http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/6f3da7c3/Interacting_with_Airavata_using_ipython_Notebook/Admin-User/Admin User.ipynb ---------------------------------------------------------------------- diff --git a/Interacting_with_Airavata_using_ipython_Notebook/Admin-User/Admin User.ipynb b/Interacting_with_Airavata_using_ipython_Notebook/Admin-User/Admin User.ipynb index 748fc23..3bb9cad 100644 --- a/Interacting_with_Airavata_using_ipython_Notebook/Admin-User/Admin User.ipynb +++ b/Interacting_with_Airavata_using_ipython_Notebook/Admin-User/Admin User.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": 15, "metadata": { "collapsed": false }, @@ -33,8 +33,9 @@ "name": "stdout", "output_type": "stream", "text": [ - "0.16.0\n", - "0.16.0\n", + "AuthzToken(claimsMap={'userName': 'admin', 'gatewayID': 'seagrid'}, accessToken='empty-token')\n", + "0.17.0\n", + "0.17.0\n", "\n", "Welcome to Airavata CLI v0.0.1 - Wirtten in python\n", "\n", @@ -62,13 +63,37 @@ "cell_type": "code", "execution_count": 3, "metadata": { - "collapsed": false + "collapsed": false, + "scrolled": false }, "outputs": [ { "data": { "text/plain": [ - "[Gateway(gatewayId='Ultrascan_Production', emailAddress=None, domain=None, gatewayName='Ultrascan_Production')]" + "[Gateway(gatewayId='Arc', emailAddress='airavata.Arc', domain='Arc', gatewayName=None),\n", + " Gateway(gatewayId='brandeis', emailAddress=None, domain='Brandeis University Science Gateway', gatewayName=None),\n", + " Gateway(gatewayId='chemcompute', emailAddress=None, domain='Chem Compute Gateway', gatewayName=None),\n", + " Gateway(gatewayId='cornelldna', emailAddress='dreg.cornell', domain='dREG DNA Sequencing', gatewayName=None),\n", + " Gateway(gatewayId='default', emailAddress=None, domain='Testdrive Portal', gatewayName=None),\n", + " Gateway(gatewayId='georgiastate', emailAddress=None, domain='Georgia State PHP Gateway', gatewayName=None),\n", + " Gateway(gatewayId='iugateway', emailAddress=None, domain='IU Gateway', gatewayName=None),\n", + " Gateway(gatewayId='lsu', emailAddress=None, domain='LSU Cybergateway', gatewayName=None),\n", + " Gateway(gatewayId='New Physics Gateway 5', emailAddress=None, domain='New Physics Gateway 5', gatewayName=None),\n", + " Gateway(gatewayId='newg', emailAddress=None, domain='newg', gatewayName=None),\n", + " Gateway(gatewayId='nsg', emailAddress=None, domain='Neuro Science Gateway', gatewayName=None),\n", + " Gateway(gatewayId='oiitandy', emailAddress=None, domain='OII Science Gateway', gatewayName=None),\n", + " Gateway(gatewayId='oscer', emailAddress=None, domain='Oklahoma University Science Gateway', gatewayName=None),\n", + " Gateway(gatewayId='phasta', emailAddress=None, domain='PHASTA Science Gateway', gatewayName=None),\n", + " Gateway(gatewayId='scigap', emailAddress=None, domain='SciGaP Portal', gatewayName=None),\n", + " Gateway(gatewayId='scigap-physics', emailAddress=None, domain='Physics Gateway', gatewayName=None),\n", + " Gateway(gatewayId='scigap-weather', emailAddress=None, domain='Wether Forecasting Gateway', gatewayName=None),\n", + " Gateway(gatewayId='sdfsdf', emailAddress=None, domain='sdfsdf', gatewayName=None),\n", + " Gateway(gatewayId='seagrid', emailAddress=None, domain='SEAGrid Portal', gatewayName=None),\n", + " Gateway(gatewayId='simvascular', emailAddress=None, domain='SimVascular', gatewayName=None),\n", + " Gateway(gatewayId='southdakota', emailAddress=None, domain='South Dakota CyberGateway', gatewayName=None),\n", + " Gateway(gatewayId='southill', emailAddress=None, domain='Southern Illinois PHP Gateway', gatewayName=None),\n", + " Gateway(gatewayId='TestResearch1', emailAddress=None, domain='TestResearch1', gatewayName=None),\n", + " Gateway(gatewayId='utah', emailAddress=None, domain='Utah-Gateway', gatewayName=None)]" ] }, "execution_count": 3, @@ -99,15 +124,47 @@ { "data": { "text/plain": [ - "[('alamo.uthscsa.edu_4793b5cc-b991-4e43-b82d-17163b64ef29',\n", + "[('jetstream.chemcompute.org_d87012a7-afbd-4439-b199-c5141045ea4d',\n", + " 'jetstream.chemcompute.org'),\n", + " ('series.usda.gov_46bd9f3e-ab96-463b-ab5e-4e7cc527694f', 'series.usda.gov'),\n", + " ('smic.hpc.lsu.edu_6b72d6d8-533b-42f5-9a67-8a596f719fe7', 'smic.hpc.lsu.edu'),\n", + " ('ember.chpc.utah.edu_6fd6fb6f-4656-40d3-afa4-3521407cf14b',\n", + " 'ember.chpc.utah.edu'),\n", + " ('mason.uits.iu.edu_4910ad55-317b-49c9-8cc1-032da55f974a',\n", + " 'mason.uits.iu.edu'),\n", + " ('JetStream_3fe9cc27-26f2-45a7-bccd-c6c07d70e881',\n", + " 'js-170-153.jetstream-cloud.org'),\n", + " ('test_511bb8bd-b2ef-423e-958e-7a0531226dbe', 'test'),\n", + " ('BlueWaterII_9db6f84b-a099-40db-8d51-0f81b716b4cd', 'BlueWaterII'),\n", + " ('tandy.oii.org_93580801-f1ae-4faa-a052-46a8e21a8772',\n", + " 'tcs.tandysupercomputing.org'),\n", + " ('gordon.sdsc.edu_bb11b481-fe7e-44d4-95ba-d3ffcd08bf08', 'gordon.sdsc.edu'),\n", + " ('TestKarst_ef43b68c-9fe6-419c-873e-f3efc63aeef7', 'TestKarst'),\n", + " ('hpclogin.gsu.edu_964e7e13-f278-4bf5-8482-c8f07b556d52', 'hpclogin.gsu.edu'),\n", + " ('hpc.usd.edu_b4bd47b0-6093-4166-8c02-c882bf6657af', 'hpc.usd.edu'),\n", + " ('schooner.oscer.ou.edu_d5a3bcef-93c9-44c0-acea-c79095b50a38',\n", + " 'schooner.oscer.ou.edu'),\n", + " ('bridges.psc.edu_8e9bcd61-1f55-4926-a9b4-0cbe3d0eee8c', 'bridges.psc.edu'),\n", + " ('stampede.tacc.xsede.org_ea585ade-831f-4ad1-91c6-d897fb170e3b',\n", + " 'stampede.tacc.xsede.org'),\n", + " ('karst.uits.iu.edu_a9a65e7d-d104-4c11-829b-412168bed7a8',\n", + " 'karst.uits.iu.edu'),\n", + " ('philip.hpc.lsu.edu_ae3007b2-93ea-4817-a7c1-2ed79061d182',\n", + " 'philip.hpc.lsu.edu'),\n", + " ('login-knl1.stampede.tacc.utexas.edu_5ea26511-1fa6-407d-93a8-7552a301ee53',\n", + " 'login-knl1.stampede.tacc.utexas.edu'),\n", + " ('js-156-20.jetstream-cloud.org_e9d76f84-2869-4d43-9d12-54320d10286f',\n", + " 'js-156-20.jetstream-cloud.org'),\n", + " ('bigred2.uits.iu.edu_ac140dca-3c88-46d8-b9ed-875d96ea6908',\n", + " 'bigred2.uits.iu.edu'),\n", + " ('kingspeak_0c37628f-ed16-414c-82a5-25d0fc031f8d', 'kingspeak.chpc.utah.edu'),\n", + " ('alamo.uthscsa.edu_5612cc49-e6ba-4e53-bb9a-7741e95ce98b',\n", " 'alamo.uthscsa.edu'),\n", - " ('Jureca_32098185-4396-4c11-afb7-26e991a03476', 'Jureca'),\n", - " ('comet.sdsc.edu_f24b0bba-5230-498d-97e2-46a975ee035b', 'comet.sdsc.edu'),\n", - " ('gordon.sdsc.edu_f9363997-4614-477f-847e-79d262ee8ef7', 'gordon.sdsc.edu'),\n", - " ('ls5.tacc.utexas.edu_6dd67b08-30e5-4f74-bdd6-aad1f8310ecf',\n", - " 'ls5.tacc.utexas.edu'),\n", - " ('stampede.tacc.xsede.org_bf7958ae-f9d4-468b-b146-a201fb89bf12',\n", - " 'stampede.tacc.xsede.org')]" + " ('comet.sdsc.edu_91b900df-0ee0-4909-89b3-98e8f64e1969', 'comet.sdsc.edu'),\n", + " ('login-ld.research.siu.edu_7e01b6fe-3e16-430c-9935-4b002fc868cd',\n", + " 'login-ld.research.siu.edu'),\n", + " ('lonestar.tacc.utexas.edu_0d2d81a2-af4f-48c3-8be9-2093ebe2b866',\n", + " 'lonestar.tacc.utexas.edu')]" ] }, "execution_count": 4, @@ -141,46 +198,194 @@ " <tbody>\n", " <tr>\n", " <th>0</th>\n", - " <td>alamo.uthscsa.edu_4793b5cc-b991-4e43-b82d-1716...</td>\n", - " <td>alamo.uthscsa.edu</td>\n", + " <td>jetstream.chemcompute.org_d87012a7-afbd-4439-b...</td>\n", + " <td>jetstream.chemcompute.org</td>\n", " </tr>\n", " <tr>\n", " <th>1</th>\n", - " <td>Jureca_32098185-4396-4c11-afb7-26e991a03476</td>\n", - " <td>Jureca</td>\n", + " <td>series.usda.gov_46bd9f3e-ab96-463b-ab5e-4e7cc5...</td>\n", + " <td>series.usda.gov</td>\n", " </tr>\n", " <tr>\n", " <th>2</th>\n", - " <td>comet.sdsc.edu_f24b0bba-5230-498d-97e2-46a975e...</td>\n", - " <td>comet.sdsc.edu</td>\n", + " <td>smic.hpc.lsu.edu_6b72d6d8-533b-42f5-9a67-8a596...</td>\n", + " <td>smic.hpc.lsu.edu</td>\n", " </tr>\n", " <tr>\n", " <th>3</th>\n", - " <td>gordon.sdsc.edu_f9363997-4614-477f-847e-79d262...</td>\n", - " <td>gordon.sdsc.edu</td>\n", + " <td>ember.chpc.utah.edu_6fd6fb6f-4656-40d3-afa4-35...</td>\n", + " <td>ember.chpc.utah.edu</td>\n", " </tr>\n", " <tr>\n", " <th>4</th>\n", - " <td>ls5.tacc.utexas.edu_6dd67b08-30e5-4f74-bdd6-aa...</td>\n", - " <td>ls5.tacc.utexas.edu</td>\n", + " <td>mason.uits.iu.edu_4910ad55-317b-49c9-8cc1-032d...</td>\n", + " <td>mason.uits.iu.edu</td>\n", " </tr>\n", " <tr>\n", " <th>5</th>\n", - " <td>stampede.tacc.xsede.org_bf7958ae-f9d4-468b-b14...</td>\n", + " <td>JetStream_3fe9cc27-26f2-45a7-bccd-c6c07d70e881</td>\n", + " <td>js-170-153.jetstream-cloud.org</td>\n", + " </tr>\n", + " <tr>\n", + " <th>6</th>\n", + " <td>test_511bb8bd-b2ef-423e-958e-7a0531226dbe</td>\n", + " <td>test</td>\n", + " </tr>\n", + " <tr>\n", + " <th>7</th>\n", + " <td>BlueWaterII_9db6f84b-a099-40db-8d51-0f81b716b4cd</td>\n", + " <td>BlueWaterII</td>\n", + " </tr>\n", + " <tr>\n", + " <th>8</th>\n", + " <td>tandy.oii.org_93580801-f1ae-4faa-a052-46a8e21a...</td>\n", + " <td>tcs.tandysupercomputing.org</td>\n", + " </tr>\n", + " <tr>\n", + " <th>9</th>\n", + " <td>gordon.sdsc.edu_bb11b481-fe7e-44d4-95ba-d3ffcd...</td>\n", + " <td>gordon.sdsc.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>10</th>\n", + " <td>TestKarst_ef43b68c-9fe6-419c-873e-f3efc63aeef7</td>\n", + " <td>TestKarst</td>\n", + " </tr>\n", + " <tr>\n", + " <th>11</th>\n", + " <td>hpclogin.gsu.edu_964e7e13-f278-4bf5-8482-c8f07...</td>\n", + " <td>hpclogin.gsu.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>12</th>\n", + " <td>hpc.usd.edu_b4bd47b0-6093-4166-8c02-c882bf6657af</td>\n", + " <td>hpc.usd.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>13</th>\n", + " <td>schooner.oscer.ou.edu_d5a3bcef-93c9-44c0-acea-...</td>\n", + " <td>schooner.oscer.ou.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>14</th>\n", + " <td>bridges.psc.edu_8e9bcd61-1f55-4926-a9b4-0cbe3d...</td>\n", + " <td>bridges.psc.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>15</th>\n", + " <td>stampede.tacc.xsede.org_ea585ade-831f-4ad1-91c...</td>\n", " <td>stampede.tacc.xsede.org</td>\n", " </tr>\n", + " <tr>\n", + " <th>16</th>\n", + " <td>karst.uits.iu.edu_a9a65e7d-d104-4c11-829b-4121...</td>\n", + " <td>karst.uits.iu.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>17</th>\n", + " <td>philip.hpc.lsu.edu_ae3007b2-93ea-4817-a7c1-2ed...</td>\n", + " <td>philip.hpc.lsu.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>18</th>\n", + " <td>login-knl1.stampede.tacc.utexas.edu_5ea26511-1...</td>\n", + " <td>login-knl1.stampede.tacc.utexas.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>19</th>\n", + " <td>js-156-20.jetstream-cloud.org_e9d76f84-2869-4d...</td>\n", + " <td>js-156-20.jetstream-cloud.org</td>\n", + " </tr>\n", + " <tr>\n", + " <th>20</th>\n", + " <td>bigred2.uits.iu.edu_ac140dca-3c88-46d8-b9ed-87...</td>\n", + " <td>bigred2.uits.iu.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>21</th>\n", + " <td>kingspeak_0c37628f-ed16-414c-82a5-25d0fc031f8d</td>\n", + " <td>kingspeak.chpc.utah.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>22</th>\n", + " <td>alamo.uthscsa.edu_5612cc49-e6ba-4e53-bb9a-7741...</td>\n", + " <td>alamo.uthscsa.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>23</th>\n", + " <td>comet.sdsc.edu_91b900df-0ee0-4909-89b3-98e8f64...</td>\n", + " <td>comet.sdsc.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>24</th>\n", + " <td>login-ld.research.siu.edu_7e01b6fe-3e16-430c-9...</td>\n", + " <td>login-ld.research.siu.edu</td>\n", + " </tr>\n", + " <tr>\n", + " <th>25</th>\n", + " <td>lonestar.tacc.utexas.edu_0d2d81a2-af4f-48c3-8b...</td>\n", + " <td>lonestar.tacc.utexas.edu</td>\n", + " </tr>\n", " </tbody>\n", "</table>\n", "</div>" ], "text/plain": [ - " Id Name\n", - "0 alamo.uthscsa.edu_4793b5cc-b991-4e43-b82d-1716... alamo.uthscsa.edu\n", - "1 Jureca_32098185-4396-4c11-afb7-26e991a03476 Jureca\n", - "2 comet.sdsc.edu_f24b0bba-5230-498d-97e2-46a975e... comet.sdsc.edu\n", - "3 gordon.sdsc.edu_f9363997-4614-477f-847e-79d262... gordon.sdsc.edu\n", - "4 ls5.tacc.utexas.edu_6dd67b08-30e5-4f74-bdd6-aa... ls5.tacc.utexas.edu\n", - "5 stampede.tacc.xsede.org_bf7958ae-f9d4-468b-b14... stampede.tacc.xsede.org" + " Id \\\n", + "0 jetstream.chemcompute.org_d87012a7-afbd-4439-b... \n", + "1 series.usda.gov_46bd9f3e-ab96-463b-ab5e-4e7cc5... \n", + "2 smic.hpc.lsu.edu_6b72d6d8-533b-42f5-9a67-8a596... \n", + "3 ember.chpc.utah.edu_6fd6fb6f-4656-40d3-afa4-35... \n", + "4 mason.uits.iu.edu_4910ad55-317b-49c9-8cc1-032d... \n", + "5 JetStream_3fe9cc27-26f2-45a7-bccd-c6c07d70e881 \n", + "6 test_511bb8bd-b2ef-423e-958e-7a0531226dbe \n", + "7 BlueWaterII_9db6f84b-a099-40db-8d51-0f81b716b4cd \n", + "8 tandy.oii.org_93580801-f1ae-4faa-a052-46a8e21a... \n", + "9 gordon.sdsc.edu_bb11b481-fe7e-44d4-95ba-d3ffcd... \n", + "10 TestKarst_ef43b68c-9fe6-419c-873e-f3efc63aeef7 \n", + "11 hpclogin.gsu.edu_964e7e13-f278-4bf5-8482-c8f07... \n", + "12 hpc.usd.edu_b4bd47b0-6093-4166-8c02-c882bf6657af \n", + "13 schooner.oscer.ou.edu_d5a3bcef-93c9-44c0-acea-... \n", + "14 bridges.psc.edu_8e9bcd61-1f55-4926-a9b4-0cbe3d... \n", + "15 stampede.tacc.xsede.org_ea585ade-831f-4ad1-91c... \n", + "16 karst.uits.iu.edu_a9a65e7d-d104-4c11-829b-4121... \n", + "17 philip.hpc.lsu.edu_ae3007b2-93ea-4817-a7c1-2ed... \n", + "18 login-knl1.stampede.tacc.utexas.edu_5ea26511-1... \n", + "19 js-156-20.jetstream-cloud.org_e9d76f84-2869-4d... \n", + "20 bigred2.uits.iu.edu_ac140dca-3c88-46d8-b9ed-87... \n", + "21 kingspeak_0c37628f-ed16-414c-82a5-25d0fc031f8d \n", + "22 alamo.uthscsa.edu_5612cc49-e6ba-4e53-bb9a-7741... \n", + "23 comet.sdsc.edu_91b900df-0ee0-4909-89b3-98e8f64... \n", + "24 login-ld.research.siu.edu_7e01b6fe-3e16-430c-9... \n", + "25 lonestar.tacc.utexas.edu_0d2d81a2-af4f-48c3-8b... \n", + "\n", + " Name \n", + "0 jetstream.chemcompute.org \n", + "1 series.usda.gov \n", + "2 smic.hpc.lsu.edu \n", + "3 ember.chpc.utah.edu \n", + "4 mason.uits.iu.edu \n", + "5 js-170-153.jetstream-cloud.org \n", + "6 test \n", + "7 BlueWaterII \n", + "8 tcs.tandysupercomputing.org \n", + "9 gordon.sdsc.edu \n", + "10 TestKarst \n", + "11 hpclogin.gsu.edu \n", + "12 hpc.usd.edu \n", + "13 schooner.oscer.ou.edu \n", + "14 bridges.psc.edu \n", + "15 stampede.tacc.xsede.org \n", + "16 karst.uits.iu.edu \n", + "17 philip.hpc.lsu.edu \n", + "18 login-knl1.stampede.tacc.utexas.edu \n", + "19 js-156-20.jetstream-cloud.org \n", + "20 bigred2.uits.iu.edu \n", + "21 kingspeak.chpc.utah.edu \n", + "22 alamo.uthscsa.edu \n", + "23 comet.sdsc.edu \n", + "24 login-ld.research.siu.edu \n", + "25 lonestar.tacc.utexas.edu " ] }, "execution_count": 5, @@ -213,8 +418,39 @@ { "data": { "text/plain": [ - "[ApplicationInterfaceDescription(applicationName='Ultrascan', applicationInputs=[InputDataObjectType(userFriendlyDescription='Ultrascan HPC Input Tar File', name='Input_Tar_File', dataStaged=False, value='', applicationArgument='', isRequired=False, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='Batches for multi-wavelength data processing', name='Parallel_Group_Count', dataStaged=False, value='-mgroupcount=1', applicationArgument='', isRequired=False, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='Wall Clock Limit on the Compute Resource', name='Wall_Time', dataStaged=False, value='-walltime=60', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=2, metaData='')], applicationInterfaceId='Ultrascan_0ed937f6-26af-4c54-8064-3be082411e46 ', applicationDescription='Ultrascan Version 3 Interface', applicationOutputs=[OutputDataObjectType(dataMovement=True, name='output', value='output/analysis-results.tar', applicationArgument='', isRequired=True, searchQuery='', location='output', requiredToAddedToCommandLine=False, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=True, name='Ultrascan-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5), OutputDataObjectType(dataMovement=True, name='Ultrascan-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=4)], applicationModules=['Ultrascan_82282f1e-284f-4999-9beb-4620c485b03d']),\n", - " ApplicationInterfaceDescription(applicationName='Ultrascan_Unicore', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='Input', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='', name='mgroupcount', dataStaged=False, value='-mgroupcount 1', applicationArgument='', isRequired=False, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=2, metaData=''), InputDataObjectType(userFriendlyDescription='', name='US3INPUTARG', dataStaged=False, value='', applicationArgument='', isRequired=False, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=4, metaData=''), InputDataObjectType(userFriendlyDescription='', name='walltime', dataStaged=False, value='-walltime 60', applicationArgument='', isRequired=False, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=3, metaData='')], applicationInterfaceId='Ultrascan_Unicore_0e7f8522-6d75-41ba-8b09-0021e728679a', applicationDescription='Unicore Service', applicationOutputs=[OutputDataObjectType(dataMovement=True, name='Ultrascan-Unicore-Standard-Error', value='', applicationArgument='', isRequired=False, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5), OutputDataObjectType(dataMovement=True, name='Ultrascan-Unicore-Standard-Out', value='', applicationArgument='', isRequired=False, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=4), OutputDataObjectType(dataMovement=True, name='US3OUT', value='analysis-results.tar', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=0)], applicationModules=['Ultrascan_Unicore_2471953d-5d87-4ffc-b0e6-b06c86c6206d'])]" + "[ApplicationInterfaceDescription(applicationName='Echo', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='Input-to-Echo', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=1, metaData='')], applicationInterfaceId='Echo_3f480d1f-ea86-4018-94bb-015423d66a1c', applicationDescription='Simple Echo Application Interface', applicationOutputs=[OutputDataObjectType(dataMovement=False, 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name='Parameter-Topology-File', dataStaged=False, value='', applicationArgument='-p', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='Constant pressure and temperature for production stage - 03_Prod.in', name='Production-Control-File', dataStaged=False, value='', applicationArgument='-i', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=2, metaData='')], applicationInter faceId='Amber_Sander_27b68571-b9c0-4bd5-bd70-e29435fa81bd', applicationDescription='Assisted Model Building with Energy Refinement MD Package', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Amber-Execution-Log', value='03_Prod.out', applicationArgument='-o', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Amber-Execution-Summary', 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requiredToAddedToCommandLine=True, outputStreaming=False, type=3)], applicationModules=['Amber-Sander_e8ce4375-aa60-4dd9-aff5-61bbe1f275c0']),\n", + " ApplicationInterfaceDescription(applicationName='Gaussian', applicationInputs=[InputDataObjectType(userFriendlyDescription='Gaussian input file specifying desired calculation type, model chemistry, molecular system and other parameters.', name='Input-File', dataStaged=False, value='gaussian.com', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData='')], applicationInterfaceId='Gaussian_4e76aecd-d504-4ce2-9ccf-da9550159e7c', applicationDescription='Gaussian provides capabilities for electronic structure modeling.', applicationOutputs=[OutputDataObjectType(dataMovement=True, name='Gaussian-Application-Output', value='gaussian.log', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=True, name='Gaussian-Checkpoint-File', value='*.chk', applicationArgument='', isRequired=False, searchQ uery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Gaussian-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Gaussian-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Gaussian_57eb2905-1cd8-400e-ad40-cadfba8f434f']),\n", + " ApplicationInterfaceDescription(applicationName='AutoDock', applicationInputs=[InputDataObjectType(userFriendlyDescription='hsg1.maps.fld', name='HSG1-Maps-FLD', dataStaged=False, value='', applicationArgument='', isRequired=True, 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requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData='')], applicationInterfaceId='GROMACS_f0773c7e-9d89-4ad4-aa76-c3aefa2ebe78', applicationDescription='GROMACS Molecular Dynamics Package', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Gromacs-Execution-Log', value='pdb1y 6l-EM-vacuum.tpr.log', applicationArgument='-g', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Gromacs-Portable-Energy-File', value='pdb1y6l-EM-vacuum.tpr.edr', applicationArgument='-e', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Gromacs-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Gromacs-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=5)], applicationModules=['Gromacs_17f97a2e-bdea-4075-9425-6bde4a8d1317']),\n", + " ApplicationInterfaceDescription(applicationName='Lammps_BR2', applicationInputs=[InputDataObjectType(userFriendlyDescription='Friction Simulation Input - in.friction', name='Friction-Simulation-Input', dataStaged=False, value='', applicationArgument='-cuda off -suffix gpu <', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData='')], applicationInterfaceId='Lammps_BR2_965cdc59-f6c8-4146-ad27-e26a53b75c12', applicationDescription='Large-scale Atomic/Molecular Massively Parallel Simulator', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Lammps-Application-Output', value='log.lammps', applicationArgument='>', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Lammps-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, out putStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Lammps-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Lammps_1f150b05-6295-43c5-8040-27992693cef6']),\n", + " ApplicationInterfaceDescription(applicationName='NWChem', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='Water-Molecule-Input', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData='')], applicationInterfaceId='NWChem_461f6aae-5bab-43cf-8db9-02f472054bad', applicationDescription='Ab initio computational chemistry software package', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='NWChem-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='NWChem-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['NWChem_2f38a95e-c2aa-4db3-b1bf-2adb006a34bc']), \n", + " ApplicationInterfaceDescription(applicationName='Gamess_BR2', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='Input-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='', name='PPN', dataStaged=False, value='16', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=4, metaData=''), InputDataObjectType(userFriendlyDescription='', name='Processes-Per-Job', dataStaged=False, value='16', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='', name='Version', dataStaged=False, value='01', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=2, metaDa ta='')], applicationInterfaceId='Gamess_BR2_55f48919-c067-4c72-9a83-3d02325857a7', applicationDescription='Gamess Application in BigRedII', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Gamess-Standard-out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5), OutputDataObjectType(dataMovement=False, name='Gamess_Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6)], applicationModules=['Gamess_BR2_5c979001-d994-47fb-a9af-5227ff5c5c55']),\n", + " ApplicationInterfaceDescription(applicationName='NEK5000', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='Basename', dataStaged=False, value='nek5kbasename', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=0, metaData=''), InputDataObjectType(userFriendlyDescription='.rea File', name='Runtime-Parameter-File', dataStaged=False, value='nek5kbasename.rea', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=2, metaData=''), InputDataObjectType(userFriendlyDescription='SIZE File', name='Size-for-Memory-Allocation', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='.usr File', name='User-Subroutine-File', dataStaged=False, value='nek5kbasename.usr', applicationArgument ='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=1, metaData='')], applicationInterfaceId='NEK5000_8759b170-f825-444a-a86c-7927c4133b7a', applicationDescription='', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='NEK5000-Compilation-Output', value='compiler.out', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='NEK5000-Output_tarball', value='nek5kbasename.tgz', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='NEK5000-Session-Out', value='session.log', applicationArgument='>', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='NEK5000-Standard -Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='NEK5000-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['NEK5000_35922b60-f0ad-41dd-8b3c-7877617767d8']),\n", + " ApplicationInterfaceDescription(applicationName='Abinit', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='ModulePath', dataStaged=False, value='$MODULEPATH', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=0, inputOrder=4, metaData=''), InputDataObjectType(userFriendlyDescription='01h.pspgth', name='Pspgth-Input-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='tbase1_files.in', name='Tbase-Input-File-1', dataStaged=False, value='', applicationArgument='<', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='tbase1_2.in', name='Tbase-Input-File-2', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=Fals e, requiredToAddedToCommandLine=False, type=3, inputOrder=2, metaData='')], applicationInterfaceId='Abinit_5d1f0755-c879-41b5-a3d0-9dc5672e33c7', applicationDescription='ABINIT is a package whose main program allows one to find the total energy, charge 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applicationInputs=[InputDataObjectType(userFriendlyDescription='AI_Metal_Input_File - Al.sample.in', name='AI-Primitive-Cell', dataStaged=False, value='', applicationArgument='<', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='Constant pressure and temperature for production stage - Al.pz-vbc.UPF', name='AI-Pseudopotential-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=0, metaData='')], applicationInterfaceId='Quantum_Espresso_d83e7aac-9ccc-451b-b856-d92f5e7b7372', applicationDescription='Nanoscale electronic-structure calculations and materials modeling', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Quantum-Espresso-Execution-Log', value='Al.sample.out', applicationArgument='> ', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='QuantumEspresso-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='QuantumEspresso-StandardOut', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Quantum_Espresso_cf47dccc-c870-4e76-be68-784a1574426e']),\n", + " ApplicationInterfaceDescription(applicationName='Lammps', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='Friction-Simulation-Input', dataStaged=False, value='', applicationArgument='<', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData='')], applicationInterfaceId='Lammps_1284f9d9-d039-47ec-a885-6792caa26510', applicationDescription='Large-scale Atomic/Molecular Massively Parallel Simulator', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Lammps-Application-Output', value='log.lammps', applicationArgument='>', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Lammps-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Lammps-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Lammps_4e799726-669e-4b87-9a7d-9d567d83c1c7']),\n", + " ApplicationInterfaceDescription(applicationName='CP2K', applicationInputs=[InputDataObjectType(userFriendlyDescription='Input file for CP2K - 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type=5)], applicationModules=['CP2K_3d1895c9-03e1-4ba7-96b3-94bf2c88c865']),\n", + " ApplicationInterfaceDescription(applicationName='Phasta_P', applicationInputs=[InputDataObjectType(userFriendlyDescription='Mesh Description - geom.sms', name='Mesh-Description-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='', name='Parasolid-Geometric-Model', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='problem definition - geom.smd', name='Problem-Definition', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=2, metaData=''), InputDataObjectType(userFriendlyDescription='solver 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requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Phasta_P_681394ed- 212a-404e-b336-e5d41593016f']),\n", + " ApplicationInterfaceDescription(applicationName='Gamess', applicationInputs=[InputDataObjectType(userFriendlyDescription='Gamess Input file', name='Input-File', dataStaged=True, value='gamess.inp', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='', name='PPN', dataStaged=False, value='4', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='', name='Version', dataStaged=False, value='00', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=2, metaData='')], applicationInterfaceId='Gamess_43fd2803-f388-4b79-b131-ec52ac023b5b', applicationDescription='Gamess Application', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Gamess-Standard-Error', v alue='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Gamess-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Gamess_6ed12ada-a6a7-4df5-b044-b9a5e2b0c49b']),\n", + " ApplicationInterfaceDescription(applicationName='Tinker_Monte', applicationInputs=[InputDataObjectType(userFriendlyDescription='Tinker monte input_4', name='Ctc', dataStaged=False, value='C', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=4, metaData=''), InputDataObjectType(userFriendlyDescription='Tinker monte input_2', name='keyf', dataStaged=False, value='O16.key', applicationArgument='-k', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=2, metaData=''), InputDataObjectType(userFriendlyDescription='Tinker monte input_7', name='Rconv', dataStaged=False, value='0.01', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=2, inputOrder=7, metaData=''), InputDataObjectType(userFriendlyDescription='Tinker monte input_3', name='stps', dataStaged=False, value='20000', applicationArgument='', isRequired=True, standardIn put=False, requiredToAddedToCommandLine=True, type=0, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='Tinker monte input_5', name='stpsZ', dataStaged=False, value='3.0', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=5, metaData=''), InputDataObjectType(userFriendlyDescription='Tinker monte input_6', name='temp', 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applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Echo-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Echo-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Echo_19dc358d-d241-43d8-918c-f5a21a3b0845']),\n", + " ApplicationInterfaceDescription(applicationName='Trinity', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='CPU', dataStaged=False, value='4', applicationArgument='--cpu', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=1, inputOrder=6, metaData=''), InputDataObjectType(userFriendlyDescription='', name='Max-Heapspace', dataStaged=False, value='2G', applicationArgument='--bflyHeapSpaceMax', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=7, metaData=''), InputDataObjectType(userFriendlyDescription='', name='Max_Memory', dataStaged=False, value='4G', applicationArgument='--max_memory', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=2, metaData=''), InputDataObjectType(userFriendlyDescription='', name='Rna-Seq-Right-Input', dataStaged=False, value='', applicationArgument='--right', isRequired=True, standardInput=False, requiredToAddedTo CommandLine=True, type=3, inputOrder=4, metaData=''), InputDataObjectType(userFriendlyDescription='', name='Rna-Seq_Left_Input', dataStaged=False, value='', applicationArgument='--left', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='', name='Seq_type', dataStaged=False, value='fq', applicationArgument='--seqType', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='', name='SS-Lib_Type', dataStaged=False, value='RF', applicationArgument='--SS_lib_typ', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=5, metaData='')], applicationInterfaceId='Trinity_82ec9f8d-790f-4909-9ad1-e010632736f9', applicationDescription='De novo reconstruction of transcriptomes from RNA-seq data', applicationOutputs=[OutputDataObjectType(dataMovement=False, nam e='Trinity_Execution-Log', value='trinity.timing', applicationArgument='--output ./trinity_out_dir', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Trinity_FASTA_File', value='Trinity.fasta', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=True, name='Trinity_Standard-Error', value='Trinity_stderror', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=0), OutputDataObjectType(dataMovement=True, name='Trinity_Stdout', value='Trinity_stdout', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=0)], applicationModules=['Trinity_b32b104d-501e-42f6-a35a-18540190cf2e']),\n", + " ApplicationInterfaceDescription(applicationName='Gaussian16', applicationInputs=[InputDataObjectType(userFriendlyDescription='Gaussian input file specifying desired calculation type, model chemistry, molecular system and other parameters.', name='Input-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData='')], applicationInterfaceId='Gaussian16_8e065560-9b1e-443c-b59c-e919b677039d', applicationDescription='Gaussian provides capabilities for electronic structure modeling.', applicationOutputs=[OutputDataObjectType(dataMovement=True, name='Gaussian-Application-Output', value='gaussian.log', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Gaussian-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', loca tion='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Gaussian-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Gaussian16_3e749c7d-6b02-4356-acc3-a58423210bda']),\n", + " ApplicationInterfaceDescription(applicationName='Amber_pmemd', applicationInputs=[InputDataObjectType(userFriendlyDescription='Heating up the system equilibration stage - 02_Heat.rst', name='Heat-Restart-File', dataStaged=False, value='', applicationArgument='-c', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='Parameter and Topology coordinates - prmtop', name='Parameter-Topology-File', dataStaged=False, value='', applicationArgument='-p', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='Constant pressure and temperature for production stage - 03_Prod.in', name='Production-Control-File', dataStaged=False, value='', applicationArgument='-i', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=2, metaData=''), InputDataObjectTyp e(userFriendlyDescription='The reference structure is specified using the -ref flag in the same manner as is used for Cartesian coordinate restraints (NTR=1). Targeted MD can be used with\\r\\nor without positional restraints.', name='Reference-coordinate-file', dataStaged=False, value='', applicationArgument='-ref', isRequired=False, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=4, metaData='')], applicationInterfaceId='Amber_pmemd_274841f0-3b5e-4b74-8eb1-dd66283c5057', applicationDescription='Assisted Model Building with Energy Refinement MD Package', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Amber-Execution-Log', value='03_Prod.out', applicationArgument='-o', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Amber-Execution-Summary', value='03_Prod.info', applicationArgument='-inf', isRequired=True, searchQuery='', loc ation='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Amber-Restart-File', value='03_Prod.rst', applicationArgument='-r', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Amber-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Amber-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5), OutputDataObjectType(dataMovement=False, name='Amber-Trajectory-File', value='03_Prod.mdcrd', applicationArgument='-x', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3)], applicationModules=['Amb er-Sander_e8ce4375-aa60-4dd9-aff5-61bbe1f275c0']),\n", + " ApplicationInterfaceDescription(applicationName='Amber-pmemd-min', applicationInputs=[InputDataObjectType(userFriendlyDescription='Heating up the system equilibration stage - 02_Heat.rst', name='Amber-Coordinates-file', dataStaged=False, value='', applicationArgument='-c', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='Parameter and Topology coordinates - prmtop', name='Parameter-Topology-File', dataStaged=False, value='', applicationArgument='-p', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='Input file with simulations conditions', name='Production-Control-Input-File', dataStaged=False, value='', applicationArgument='-i', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=2, metaData='')], applicationInterfaceId='Amber-p memd-min_10df4de9-bc80-491b-878b-97742b9519ae', applicationDescription='Assisted Model Building with Energy Refinement MD Package', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Amber-Execution-Log', value='03_Prod.out', applicationArgument='-o', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Amber-Execution-Summary', value='03_Prod.info', applicationArgument='-inf', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Amber-Restart-File', value='03_Prod.rst', applicationArgument='-r', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='Amber-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', re quiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Amber-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5), OutputDataObjectType(dataMovement=False, name='Amber-Trajectory-File', value='03_Prod.mdcrd', applicationArgument='-x', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3)], applicationModules=['Amber-Sander_e8ce4375-aa60-4dd9-aff5-61bbe1f275c0'])]" ] }, "execution_count": 6, @@ -223,22 +459,51 @@ } ], "source": [ - "airavata_cli.list_of_applications('Ultrascan_Production')" + "airavata_cli.list_of_applications('seagrid')" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { - "collapsed": false, - "scrolled": true + "collapsed": false }, "outputs": [ { "data": { "text/plain": [ - "[ApplicationModule(appModuleName='Ultrascan', appModuleVersion='Ultrascan Application', appModuleId='Ultrascan_82282f1e-284f-4999-9beb-4620c485b03d', appModuleDescription=''),\n", - " ApplicationModule(appModuleName='Ultrascan_Unicore', appModuleVersion='', appModuleId='Ultrascan_Unicore_2471953d-5d87-4ffc-b0e6-b06c86c6206d', appModuleDescription='Ultrascan Unicore Application')]" + "[ApplicationModule(appModuleName='Echo', appModuleVersion='', appModuleId='Echo_19dc358d-d241-43d8-918c-f5a21a3b0845', appModuleDescription='A Simple Echo Application'),\n", + " ApplicationModule(appModuleName='Amber_Sander', appModuleVersion='', appModuleId='Amber-Sander_e8ce4375-aa60-4dd9-aff5-61bbe1f275c0', appModuleDescription='Assisted Model Building with Energy Refinement MD Package'),\n", + " ApplicationModule(appModuleName='Gaussian', appModuleVersion='', appModuleId='Gaussian_57eb2905-1cd8-400e-ad40-cadfba8f434f', appModuleDescription='Gaussian provides capabilities for electronic structure modeling.'),\n", + " ApplicationModule(appModuleName='AutoDock', appModuleVersion='', appModuleId='AutoDock_24d6d7da-1160-45b0-9958-63bcc9044804', appModuleDescription='AutoDock suite of automated docking tools'),\n", + " ApplicationModule(appModuleName='Gromacs', appModuleVersion='', appModuleId='Gromacs_17f97a2e-bdea-4075-9425-6bde4a8d1317', appModuleDescription='GROMACS Molecular Dynamics Package'),\n", + " ApplicationModule(appModuleName='Lammps_BR2', appModuleVersion='', appModuleId='Lammps_1f150b05-6295-43c5-8040-27992693cef6', appModuleDescription='Large-scale Atomic/Molecular Massively Parallel Simulator for BigRedII'),\n", + " ApplicationModule(appModuleName='NWChem', appModuleVersion='', appModuleId='NWChem_2f38a95e-c2aa-4db3-b1bf-2adb006a34bc', appModuleDescription='Ab initio computational chemistry software package'),\n", + " ApplicationModule(appModuleName='Gamess_BR2', appModuleVersion='', appModuleId='Gamess_BR2_5c979001-d994-47fb-a9af-5227ff5c5c55', appModuleDescription='A Gamess Application in BigRedII'),\n", + " ApplicationModule(appModuleName='NEK5000', appModuleVersion='', appModuleId='NEK5000_35922b60-f0ad-41dd-8b3c-7877617767d8', appModuleDescription='Open source, highly scalable and portable spectral element code designed to simulate fluid flows about objects.'),\n", + " ApplicationModule(appModuleName='Abinit', appModuleVersion='', appModuleId='Abinit_34e497ac-28cd-42a2-afe0-1ee99f173c6d', appModuleDescription='ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT)'),\n", + " ApplicationModule(appModuleName='Quantum_Espresso', appModuleVersion='', appModuleId='Quantum_Espresso_cf47dccc-c870-4e76-be68-784a1574426e', appModuleDescription='Nanoscale electronic-structure calculations and materials modeling'),\n", + " ApplicationModule(appModuleName='Lammps', appModuleVersion='', appModuleId='Lammps_4e799726-669e-4b87-9a7d-9d567d83c1c7', appModuleDescription='Large-scale Atomic/Molecular Massively Parallel Simulator'),\n", + " ApplicationModule(appModuleName='CP2K', appModuleVersion='', appModuleId='CP2K_3d1895c9-03e1-4ba7-96b3-94bf2c88c865', appModuleDescription='CP2K Test Application Module'),\n", + " ApplicationModule(appModuleName='Phasta_P', appModuleVersion='', appModuleId='Phasta_P_681394ed-212a-404e-b336-e5d41593016f', appModuleDescription='Parallel version of PHASTA'),\n", + " ApplicationModule(appModuleName='Gamess', appModuleVersion='', appModuleId='Gamess_6ed12ada-a6a7-4df5-b044-b9a5e2b0c49b', appModuleDescription='Gamess Application'),\n", + " ApplicationModule(appModuleName='Tinker_Monte', appModuleVersion='', appModuleId='Tinker_Monte_b11b893a-626b-4778-997a-2da92537b4b7', appModuleDescription='GridChem Tinker Monte Application'),\n", + " ApplicationModule(appModuleName='CPMD', appModuleVersion='', appModuleId='CPMD_6870dafa-e2e3-4fe6-a0e2-5b11c1436af4', appModuleDescription='parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.'),\n", + " ApplicationModule(appModuleName='QChem', appModuleVersion='', appModuleId='QChem_9214bc96-2bf8-4ba2-b717-a1cd4dc98a4f', appModuleDescription='Quantum Chemistry Application'),\n", + " ApplicationModule(appModuleName='DDSCat', appModuleVersion='', appModuleId='DDSCat_b01bf3eb-7e19-4ebe-bd18-32af7c81e5df', appModuleDescription='Discrete Dipole Approximation Scattering (DDSCAT) code'),\n", + " ApplicationModule(appModuleName='DFTB+', appModuleVersion='', appModuleId='DFTB+_9add4ce4-7f57-495a-bb1a-eff570b56441', appModuleDescription='Semi empirical Quantum Chemistry'),\n", + " ApplicationModule(appModuleName='WRF', appModuleVersion='', appModuleId='WRF_17f339d1-92e3-4eb9-a72e-cb4961d685a9', appModuleDescription='Weather Research and Forecasting'),\n", + " ApplicationModule(appModuleName='Gamess_Stampede', appModuleVersion='', appModuleId='Gamess_Stampede_1eb6c1f7-9292-456d-b1c3-1b88c3936b68', appModuleDescription='Gamess Application Module in Stampede'),\n", + " ApplicationModule(appModuleName='Molcas', appModuleVersion='', appModuleId='Molcas_f7dd5a10-0f8d-43b0-9c88-ec1a648dd037', appModuleDescription='Computational Chemistry QM'),\n", + " ApplicationModule(appModuleName='Abaqus', appModuleVersion='', appModuleId='Abaqus_96a88449-b4cd-4a39-8ad2-26abfbdd4b3e', appModuleDescription='Finite Element Analysis, Enginnering'),\n", + " ApplicationModule(appModuleName='test', appModuleVersion='', appModuleId='test_0282ea6b-8203-405f-b115-f86b4cd3b9e3', appModuleDescription=''),\n", + " ApplicationModule(appModuleName='AutoDock_Vina', appModuleVersion='', appModuleId='AutoDock_Vina_2bf91893-d75b-4478-9039-1aed216b5866', appModuleDescription=''),\n", + " ApplicationModule(appModuleName='Vina_Multiple', appModuleVersion='', appModuleId='Vina_Multiple_d0292a2f-6555-4364-b3be-d84b47ceeced', appModuleDescription='AutoDock Vina to launch with multiple Ligands'),\n", + " ApplicationModule(appModuleName='PSI4.0', appModuleVersion='', appModuleId='PSI4.0_80cfebe1-fef8-49c3-a8eb-00b735bd817f', appModuleDescription='Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties.'),\n", + " ApplicationModule(appModuleName='Abaqus-6.13-3', appModuleVersion='6.13-3', appModuleId='Abaqus-6.13-3_be287dc9-4347-4fba-a308-465010e5f7d0', appModuleDescription='Finite Element Analysis, Engineering'),\n", + " ApplicationModule(appModuleName='Trinity', appModuleVersion='2.2.0', appModuleId='Trinity_b32b104d-501e-42f6-a35a-18540190cf2e', appModuleDescription='De novo reconstruction of transcriptomes from RNA-seq data'),\n", + " ApplicationModule(appModuleName='Gaussian16', appModuleVersion='Gaussian 16: ES64L-G16RevA.03', appModuleId='Gaussian16_3e749c7d-6b02-4356-acc3-a58423210bda', appModuleDescription='Gaussian computes molecular electronic properties using ab inito and dft techniques'),\n", + " ApplicationModule(appModuleName='Amber_pmemd', appModuleVersion='', appModuleId='Amber_pmemd_d5011de7-7544-4af0-a6e0-384f85127766', appModuleDescription='Assisted Model Building with Energy Refinement MD Package with Particle Mesh Ewald summation for electrostatic interactions')]" ] }, "execution_count": 7, @@ -247,7 +512,7 @@ } ], "source": [ - "airavata_cli.module_descriptions('Ultrascan_Production') " + "airavata_cli.module_descriptions('seagrid') " ] }, { @@ -290,7 +555,7 @@ }, "outputs": [], "source": [ - "ds=airavata_cli.experiment_statistics(\"Ultrascan_Production\", fromTime*1000, toTime*1000)\n", + "ds=airavata_cli.experiment_statistics(\"seagrid\", fromTime*1000, t
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