Amber/Coco on ARCHER

[ebreitmo]

Running ExTASY from ARCHER as localhost. I use anaconda and the conda environment instead of virtualenv.

/home/e290/e290/ebreitmo/.local/bin/extasy --RPconfig $HOME/ExTASY/config/RP_config.py --Kconfig $HOME/ExTASY/config/amber_coco_config.py

Session UID: 542a891df6da63ace6571fff Pilot UID : 542a8920f6da63ace6572001 Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/sleep.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/coco.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/gromacs.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/mmpbsa.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/lsdmap.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/namd.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/amber.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/test.json Cycle 0 Starting Simulation Traceback (most recent call last): File "/home/e290/e290/ebreitmo/.local/bin/extasy", line 9, in load_entry_point('radical.ensemblemd.extasy==0.1', 'console_scripts', 'extasy')() File "/home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/runme.py", line 130, in main Simulator(umgr,RPconfig,Kconfig,i) File "/home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Amber/simulator.py", line 19, in Simulator dict['crdfile'] = Kconfig.crdfile AttributeError: 'module' object has no attribute 'crdfile'

Elena

[oleweidner]

Hi Elena -- there were a few inconsistencies in the instructions as well as the configuration files. We have completely rewritten everything and things should be consistent now.

Can you please try again from scratch following the instructions at https://github.com/radical-cybertools/ExTASY/blob/devel/README.md?

Also, if you don't mind, please use virtualenv. We are not familiar with the anaconda environment and it will be difficult to debug.

[ebreitmo]

Hi Ole,

I list all the commands I execute on my Mac. Do I use any outdated stuff from github?

vitrualenv Test01 source Test01/bin/activate

python -c "import pymongo; print pymongo.version" Traceback (most recent call last): File "", line 1, in ImportError: No module named pymongopip install radical.pilot

pip install --upgrade git+https://github.com/radical-cybertools/radical.ensemblemd.mdkernels.git@master#egg=radical.ensemblemd.mdkernels pip install --upgrade git+https://github.com/radical-cybertools/ExTASY.git@devel#egg=radical.ensemblemd.extasy python -c "import pymongo; print pymongo.version" 2.7.2

extasy Traceback (most recent call last): File "/Users/elenabreitmoser/Test0210/bin/extasy", line 5, in from pkg_resources import load_entry_point File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 2603, in working_set.require(requires) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 666, in require needed = self.resolve(parse_requirements(requirements)) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: pymongo>=2.5

Cheers, Elena

---

Dr Elena Breitmoser

EPCC, University of Edinburgh JCMB, Room 3401 Peter Guthrie Tait Road UK-Edinburgh EH9 3FD

Tel: +44 131 650 6494

On 30 Sep 2014, at 19:16, Ole Weidner notifications@github.com wrote:

Hi Elena -- there were a few inconsistencies in the instructions as well as the configuration files. We have completely rewritten everything and things should be consistent now.

Can you please try again from scratch following the instructions at https://github.com/radical-cybertools/ExTASY/blob/devel/README.md?

Also, if you don't mind, please use virtualenv. We are not familiar with the anaconda environment and it will be difficult to debug.

— Reply to this email directly or view it on GitHub.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

[ebreitmo]

I now use virtualenv on ARCHER.

extasy --RPconfig archer.rcfg --Kconfig cocoamber.wcfg Session UID: 542d576f6b5be34574840a36 Pilot UID : 542d57726b5be34574840a38 Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/mmpbsa.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/gromacs.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/amber.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/sleep.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/test.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/lsdmap.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/namd.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/coco.json Cycle 0 Starting Simulation [Callback]: ComputeUnit '542d57726b5be34574840a3b' state changed to PendingInputStaging. [Callback]: ComputeUnit '542d57726b5be34574840a40' state changed to PendingInputStaging. [Callback]: ComputePilot '542d57726b5be34574840a38' state changed to Failed. pilot manager controller thread caught system exit -- forcing application shutdown Traceback (most recent call last): File "/home/e290/e290/ebreitmo/.local/bin/extasy", line 9, in load_entry_point('radical.ensemblemd.extasy==0.1', 'console_scripts', 'extasy')() File "/home/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/runme.py", line 130, in main Simulator(umgr,RPconfig,Kconfig,i) File "/home/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Simulator/Amber/simulator.py", line 54, in Simulator units = umgr.submit_units(compute_units) File "/home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/unit_manager.py", line 452, in submit_units self.handle_schedule (schedule) File "/home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/unit_manager.py", line 545, in handle_schedule units=units_to_schedule File "/home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/controller/unit_manager_controller.py", line 576, in schedule_compute_units self._db.set_compute_unit_state(unit.uid, PENDING_INPUT_STAGING, log) File "/home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/db/database.py", line 541, in set_compute_unit_state "$pushAll": {"log": log}}) File "build/bdist.linux-x86_64/egg/pymongo/collection.py", line 572, in update File "build/bdist.linux-x86_64/egg/pymongo/mongo_client.py", line 1123, in _send_message File "build/bdist.linux-x86_64/egg/pymongo/mongo_client.py", line 1158, in __receive_message_on_socket File "build/bdist.linux-x86_64/egg/pymongo/mongo_client.py", line 1146, in __receive_data_on_socket KeyboardInterrupt

[vivek-bala]

Seems like the pilot fails before even starting, could you set environment variable RADICAL_PILOT_VERBOSE to DEBUG and run it again and paste the entire output here again please ?

export RADICAL_PILOT_VERBOSE=DEBUG

[ebreitmo]

with export RADICAL_PILOT_VERBOSE=DEBUG, and 'archer.ac.uk:local'

extasy --RPconfig archer.rcfg --Kconfig cocoamber.wcfg 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] radical.pilot version: 0.20 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] using database url mongodb://ec2-184-72-89-141.compute-1.amazonaws.com:27017/ 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] using database name radicalpilot 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/das4.json 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/epsrc.json 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/futuregrid.json 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/iu.json 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/localhost.json 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/lrz.json 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/ncar.json 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/radical.json 2014:10:02 16:36:27 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/xsede.json 2014:10:02 16:36:30 radical.pilot.MainProcess: [INFO ] New Session created{'database_url': 'mongodb://ec2-184-72-89-141.compute-1.amazonaws.com:27017/', 'database_name': 'radicalpilot', 'last_reconnect': None, 'uid': '542d70fb6b5be31b1323011a', 'created': datetime.datetime(2014, 10, 2, 15, 36, 27, 959992)}. Session UID: 542d70fb6b5be31b1323011a 2014:10:02 16:36:30 radical.pilot.MainProcess: [DEBUG ] Worker thread (ID: Thread-1[46912618166016]) for PilotManager 542d70fe6b5be31b1323011b started. 2014:10:02 16:36:30 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for PilotManager 542d70fe6b5be31b1323011b. Pilot UID : 542d70fe6b5be31b1323011c 2014:10:02 16:36:30 radical.pilot.MainProcess: [INFO ] Starting InputFileTransferWorker 2014:10:02 16:36:30 radical.pilot.MainProcess: [INFO ] Starting InputFileTransferWorker 2014:10:02 16:36:30 radical.pilot.MainProcess: [INFO ] Loaded scheduler: DirectSubmissionScheduler. 2014:10:02 16:36:30 radical.pilot.MainProcess: [DEBUG ] Worker thread (ID: Thread-3[46912632592128]) for UnitManager 542d70fe6b5be31b1323011d started. 2014:10:02 16:36:31 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 542d70fe6b5be31b1323011d. 2014:10:02 16:36:31 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 542d70fe6b5be31b1323011d. 2014:10:02 16:36:31 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 542d70fe6b5be31b1323011d. 2014:10:02 16:36:31 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 542d70fe6b5be31b1323011d. Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/mmpbsa.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/gromacs.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/amber.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/sleep.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/test.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/lsdmap.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/namd.json Loading kernel configurations from /home4/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/coco.json Cycle 0 Starting Simulation Traceback (most recent call last): File "/home/e290/e290/ebreitmo/.local/bin/extasy", line 9, in load_entry_point('radical.ensemblemd.extasy==0.1', 'console_scripts', 'extasy')() File "/home/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/runme.py", line 130, in main Simulator(umgr,RPconfig,Kconfig,i) File "/home/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Simulator/Amber/simulator.py", line 41, in Simulator mdtd_bound = mdtd.bind(resource=RPconfig.REMOTE_HOST)

[vivek-bala]

I think this might be different from what you posted earlier ? Could you also mention the error that it reports, might be after mdtd_bound = mdtd.bind(resource=RPconfig.REMOTE_HOST)

[oleweidner]

Ah -- this is because MD Kernels don't support :local -- I'll fix this ASAP.

[ebreitmo]

Hi Ole,

Have you finished testing it?

Thanks, Elena

---

Dr Elena Breitmoser

EPCC, University of Edinburgh JCMB, Room 3401 Peter Guthrie Tait Road UK-Edinburgh EH9 3FD

Tel: +44 131 650 6494

On 6 Oct 2014, at 14:11, Ole Weidner notifications@github.com wrote:

Ah -- this is because MD Kernels don't support :local -- I'll fix this ASAP.

— Reply to this email directly or view it on GitHub.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

[ebreitmo]

I installed everything from scratch again on ARCHER as localhost, using 'export SAGA_VERBOSE=DEBUG:

2014:10:08 11:08:01 26209 MainThread saga.Engine : [ERROR ] Skipping adaptor saga.adaptors.irods.irods_replica: failed self test: Could not run iRODS/ils. Check iRODSenvironment and certificates ('module' object has no attribute 'logger') (/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/saga_python-0.18-py2.7.egg/saga/adaptors/irods/irods_replica.py +200 (sanity_check) : "environment and certificates (%s)" % ex))

[andre-merzky]

The irods adaptor is not used by ExTASY, so feel free to ignore that error.

[ebreitmo]

Ok, then it ends with:

Cycle 0 Starting Simulation Traceback (most recent call last): File "/home/e290/e290/ebreitmo/.local/bin/extasy", line 9, in load_entry_point('radical.ensemblemd.extasy==0.1', 'console_scripts', 'extasy')() File "/home/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/runme.py", line 130, in main Simulator(umgr,RPconfig,Kconfig,i) File "/home/e290/e290/ebreitmo/.local/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Simulator/Amber/simulator.py", line 48, in Simulator cu.input_staging = ['%s > min%s.crd'%(dict['crdfile'],cycle),'%s'%(dict['topfile']),'%s'%(dict['minin']),'%s'%(dict['mdin'])] File "/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/saga_python-0.18-py2.7.egg/saga/attributes.py", line 2641, in setattr return self._attributes_i_set (key, val, flow=self._DOWN) File "/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/saga_python-0.18-py2.7.egg/saga/attributes.py", line 1065, in _attributes_i_set raise se.IncorrectState ("attribute set is not extensible/private (key %s)" % key) saga.exceptions.IncorrectState: attribute set is not extensible/private (key input_staging) (/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/saga_python-0.18-py2.7.egg/saga/attributes.py +1065 (_attributes_i_set) : raise se.IncorrectState ("attribute set is not extensible/private (key %s)" % key))

[andre-merzky]

cu.input_staging should be perfectly valid, but the radical.pilot version used here does not seem to like it. That would indicate a relatively old radical.pilot installation? Would you mind running:

  python -c 'import radical.pilot as rp; print rp.version; print rp.version_detail'

please?

[ebreitmo]

That was it, there was some legacy stuff which is deleted now. I think it works fine. The output is

... Cycle 1 Starting Simulation ... Total Simulation Time : 135.34899807 Simulation Execution Time : 130.073 Starting Analysis Submitting COCO Compute Unit [Callback]: ComputeUnit '5435220ea7ed1db823ace456' state changed to PendingInputStaging. [Callback]: ComputeUnit '5435220ea7ed1db823ace456' state changed to StagingInput. [Callback]: ComputeUnit '5435220ea7ed1db823ace456' state changed to Scheduling. [Callback]: ComputeUnit '5435220ea7ed1db823ace456' state changed to Executing. [Callback]: ComputeUnit '5435220ea7ed1db823ace456' state changed to StagingOutput. [Callback]: ComputeUnit '5435220ea7ed1db823ace456' state changed to Done. Analysis Execution time : 40.163 [Callback]: ComputePilot '5435206fa7ed1db823ace443' state changed to Canceled.

And the issue can be closed.

[andre-merzky]

Great! :)

[shantenujha]

The irods adaptor is not used by ExTASY, so feel free to ignore that error.

Please fix the cause of the error rather than ignoring the error message.

If it isn't required I don't see any justification for why that error should arise.

— Reply to this email directly or view it on GitHub https://github.com/radical-cybertools/ExTASY/issues/57#issuecomment-58337187.