You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@airavata.apache.org by sc...@apache.org on 2017/05/09 16:20:39 UTC
[2/3] airavata-sandbox git commit: fixing the issues in notebooks and
making them compatible with new master deployment for seagrid
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, 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=['Amber-Sander_e8ce4375-aa60-4dd9-aff5-61bbe1f275c0', 'Echo_19dc358d-d241-43d8-91
8c-f5a21a3b0845']),\n",
+ " ApplicationInterfaceDescription(applicationName='Amber_Sander', 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='')], 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', 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='', loc
ation='', 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=['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, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='AD4_parameters.dat', name='Input-File-DAT', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=2, metaData=''), InputDataObjectType(userFriendlyDescription='ind.dpf', name='Input-File-DPF', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData='')], applicationInterfaceId='AutoDock_a43d41f6-febf-4172-963c-4b67b8452180', applicationDescription='AutoDock suite of automated docking tools', applicationOutputs=[OutputDataObj
ectType(dataMovement=False, name='AutoDock-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='AutoDock-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['AutoDock_24d6d7da-1160-45b0-9958-63bcc9044804']),\n",
+ " ApplicationInterfaceDescription(applicationName='Gromacs', applicationInputs=[InputDataObjectType(userFriendlyDescription='Trajectory Coordinates Molecular Structure in Gromos87 format - pdb1y6l-EM-vacuum.gro', name='Coordinate-File', dataStaged=False, value='', applicationArgument='-c', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=2, metaData=''), InputDataObjectType(userFriendlyDescription='Coordinates velocities, molecular topology and simulation parameters - pdb1y6l-EM-vacuum.tpr\\r\\n-v -deffnm', name='Portable-Input-Binary-File', dataStaged=False, value='', applicationArgument='-s', isRequired=True, standardInput=False, 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 density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT)', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Abinit-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Abinit-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5), OutputDataObjectType(dataMovement=False, name='Application-Out', value='tbase1_2.out', applicationArgument='', isRequired=True, searchQuery=''
, location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=3)], applicationModules=['Abinit_34e497ac-28cd-42a2-afe0-1ee99f173c6d']),\n",
+ " ApplicationInterfaceDescription(applicationName='Quantum_Espresso', 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 - fayalite.inp', name='Input-File-INP', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData='')], applicationInterfaceId='CP2K_b53107d7-bda8-44a2-a724-fed43d056e4e', applicationDescription='CP2K Test Application Module', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='CP2K-Application-Output', value='cp2k.out', applicationArgument='>&', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='CP2K-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='CP2K-Stan
dard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, 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 parameters solver.inp', name='Solver-Input-Parameters', dataStaged=False, value=
'', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=4, metaData='')], applicationInterfaceId='Phasta_P_f5398ee4-d6f0-4ada-8add-46747ea59449', applicationDescription='Parallel version of PHASTA', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Phasta-Output-TAR', value='PHASTA_Output.tar.gz', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='PhastaP-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='PhastaP-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', 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', dataStaged=False, value='298', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=6, metaData=''), InputDataObjectType(userFriendlyDescription='Tinker monte input_1', name='xyzf', dataStaged=False, value='O16.xyz', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData='')], applicationInterfaceId='Tinker_monte_d80b010e-c22c-471d-a5d8-ac7c4dd2e429', applicationDescription='Grid Chem Tinker Monte Application', applicationOutputs=[OutputDataObjectT
ype(dataMovement=False, name='TinkerMonte-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='TinkerMonte-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Tinker_Monte_b11b893a-626b-4778-997a-2da92537b4b7']),\n",
+ " ApplicationInterfaceDescription(applicationName='CPMD', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='INP-Input-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='Define PLIBRARY as a prejob command', name='PPLibrary', dataStaged=False, value='$PPLIBRARY', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=2, metaData='')], applicationInterfaceId='CPMD_3afef8de-1252-407b-b768-28f58ed41fa3', applicationDescription='parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='CPMD-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', re
quiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='CPMD-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5), OutputDataObjectType(dataMovement=True, name='CPMD.Out', value='CPMD.out', applicationArgument='>', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=True, name='CPMD.restart', value='RESTART.1', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=3)], applicationModules=['CPMD_6870dafa-e2e3-4fe6-a0e2-5b11c1436af4']),\n",
+ " ApplicationInterfaceDescription(applicationName='QChem', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='IN-Input-File', dataStaged=False, value='', applicationArgument='-nt 24', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=2, metaData='')], applicationInterfaceId='QChem_5e5a711f-18a3-459a-bfe2-c6fbf686b5b1', applicationDescription='Quantum Chemistry Application', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='QChem-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='QChem-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5), OutputDataObjectType(dataMovement=False, name='Qchem.Output', value='QChem.out', applicationArg
ument='>', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=True, outputStreaming=False, type=3)], applicationModules=['QChem_9214bc96-2bf8-4ba2-b717-a1cd4dc98a4f']),\n",
+ " ApplicationInterfaceDescription(applicationName='DDSCat', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='PAR-Input-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='', name='TAB-Input-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=2, metaData='')], applicationInterfaceId='DDSCat_e6ab3de1-9d8c-4c89-878a-d8cb84b6619b', applicationDescription='Discrete Dipole Approximation Scattering (DDSCAT) code', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='DDSCat-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='DDSCat-
Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5), OutputDataObjectType(dataMovement=False, name='DDSCat.out', value='DDSCat.out', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=3)], applicationModules=['DDSCat_b01bf3eb-7e19-4ebe-bd18-32af7c81e5df']),\n",
+ " ApplicationInterfaceDescription(applicationName='DFTB+', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='DFTB-Input', dataStaged=False, value='dftb_in.hsd', applicationArgument='', isRequired=True, standardInput=True, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData='')], applicationInterfaceId='DFTB+_ac6c3ae2-8367-4433-b3bd-8146b9125c4a', applicationDescription='Semi empirical Quantum Chemistry', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='DFTB-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='DFTB-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['DFTB+_9add4ce4-7f57-495a-bb1a-eff570b56441']),\n",
+ " ApplicationInterfaceDescription(applicationName='WRF', applicationInputs=[InputDataObjectType(userFriendlyDescription='Namelist Configuration File - namelist.input', name='Configuration-Namelist-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='Boundary Conditions File - wrfbdy_d01', name='WRF-Boundary-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='Initial Conditions File - wrfinput_d01', name='WRF-Initial-Conditions', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=2, metaData='')], applicationInterfaceId='WRF_b9c0e9df-8a39-4317-a689-36025a45ec20', applica
tionDescription='Weather Research and Focasting Application', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='WRF-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='WRF-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5), OutputDataObjectType(dataMovement=False, name='WRF_Application_Execution_Log', value='rsl.out.0000', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=3)], applicationModules=['WRF_17f339d1-92e3-4eb9-a72e-cb4961d685a9']),\n",
+ " ApplicationInterfaceDescription(applicationName='Gamess_Stampede', applicationInputs=[InputDataObjectType(userFriendlyDescription='Gamess Input file', 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='8', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=2, metaData='')], applicationInterfaceId='Gamess_Stampede_c892ddc8-9da3-4d2d-98da-b5ccbe937f4e', applicationDescription='Gamess Application on Stampede', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Gamess-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Gamess-Stand
ard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Gamess_Stampede_1eb6c1f7-9292-456d-b1c3-1b88c3936b68']),\n",
+ " ApplicationInterfaceDescription(applicationName='Molcas', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='Molcas-Input', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=True, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData='')], applicationInterfaceId='Molcas_1b42f617-a3eb-4d38-b9ad-986fc57a36ed', applicationDescription='Computational Chemistry QM', applicationOutputs=[OutputDataObjectType(dataMovement=True, name='Molcas-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=True, name='Molcas-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Molcas_f7dd5a10-0f8d-43b0-9c88-ec1a648dd037']),\n",
+ " ApplicationInterfaceDescription(applicationName='Abaqus', applicationInputs=[InputDataObjectType(userFriendlyDescription='Main input files for the application', name='Abacus-INP-File', dataStaged=False, value='', applicationArgument='-input', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='String for job canonical name', name='ABQ_JOB', dataStaged=False, value='$abq_job', applicationArgument='-job', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=2, metaData=''), InputDataObjectType(userFriendlyDescription='cpus for the job', name='CPUs', dataStaged=False, value='24', applicationArgument='-cpus', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=4, metaData=''), InputDataObjectType(userFriendlyDescription='--datafile_file or --datafile2_file2.tar', name='Datach', dataStaged=False, valu
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ionInterfaceId='Abaqus_cfdf8945-e173-4265-b15a-ec6ae4ccedfa', applicationDescription='Finite Element Analysis, Enginnering', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Abaqus-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Abaqus-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Abaqus_96a88449-b4cd-4a39-8ad2-26abfbdd4b3e']),\n",
+ " ApplicationInterfaceDescription(applicationName='Vina_Multiple', applicationInputs=[InputDataObjectType(userFriendlyDescription='config\\r\\nShould not contain ligand description', name='Config-File', dataStaged=False, value='conf.txt', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='ligands.zip', name='Multi-Ligand-Zip-File', dataStaged=False, value='ligands.zip', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=2, metaData=''), InputDataObjectType(userFriendlyDescription='receptor.pdbqt', name='Receptor-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=1, metaData='')], applicationInterfaceId='Vina_Multiple_53fc0aaa-20d4-4c80-8797-0a4bcc20bc61', applicationDescription='Autodoc
k Vina with multiple ligands', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='AutoDock-Vina-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='AutoDock-Vina-Standard-out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Vina_Multiple_d0292a2f-6555-4364-b3be-d84b47ceeced']),\n",
+ " ApplicationInterfaceDescription(applicationName='AutoDock_Vina', applicationInputs=[InputDataObjectType(userFriendlyDescription='config', name='Config-File', dataStaged=False, value='', applicationArgument='--config', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=3, metaData=''), InputDataObjectType(userFriendlyDescription='ligand1.pdbqt', name='Ligand-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=2, metaData=''), InputDataObjectType(userFriendlyDescription='receptor.pdbqt', name='Receptor-File', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=1, metaData='')], applicationInterfaceId='AutoDock_Vina_c9436341-aa2e-4ccd-8ac0-1db3e176f962', applicationDescription='', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='
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+ " ApplicationInterfaceDescription(applicationName='PSI4.0', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='Psi-Input-File', dataStaged=False, value='input.dat', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=False, type=3, inputOrder=1, metaData='')], applicationInterfaceId='PSI4.0_440faf02-3db3-4537-b66b-0465099e0f7e', applicationDescription='Psi4 is an ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties.', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Psi-Output', value='output.dat', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=3), OutputDataObjectType(dataMovement=False, name='PSI4.0-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStrea
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+ " ApplicationInterfaceDescription(applicationName='Abaqus-6.13-3', applicationInputs=[InputDataObjectType(userFriendlyDescription='Main input files for the application', name='Abacus-INP-File', dataStaged=False, value='', applicationArgument='-input', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=3, inputOrder=1, metaData=''), InputDataObjectType(userFriendlyDescription='String for job canonical name', name='ABQ_JOB', dataStaged=False, value='$abq_job', applicationArgument='-job', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=2, metaData=''), InputDataObjectType(userFriendlyDescription='cpus for the job', name='CPUs', dataStaged=False, value='24', applicationArgument='-cpus', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=4, metaData=''), InputDataObjectType(userFriendlyDescription='--datafile_file or --datafile2_file2.tar', name='Datach', dataStaged=Fals
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pplicationInterfaceId='Abaqus-6.13-3_43054f54-87e5-493b-8788-899028534465', applicationDescription='Finite Element Analysis, Enginnering', applicationOutputs=[OutputDataObjectType(dataMovement=False, name='Abaqus-Standard-Error', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=6), OutputDataObjectType(dataMovement=False, name='Abaqus-Standard-Out', value='', applicationArgument='', isRequired=True, searchQuery='', location='', requiredToAddedToCommandLine=False, outputStreaming=False, type=5)], applicationModules=['Abaqus-6.13-3_be287dc9-4347-4fba-a308-465010e5f7d0']),\n",
+ " ApplicationInterfaceDescription(applicationName='Echo-Marcus', applicationInputs=[InputDataObjectType(userFriendlyDescription='', name='Input to Echo', dataStaged=False, value='', applicationArgument='', isRequired=True, standardInput=False, requiredToAddedToCommandLine=True, type=0, inputOrder=1, metaData='')], applicationInterfaceId='Echo-Marcus_c12b0256-8033-4a2b-938c-7bcadb2e87e3', applicationDescription='Simple Echo Application Interface', 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
<TRUNCATED>