"exp = md.AMBER.initialize(\n",
" name=\"AMBER_test\",\n",
" coord_file=\"data/amber/RAMP1_equil.rst7\",\n",
" control_file=\"data/amber/md.in\",\n",
" topology_file=\"data/amber/RAMP1.prmtop\",\n",
" ref_coord_file=\"data/amber/RAMP1.prmtop\",\n",
")\n",
"exp.create_task(*ae.list_runtimes(cluster=\"login.expanse.sdsc.edu\", category=\"gpu\", group=\"Default\", walltime=60))\n",
"ae.display(exp)\n",
"plan = exp.plan()\n",
"plan.launch()\n",
"plan.save_json(\"plan_amber.json\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Gaussian"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"exp = md.Gaussian.initialize(\n",
" name=\"Gaussian_test\",\n",
" input_file=\"data/gaussian/NOR0N-RAD21-freq.gjf\",\n",
" gpu_version=\"g16\",\n",
")\n",
"exp.create_task(*ae.list_runtimes(cluster=\"login.expanse.sdsc.edu\", category=\"gpu\", group=\"GaussianGroup\", walltime=60))\n",
"ae.display(exp)\n",
"plan = exp.plan()\n",
"plan.launch()\n",
"plan.save_json(\"plan_gaussian.json\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## GROMACS"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"exp = md.GROMACS.initialize(\n",
" name=\"GROMACS_test\",\n",
" pib_file=\"data/gromacs/npt.tpr\",\n",
" coord_file=\"data/gromacs/npt.gro\",\n",
" optional_files=[\"data/gromacs/md.mdp\"],\n",
" environment=\"I_MPI_FABRICS shm:ofa\",\n",
")\n",
"exp.create_task(*ae.list_runtimes(cluster=\"login.expanse.sdsc.edu\", category=\"gpu\", group=\"Default\", walltime=60))\n",
"ae.display(exp)\n",
"plan = exp.plan()\n",
"plan.launch()\n",
"plan.save_json(\"plan_gromacs.json\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## NAMD"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"exp = md.NAMD.initialize(\n",
" name=\"SMD\",\n",
" config_file=\"data/namd/pull_cpu.conf\",\n",
" pdb_file=\"data/namd/structure.pdb\",\n",
" psf_file=\"data/namd/structure.psf\",\n",
" ffp_files=[\n",
" \"data/namd/par_all36_water.prm\",\n",
" \"data/namd/par_all36m_prot.prm\"\n",
" ],\n",
" other_files=[\n",
" \"data/namd/b4pull.pdb\",\n",
" \"data/namd/b4pull.restart.coor\",\n",
" \"data/namd/b4pull.restart.vel\",\n",
" \"data/namd/b4pull.restart.xsc\",\n",
" ],\n",
" parallelism=\"CPU\",\n",
")\n",
"exp.create_task(*ae.list_runtimes(cluster=\"login.expanse.sdsc.edu\", category=\"gpu\", group=\"Default\", walltime=60))\n",
"ae.display(exp)\n",
"plan = exp.plan()\n",
"plan.launch()\n",
"plan.save_json(\"plan_namd.json\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Check Status"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <table border='1'>\n",
" <tr>\n",
" <th><b>Plan Id</b></th>\n",
" <th><b>Task Id</b></th>\n",
" <th><b>State</b></th>\n",
" <th><b>Name</b></th>\n",
" <th><b>App</b></th>\n",
" <th><b>Inputs</b></th>\n",
" <th><b>Cluster</b></th>\n",
" <th><b>Group</b></th>\n",
" <th><b>Category</b></th>\n",
" <th><b>Queue</b></th>\n",
" <th><b>Nodes</b></th>\n",
" <th><b>CPUs</b></th>\n",
" <th><b>GPUs</b></th>\n",
" <th><b>Time</b></th>\n",
" </tr>\n",
" \n",
" <tr>\n",
" <td>002cdb22...</td>\n",
" <td>37157371</td>\n",
" <td>COMPLETE</td>\n",
" <td>SMD_6C35</td>\n",
" <td>NAMD</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>MD-Instructions-Input</th><th>uri</th><th>data/namd/pull_cpu.conf</th></tr><tr><th>Coordinates-PDB-File</th><th>uri</th><th>data/namd/structure.pdb</th></tr><tr><th>Protein-Structure-File_PSF</th><th>uri</th><th>data/namd/structure.psf</th></tr><tr><th>FF-Parameter-Files</th><th>uri[]</th><th>['data/namd/par_all36_water.prm', 'data/namd/par_all36m_prot.prm']</th></tr><tr><th>Execution_Type</th><th>str</th><th>CPU</th></tr><tr><th>Optional_Inputs</th><th>uri[]</th><th>['data/namd/b4pull.pdb', 'data/namd/b4pull.restart.coor', 'data/namd/b4pull.restart.vel', 'data/namd/b4pull.restart.xsc']</th></tr><tr><th>Number of Replicas</th><th>str</th><th>1</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>028efdd0...</td>\n",
" <td>37158683</td>\n",
" <td>COMPLETE</td>\n",
" <td>AlphaFold2_test_4AD5</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>05b26b44...</td>\n",
" <td>37159387</td>\n",
" <td>FAILED</td>\n",
" <td>Gaussian_test_6A32</td>\n",
" <td>Gaussian16</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_File</th><th>uri</th><th>data/gaussian/NOR0N-RAD21-freq.gjf</th></tr><tr><th>GPU_Version?</th><th>str</th><th>g16</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>GaussianGroup</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>0abf4aaf...</td>\n",
" <td>37145654</td>\n",
" <td>FAILED</td>\n",
" <td>AlphaFold2_test_EAFE</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>0acf9ab1...</td>\n",
" <td>37128161</td>\n",
" <td>COMPLETE</td>\n",
" <td>SMD_4092</td>\n",
" <td>NAMD</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>MD-Instructions-Input</th><th>uri</th><th>data/namd/pull_cpu.conf</th></tr><tr><th>Coordinates-PDB-File</th><th>uri</th><th>data/namd/structure.pdb</th></tr><tr><th>Protein-Structure-File_PSF</th><th>uri</th><th>data/namd/structure.psf</th></tr><tr><th>FF-Parameter-Files</th><th>uri[]</th><th>['data/namd/par_all36_water.prm', 'data/namd/par_all36m_prot.prm']</th></tr><tr><th>Execution_Type</th><th>str</th><th>CPU</th></tr><tr><th>Optional_Inputs</th><th>uri[]</th><th>['data/namd/b4pull.pdb', 'data/namd/b4pull.restart.coor', 'data/namd/b4pull.restart.vel', 'data/namd/b4pull.restart.xsc']</th></tr><tr><th>Number of Replicas</th><th>str</th><th>1</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>0d73cff1...</td>\n",
" <td>37128815</td>\n",
" <td>COMPLETE</td>\n",
" <td>SMD_C47F</td>\n",
" <td>NAMD</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>MD-Instructions-Input</th><th>uri</th><th>data/namd/pull_cpu.conf</th></tr><tr><th>Coordinates-PDB-File</th><th>uri</th><th>data/namd/structure.pdb</th></tr><tr><th>Protein-Structure-File_PSF</th><th>uri</th><th>data/namd/structure.psf</th></tr><tr><th>FF-Parameter-Files</th><th>uri[]</th><th>['data/namd/par_all36_water.prm', 'data/namd/par_all36m_prot.prm']</th></tr><tr><th>Execution_Type</th><th>str</th><th>CPU</th></tr><tr><th>Optional_Inputs</th><th>uri[]</th><th>['data/namd/b4pull.pdb', 'data/namd/b4pull.restart.coor', 'data/namd/b4pull.restart.vel', 'data/namd/b4pull.restart.xsc']</th></tr><tr><th>Number of Replicas</th><th>str</th><th>1</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>1c45a65a...</td>\n",
" <td>37184027</td>\n",
" <td>FAILED</td>\n",
" <td>AMBER_test_576E</td>\n",
" <td>Amber_pmemd_CUDA</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_Coordinates</th><th>uri</th><th>data/amber/RAMP1_equil.rst7</th></tr><tr><th>MD_control_Input</th><th>uri</th><th>data/amber/md.in</th></tr><tr><th>Parameter-Topology-File</th><th>uri</th><th>data/amber/RAMP1.prmtop</th></tr><tr><th>Reference-coordinate-file</th><th>uri</th><th>data/amber/RAMP1.prmtop</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>1c5d2f3e...</td>\n",
" <td>37156961</td>\n",
" <td>COMPLETE</td>\n",
" <td>GROMACS_test_1B9D</td>\n",
" <td>Gromacs_with_OptionalRestart</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Portable-Input-Binary-File</th><th>uri</th><th>data/gromacs/npt.tpr</th></tr><tr><th>Coordinate-File</th><th>uri</th><th>data/gromacs/npt.gro</th></tr><tr><th>Optional_Files</th><th>uri[]</th><th>['data/gromacs/md.mdp']</th></tr><tr><th>environment</th><th>str</th><th>I_MPI_FABRICS shm:ofa</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>23713115...</td>\n",
" <td>37148952</td>\n",
" <td>FAILED</td>\n",
" <td>AlphaFold2_test_0749</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>2ace80fe...</td>\n",
" <td>37158900</td>\n",
" <td>COMPLETE</td>\n",
" <td>AlphaFold2_test_33A3</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>3692591e...</td>\n",
" <td>37146953</td>\n",
" <td>FAILED</td>\n",
" <td>AlphaFold2_test_B78A</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>36a1bb44...</td>\n",
" <td>37128793</td>\n",
" <td>FAILED</td>\n",
" <td>Gaussian_test_1093</td>\n",
" <td>Gaussian16</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_File</th><th>uri</th><th>data/gaussian/NOR0N-RAD21-freq.gjf</th></tr><tr><th>GPU_Version?</th><th>str</th><th>g16</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>3722fc9c...</td>\n",
" <td>N/A</td>\n",
" <td>N/A</td>\n",
" <td>SMD_B065</td>\n",
" <td>NAMD</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>MD-Instructions-Input</th><th>uri</th><th>data/pull_cpu.conf</th></tr><tr><th>Coordinates-PDB-File</th><th>uri</th><th>data/structure.pdb</th></tr><tr><th>Protein-Structure-File_PSF</th><th>uri</th><th>data/structure.psf</th></tr><tr><th>FF-Parameter-Files</th><th>uri[]</th><th>['data/par_all36_water.prm', 'data/par_all36m_prot.prm']</th></tr><tr><th>Execution_Type</th><th>str</th><th>CPU</th></tr><tr><th>Optional_Inputs</th><th>uri[]</th><th>['data/b4pull.pdb', 'data/b4pull.restart.coor', 'data/b4pull.restart.vel', 'data/b4pull.restart.xsc']</th></tr><tr><th>Number of Replicas</th><th>str</th><th>1</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>GaussianGroup</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>3a8cdc1e...</td>\n",
" <td>37158931</td>\n",
" <td>COMPLETE</td>\n",
" <td>SMD_5163</td>\n",
" <td>NAMD</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>MD-Instructions-Input</th><th>uri</th><th>data/namd/pull_cpu.conf</th></tr><tr><th>Coordinates-PDB-File</th><th>uri</th><th>data/namd/structure.pdb</th></tr><tr><th>Protein-Structure-File_PSF</th><th>uri</th><th>data/namd/structure.psf</th></tr><tr><th>FF-Parameter-Files</th><th>uri[]</th><th>['data/namd/par_all36_water.prm', 'data/namd/par_all36m_prot.prm']</th></tr><tr><th>Execution_Type</th><th>str</th><th>CPU</th></tr><tr><th>Optional_Inputs</th><th>uri[]</th><th>['data/namd/b4pull.pdb', 'data/namd/b4pull.restart.coor', 'data/namd/b4pull.restart.vel', 'data/namd/b4pull.restart.xsc']</th></tr><tr><th>Number of Replicas</th><th>str</th><th>1</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>3b0f2474...</td>\n",
" <td>37128788</td>\n",
" <td>FAILED</td>\n",
" <td>AlphaFold2_test_5352</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>41c7372a...</td>\n",
" <td>37159118</td>\n",
" <td>COMPLETE</td>\n",
" <td>AlphaFold2_test_97FE</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>42311487...</td>\n",
" <td>37128093</td>\n",
" <td>FAILED</td>\n",
" <td>AlphaFold2_test_E7A2</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>4573ab6d...</td>\n",
" <td>37158794</td>\n",
" <td>FAILED</td>\n",
" <td>Gaussian_test_CE4D</td>\n",
" <td>Gaussian16</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_File</th><th>uri</th><th>data/gaussian/NOR0N-RAD21-freq.gjf</th></tr><tr><th>GPU_Version?</th><th>str</th><th>g16</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>GaussianGroup</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>484cd917...</td>\n",
" <td>37158689</td>\n",
" <td>FAILED</td>\n",
" <td>AMBER_test_F168</td>\n",
" <td>Amber_pmemd_CUDA</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_Coordinates</th><th>uri</th><th>data/amber/RAMP1_equil.rst7</th></tr><tr><th>MD_control_Input</th><th>uri</th><th>data/amber/md.in</th></tr><tr><th>Parameter-Topology-File</th><th>uri</th><th>data/amber/RAMP1.prmtop</th></tr><tr><th>Reference-coordinate-file</th><th>uri</th><th>data/amber/RAMP1.prmtop</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>4b0daa9c...</td>\n",
" <td>37158912</td>\n",
" <td>FAILED</td>\n",
" <td>Gaussian_test_F4BC</td>\n",
" <td>Gaussian16</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_File</th><th>uri</th><th>data/gaussian/NOR0N-RAD21-freq.gjf</th></tr><tr><th>GPU_Version?</th><th>str</th><th>g16</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>GaussianGroup</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>5ef70f99...</td>\n",
" <td>37145563</td>\n",
" <td>FAILED</td>\n",
" <td>AlphaFold2_test_6640</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>67af14b4...</td>\n",
" <td>37148975</td>\n",
" <td>COMPLETE</td>\n",
" <td>AlphaFold2_test_A6A3</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>6909909c...</td>\n",
" <td>37148226</td>\n",
" <td>FAILED</td>\n",
" <td>AlphaFold2_test_7F8C</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>6bce1ff1...</td>\n",
" <td>37156950</td>\n",
" <td>COMPLETE</td>\n",
" <td>AlphaFold2_test_8ED9</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>6e30ec26...</td>\n",
" <td>37148358</td>\n",
" <td>FAILED</td>\n",
" <td>AlphaFold2_test_D85A</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>735722fc...</td>\n",
" <td>37148999</td>\n",
" <td>COMPLETE</td>\n",
" <td>SMD_B041</td>\n",
" <td>NAMD</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>MD-Instructions-Input</th><th>uri</th><th>data/pull_cpu.conf</th></tr><tr><th>Coordinates-PDB-File</th><th>uri</th><th>data/structure.pdb</th></tr><tr><th>Protein-Structure-File_PSF</th><th>uri</th><th>data/structure.psf</th></tr><tr><th>FF-Parameter-Files</th><th>uri[]</th><th>['data/par_all36_water.prm', 'data/par_all36m_prot.prm']</th></tr><tr><th>Execution_Type</th><th>str</th><th>CPU</th></tr><tr><th>Optional_Inputs</th><th>uri[]</th><th>['data/b4pull.pdb', 'data/b4pull.restart.coor', 'data/b4pull.restart.vel', 'data/b4pull.restart.xsc']</th></tr><tr><th>Number of Replicas</th><th>str</th><th>1</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>7d852bde...</td>\n",
" <td>37128547</td>\n",
" <td>COMPLETE</td>\n",
" <td>GROMACS_test_2CF3</td>\n",
" <td>Gromacs_with_OptionalRestart</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Portable-Input-Binary-File</th><th>uri</th><th>data/gromacs/npt.tpr</th></tr><tr><th>Coordinate-File</th><th>uri</th><th>data/gromacs/npt.gro</th></tr><tr><th>Optional_Files</th><th>uri[]</th><th>['data/gromacs/md.mdp']</th></tr><tr><th>environment</th><th>str</th><th>I_MPI_FABRICS shm:ofa</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>8aeee8bf...</td>\n",
" <td>37147790</td>\n",
" <td>FAILED</td>\n",
" <td>AlphaFold2_test_84B5</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>8e3f8daa...</td>\n",
" <td>37145575</td>\n",
" <td>FAILED</td>\n",
" <td>AlphaFold2_test_37D7</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>944aa057...</td>\n",
" <td>37159120</td>\n",
" <td>FAILED</td>\n",
" <td>AMBER_test_01C9</td>\n",
" <td>Amber_pmemd_CUDA</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_Coordinates</th><th>uri</th><th>data/amber/RAMP1_equil.rst7</th></tr><tr><th>MD_control_Input</th><th>uri</th><th>data/amber/md.in</th></tr><tr><th>Parameter-Topology-File</th><th>uri</th><th>data/amber/RAMP1.prmtop</th></tr><tr><th>Reference-coordinate-file</th><th>uri</th><th>data/amber/RAMP1.prmtop</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>9e0591d3...</td>\n",
" <td>37128101</td>\n",
" <td>FAILED</td>\n",
" <td>Gaussian_test_9B67</td>\n",
" <td>Gaussian16</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_File</th><th>uri</th><th>data/gaussian/NOR0N-RAD21-freq.gjf</th></tr><tr><th>GPU_Version?</th><th>str</th><th>g16</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>a3ff00ae...</td>\n",
" <td>37158907</td>\n",
" <td>FAILED</td>\n",
" <td>AMBER_test_8791</td>\n",
" <td>Amber_pmemd_CUDA</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_Coordinates</th><th>uri</th><th>data/amber/RAMP1_equil.rst7</th></tr><tr><th>MD_control_Input</th><th>uri</th><th>data/amber/md.in</th></tr><tr><th>Parameter-Topology-File</th><th>uri</th><th>data/amber/RAMP1.prmtop</th></tr><tr><th>Reference-coordinate-file</th><th>uri</th><th>data/amber/RAMP1.prmtop</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>a5940a9d...</td>\n",
" <td>37184023</td>\n",
" <td>COMPLETE</td>\n",
" <td>AlphaFold2_test_8F4B</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>a7d625fa...</td>\n",
" <td>37157200</td>\n",
" <td>COMPLETE</td>\n",
" <td>AlphaFold2_test_10E8</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>ace1270d...</td>\n",
" <td>37157347</td>\n",
" <td>COMPLETE</td>\n",
" <td>GROMACS_test_4700</td>\n",
" <td>Gromacs_with_OptionalRestart</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Portable-Input-Binary-File</th><th>uri</th><th>data/gromacs/npt.tpr</th></tr><tr><th>Coordinate-File</th><th>uri</th><th>data/gromacs/npt.gro</th></tr><tr><th>Optional_Files</th><th>uri[]</th><th>['data/gromacs/md.mdp']</th></tr><tr><th>environment</th><th>str</th><th>I_MPI_FABRICS shm:ofa</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>b81ff213...</td>\n",
" <td>37184028</td>\n",
" <td>FAILED</td>\n",
" <td>Gaussian_test_87BA</td>\n",
" <td>Gaussian16</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_File</th><th>uri</th><th>data/gaussian/NOR0N-RAD21-freq.gjf</th></tr><tr><th>GPU_Version?</th><th>str</th><th>g16</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>GaussianGroup</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>bfdbe51b...</td>\n",
" <td>37128804</td>\n",
" <td>COMPLETE</td>\n",
" <td>GROMACS_test_EB99</td>\n",
" <td>Gromacs_with_OptionalRestart</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Portable-Input-Binary-File</th><th>uri</th><th>data/gromacs/npt.tpr</th></tr><tr><th>Coordinate-File</th><th>uri</th><th>data/gromacs/npt.gro</th></tr><tr><th>Optional_Files</th><th>uri[]</th><th>['data/gromacs/md.mdp']</th></tr><tr><th>environment</th><th>str</th><th>I_MPI_FABRICS shm:ofa</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>c20a8467...</td>\n",
" <td>37158691</td>\n",
" <td>FAILED</td>\n",
" <td>Gaussian_test_0BD5</td>\n",
" <td>Gaussian16</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_File</th><th>uri</th><th>data/gaussian/NOR0N-RAD21-freq.gjf</th></tr><tr><th>GPU_Version?</th><th>str</th><th>g16</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>GaussianGroup</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>c426ebf5...</td>\n",
" <td>37184034</td>\n",
" <td>COMPLETE</td>\n",
" <td>SMD_D8F1</td>\n",
" <td>NAMD</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>MD-Instructions-Input</th><th>uri</th><th>data/namd/pull_cpu.conf</th></tr><tr><th>Coordinates-PDB-File</th><th>uri</th><th>data/namd/structure.pdb</th></tr><tr><th>Protein-Structure-File_PSF</th><th>uri</th><th>data/namd/structure.psf</th></tr><tr><th>FF-Parameter-Files</th><th>uri[]</th><th>['data/namd/par_all36_water.prm', 'data/namd/par_all36m_prot.prm']</th></tr><tr><th>Execution_Type</th><th>str</th><th>CPU</th></tr><tr><th>Optional_Inputs</th><th>uri[]</th><th>['data/namd/b4pull.pdb', 'data/namd/b4pull.restart.coor', 'data/namd/b4pull.restart.vel', 'data/namd/b4pull.restart.xsc']</th></tr><tr><th>Number of Replicas</th><th>str</th><th>1</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>c6a75c4d...</td>\n",
" <td>37158704</td>\n",
" <td>COMPLETE</td>\n",
" <td>SMD_BC1A</td>\n",
" <td>NAMD</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>MD-Instructions-Input</th><th>uri</th><th>data/namd/pull_cpu.conf</th></tr><tr><th>Coordinates-PDB-File</th><th>uri</th><th>data/namd/structure.pdb</th></tr><tr><th>Protein-Structure-File_PSF</th><th>uri</th><th>data/namd/structure.psf</th></tr><tr><th>FF-Parameter-Files</th><th>uri[]</th><th>['data/namd/par_all36_water.prm', 'data/namd/par_all36m_prot.prm']</th></tr><tr><th>Execution_Type</th><th>str</th><th>CPU</th></tr><tr><th>Optional_Inputs</th><th>uri[]</th><th>['data/namd/b4pull.pdb', 'data/namd/b4pull.restart.coor', 'data/namd/b4pull.restart.vel', 'data/namd/b4pull.restart.xsc']</th></tr><tr><th>Number of Replicas</th><th>str</th><th>1</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>d48ff41d...</td>\n",
" <td>37157337</td>\n",
" <td>FAILED</td>\n",
" <td>Gaussian_test_6544</td>\n",
" <td>Gaussian16</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_File</th><th>uri</th><th>data/gaussian/NOR0N-RAD21-freq.gjf</th></tr><tr><th>GPU_Version?</th><th>str</th><th>g16</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>d7714d3f...</td>\n",
" <td>37157326</td>\n",
" <td>FAILED</td>\n",
" <td>AMBER_test_CB84</td>\n",
" <td>Amber_pmemd_CUDA</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input_Coordinates</th><th>uri</th><th>data/amber/RAMP1_equil.rst7</th></tr><tr><th>MD_control_Input</th><th>uri</th><th>data/amber/md.in</th></tr><tr><th>Parameter-Topology-File</th><th>uri</th><th>data/amber/RAMP1.prmtop</th></tr><tr><th>Reference-coordinate-file</th><th>uri</th><th>data/amber/RAMP1.prmtop</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>d983f156...</td>\n",
" <td>37184031</td>\n",
" <td>COMPLETE</td>\n",
" <td>GROMACS_test_0DD8</td>\n",
" <td>Gromacs_with_OptionalRestart</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Portable-Input-Binary-File</th><th>uri</th><th>data/gromacs/npt.tpr</th></tr><tr><th>Coordinate-File</th><th>uri</th><th>data/gromacs/npt.gro</th></tr><tr><th>Optional_Files</th><th>uri[]</th><th>['data/gromacs/md.mdp']</th></tr><tr><th>environment</th><th>str</th><th>I_MPI_FABRICS shm:ofa</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>da980cad...</td>\n",
" <td>37158692</td>\n",
" <td>COMPLETE</td>\n",
" <td>GROMACS_test_1509</td>\n",
" <td>Gromacs_with_OptionalRestart</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Portable-Input-Binary-File</th><th>uri</th><th>data/gromacs/npt.tpr</th></tr><tr><th>Coordinate-File</th><th>uri</th><th>data/gromacs/npt.gro</th></tr><tr><th>Optional_Files</th><th>uri[]</th><th>['data/gromacs/md.mdp']</th></tr><tr><th>environment</th><th>str</th><th>I_MPI_FABRICS shm:ofa</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>ef41cce1...</td>\n",
" <td>37147992</td>\n",
" <td>COMPLETE</td>\n",
" <td>SMD_27D3</td>\n",
" <td>NAMD</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>MD-Instructions-Input</th><th>uri</th><th>data/pull_cpu.conf</th></tr><tr><th>Coordinates-PDB-File</th><th>uri</th><th>data/structure.pdb</th></tr><tr><th>Protein-Structure-File_PSF</th><th>uri</th><th>data/structure.psf</th></tr><tr><th>FF-Parameter-Files</th><th>uri[]</th><th>['data/par_all36_water.prm', 'data/par_all36m_prot.prm']</th></tr><tr><th>Execution_Type</th><th>str</th><th>CPU</th></tr><tr><th>Optional_Inputs</th><th>uri[]</th><th>['data/b4pull.pdb', 'data/b4pull.restart.coor', 'data/b4pull.restart.vel', 'data/b4pull.restart.xsc']</th></tr><tr><th>Number of Replicas</th><th>str</th><th>1</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>cpu</td>\n",
" <td>shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>0</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>f63326f2...</td>\n",
" <td>37158920</td>\n",
" <td>COMPLETE</td>\n",
" <td>GROMACS_test_50D5</td>\n",
" <td>Gromacs_with_OptionalRestart</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Portable-Input-Binary-File</th><th>uri</th><th>data/gromacs/npt.tpr</th></tr><tr><th>Coordinate-File</th><th>uri</th><th>data/gromacs/npt.gro</th></tr><tr><th>Optional_Files</th><th>uri[]</th><th>['data/gromacs/md.mdp']</th></tr><tr><th>environment</th><th>str</th><th>I_MPI_FABRICS shm:ofa</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>f7482df7...</td>\n",
" <td>37185688</td>\n",
" <td>COMPLETE</td>\n",
" <td>AlphaFold2_test_E7B6</td>\n",
" <td>AlphaFold2</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Input Sequence(s) File</th><th>uri</th><th>data/alphafold2/Abeta42_Dimer.fasta</th></tr><tr><th>Maximum Template Date</th><th>str</th><th>2023-09-18</th></tr><tr><th>MODEL_PRESET</th><th>str</th><th>multimer</th></tr><tr><th>Number_Of_Multimers_Per_Model</th><th>str</th><th>6</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr>\n",
" <tr>\n",
" <td>f91d0f8d...</td>\n",
" <td>37159397</td>\n",
" <td>COMPLETE</td>\n",
" <td>GROMACS_test_C4FE</td>\n",
" <td>Gromacs_with_OptionalRestart</td>\n",
" <td>\n",
" <div style=\"position:relative;\" class=\"hover-container\">\n",
" [Hover]\n",
" <div class=\"hover-content\" style=\"visibility:hidden; position:absolute; top:20px; left:0; background:white; border:1px solid black; padding:5px; z-index:10;\">\n",
" \n",
" <table border='1'>\n",
" <tr><th><b>Input</b></th><th><b>Type</b></th><th><b>Value</b></th></tr>\n",
" <tr><th>Portable-Input-Binary-File</th><th>uri</th><th>data/gromacs/npt.tpr</th></tr><tr><th>Coordinate-File</th><th>uri</th><th>data/gromacs/npt.gro</th></tr><tr><th>Optional_Files</th><th>uri[]</th><th>['data/gromacs/md.mdp']</th></tr><tr><th>environment</th><th>str</th><th>I_MPI_FABRICS shm:ofa</th></tr></table>\n",
" </div>\n",
" </div>\n",
" </td>\n",
" <td>login.expanse.sdsc.edu</td>\n",
" <td>Default</td>\n",
" <td>gpu</td>\n",
" <td>gpu-shared</td>\n",
" <td>1</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" </tr>\n",
" <tr></tr></table>\n",
" <script type=\"text/javascript\">\n",
" document.querySelectorAll('.hover-container').forEach(item => {\n",
" item.addEventListener('mouseover', () => item.querySelector('.hover-content').style.visibility = 'visible');\n",
" item.addEventListener('mouseout', () => item.querySelector('.hover-content').style.visibility = 'hidden');\n",
" });\n",
" </script>\n",
" "
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"plans = ae.plan.query()\n",
"ae.display(plans)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "airavata_examples",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.16"
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},
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}