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simWS.py
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simWS.py
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# Copyright 2012 University of Pittsburgh
# Copyright 2012 Pittsburgh Supercomputing Center
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not
# use this file except in compliance with the License. You may obtain a copy of
# the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations under
# the License.
'''
Created on Jun 2013
@author: Shawn Brown
'''
configuration = {
'local': {
'scratchDir':'/tmp',
'serviceDir':'/usr/local/packages/Simulator-WS-v3.1.0',
'templateDir':'/usr/local/packages/Simulator-WS-v3.1.0/templates',
'logFile':'/usr/local/packages/Simulator-WS-v3.1.0/sim.log',
'wsdlFile':'/usr/local/packages/Simulator-WS-v3.1.0/simulator_service_3.1.0.wsdl',
'apolloPyDir':'/usr/local/packages/apollo-db-python-module',
'port':'8094',
'version':'3.1.0',
'apolloDBName':'apollo_310_snapshot',
'apolloDBHost':'',
'apolloDBUser':'',
'apolloDBPword':''
},
# Private key files will have to be updated by the user
'machines':{
'pscss.olympus.psc.edu':{
'hostname':'pscss.olympus.psc.edu',
'username':'ows_simulator',
'password':'',
'privateKeyFile':'/usr/local/packages/.k/id_rsa.login.olympus',
'queueType':'PBS',
'priorityQueue':'batch',
'remoteDir':'/mnt/beegfs0/users/ows_simulator/apolloTemp',
'submitCommand':'/opt/bin/qsub',
'special':'source /opt/packages/virtualenvs/ows2.7/bin/activate.csh; module load gnu_parallel',
#'apolloPyLoc':'/mnt/beegfs/users/ows_simulator/apollo-db-files',
'apolloPyLoc':'',
'apolloPyModule':'module load apollo/apollo-3.0.2',
'qstatCommand':'qstat',
'useModules':True,
'big':'-l nodes=4:ppn=16',
'medium':'-l nodes=1:ppn=16 -l walltime=60:00:00',
'small':'-l nodes=1:ppn=16',
'debug':'-l nodes=1:ppn=8',
'getID':"set words = `echo $PBS_JOBID | sed 's/\./ /g'`; set id = $words[1]",
'ppn':8,
'mediumBatch':144,
'useParallel':True,
'env':'/bin/env'
},
},
'simulators':{
'mappings':{
'UPitt,PSC,CMU_FRED_2.0.1_':'fred_V1',
'UPitt,PSC,CMU_FRED_2.0.1_i_':'fred_V1_i',
'Chao-FredHutchinsonCancerCenter_FluTE_1.15_':'flute_v1.15',
'PSC_CLARA_0.5_':'clara_v0.5',
'UPitt_SEIR_3.0':'seir_30',
'Swiss TPH_OpenMalaria_1.0_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0063_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0065_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0068_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0111_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0115_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0121_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0131_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0132_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0133_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0670_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0674_':'openmalaria_32',
'Swiss TPH_OpenMalaria_R0678_':'openmalaria_32',
'Swiss TPH_OpenMalaria_base_':'openmalaria_32',
'test':'test',
'fred':'fred_V1'
},
'fred_V1':{
'stagedMachines':['blacklight.psc.xsede.org'],
'defaultMachine':['blacklight.psc.xsede.org'],
'runDirPrefix':'fred.tmp',
'preProcessCommand':'',
'moduleCommand':['module load fred; module load python'],
'runCommand':'fred_job -p config.txt -k apollo_<<ID>>$id',
'dbCommand':'python $FRED_HOME/bin/fred_to_apollo_parallel.py -k apollo_<<ID>>$id',
'big':'-m 1 -n 2 -t 32',
'medium':'-m 2 -n 4 -t 8',
'small':'-m 4 -n 4 -t 2',
'debug':'-m 8 -n 4 -t 4'
},
'fred_V1_i':{
'stagedMachines':['pscss.olympus.psc.edu'],
'defaultMachine':['pscss.olympus.psc.edu'],
'runDirPrefix':'fred.tmp',
'preProcessCommand':'',
'moduleCommand':['module load fred/pfred-0.0.3'],
'moduleName':['fred/pfred-0.0.3'],
'runCommand':'run_fred_apollo.bash ',
'dependencies':['fred_to_apollo.py','apollo.py','apollo_update_status.py','apollo_batch_update_status.py','logger.py'],
'dbCommand':'python $APOLLO_HOME/fred_to_apollo.py -o OUT -i <<ID>>',
'statusCommand':'python $APOLLO_HOME/apollo_update_status.py -r <<ID>>',
'batchStatusCommand':'python $APOLLO_HOME/apollo_batch_update_status.py -b <<bID>>',
'big':'-m 1 -n 1 -t 16',
'medium':'-m 8 -n 8 -t 4',
'small':'-m 8 -n 8 -t 2',
'debug':'-m 8 -n 4 -t 4',
'mediumPPR':1,
'mediumTPR':2,
'mediumReals':4,
'singlePPR':4,
'singleTPR':2,
'singleReals':8
},
'flute_v1.15':{
'stagedMachines':['fe-sandbox.psc.edu','pscss.olympus.psc.edu'],
'defaultMachine':['pscss.olympus.psc.edu'],
'runDirPrefix':'flute.tmp',
'preProcessCommand':'',
'dependencies':['apollo.py','apollo_update_status.py','apollo_batch_update_status.py','logger.py'],
'moduleCommand':['','module load flute/flute-1.15.1-psc'],
'moduleName':['','flute/flute-1.15.1-psc'],
'runCommand':'run_flute_apollo.bash',
'dbCommand':'python $APOLLO_HOME/flute_to_apollo-snap.py -o OUT -i <<ID>>',
'statusCommand':'python $APOLLO_HOME/apollo_update_status.py -r <<ID>>',
'big':'',
'medium':'',
'small':'',
'debug':'',
'mediumPPR':4,
'mediumTPR':1,
'mediumReals':4,
'singlePPR':4,
'singleTPR':1,
},
'openmalaria_32':{
'stagedMachines':['pscss.olympus.psc.edu'],
'defaultMachine':['pscss.olympus.psc.edu'],
'runDirPrefix':'om.tmp',
'preProcessCommand':'module load openmalaria_resources',
'dependencies':['apollo.py','apollo_update_status.py','apollo_batch_update_status.py','logger.py'],
'moduleCommand':['module load openmalaria/32'],
'moduleName':['openmalaria/32'],
'runCommand':'run_om_apollo.bash',
'dbCommand':'',
'dbCommand':'python $APOLLO_HOME/om_to_apollo.py -o OUT -i <<ID>>',
'statusCommand':'python $APOLLO_HOME/apollo_update_status.py -r <<ID>>',
'big':'',
'medium':'',
'small':'',
'debug':'',
'mediumPPR':4,
'mediumTPR':1,
'mediumReals':4,
'singlePPR':4,
'singleTPR':1,
},
'clara_v0.5':{
'stagedMachines':['fe-sandbox.psc.edu'],
'defaultMachine':['fe-sandbox.psc.edu'],
'runDirPrefix':'clara.tmp',
'preProcessCommand':'mkdir Apollo; ln -s /data/fs/packages/clara-netlogo/inputs .; ln -s /data/fs/packages/clara-netlogo/CLARA.* .; ln -s /data/fs/packages/clara-netlogo/*.dat .; ln -s /data/fs/packages/clara-netlogo/extensions .; setenv THREADS $PBS_NUM_PPN',
'moduleCommand':['module load java'],
'runCommand':'java -server -Xmx65536M -XX:+AggressiveOpts -XX:+AggressiveHeap -XX:+UseNUMA -XX:+UseParallelGC -cp .:/data/fs/packages/netlogo-5.0.4/NetLogo.jar org.nlogo.headless.Main --threads $THREADS --model CLARA.nlogo --experiment Apollo --spreadsheet Apollo.csv',
'dbCommand':'python $APOLLO_HOME/clara_to_apollo.py -i <<ID>>',
'statusCommand':'python $APOLLO_HOME/apollo_update_status.py -r <<ID>>',
'big':'',
'medium':'',
'small':'',
'debug':''
},
'seir_30':{
'stagedMachines':['pscss.olympus.psc.edu'],
'defaultMachine':['pscss.olympus.psc.edu'],
'runDirPrefix':'seir.tmp',
'preProcessCommand':'',
'moduleCommand':['module load pitt_seir/pitt_seir-3.0.0'],
'moduleName':['pitt_seir/pitt_seir-3.0.0'],
'runCommand':'$SEIR_HOME/run_seir_apollo.bash',
'dbCommand':'python $APOLLO_HOME/seir_to_apollo.py -o OUT -i <<ID>>',
'statusCommand':'python $APOLLO_HOME/apollo_update_status.py -r <<ID>>',
'big':'',
'medium':'',
'small':'',
'debug':'',
'mediumPPR':1,
'mediumTPR':1,
'mediumReals':1,
'singlePPR':1,
'singleTPR':1
},
'test':{
'stagedMachine':['olympus.psc.edu', 'blacklight.psc.xsede.org', 'unicron.psc.edu'],
'defaultMachine':['olumpus.psc.edu'],
'runDirPrefix':'test.tmp',
'preProcessCommand':'',
'moduleCommand':'module load fred',
'runCommand':'echo Testing <<ID>>; sleep 10; echo Testing <<ID>>; sleep 10',
'statusCommand':'echo "running"',
'dbCommand':'echo "db"',
'big':'',
'medium':'',
'small':'',
'debug':''
}
}
}