{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_time"},{"status":"SUCCEEDED","id":"data_set_rabbit"},{"status":"SUCCEEDED","id":"data_set_fox"}],"duration":0.125963,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_rabbit"},{"status":"SUCCEEDED","id":"curve_fox"}],"duration":0.23429,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"Figure"}],"tasks":[{"simulatorDetails":[{"value":"smoldyn.Simulation","key":"class"},{"key":"instanceAttributes"},{"value":"run","key":"method"},{"value":{"dt":0.01,"start":0,"stop":20},"key":"methodArguments"}],"algorithm":"KISAO_0000057","duration":5.661178,"output":"--------------------------------------------------------------\r\nRunning Smoldyn 2.67.2\r\n\r\nCONFIGURATION FILE\r\n Path: '/tmp/'\r\n Name: 'tmpmr0t_4d_.txt'\r\n Reading file: '/tmp/tmpmr0t_4d_.txt'\r\nWarning: 'define K_RABBIT_REPRODUCTION 10' is ignored because it is a re-definition\r\n Loaded file successfully\r\n setting up molecules\r\n setting up virtual boxes\r\n setting up reactions\r\n setting up graphics\r\n\r\nSIMULATION PARAMETERS\r\n file: /tmp/tmpmr0t_4d_.txt\r\n starting clock time: Sat Feb  5 11:24:08 2022\r\n 3 dimensions\r\n Random number seed: 1644078248\r\n Time from 0 to 20 step 0.001\r\n\r\nGRAPHICS PARAMETERS\r\n No graphical output\r\n\r\nWALL PARAMETERS\r\n wall 0: dimension x, at -100, periodic\r\n wall 1: dimension x, at 100, periodic\r\n wall 2: dimension y, at -100, periodic\r\n wall 3: dimension y, at 100, periodic\r\n wall 4: dimension z, at -10, periodic\r\n wall 5: dimension z, at 10, periodic\r\n system volume: 800000\r\n system corners: (-100,-100,-10) and (100,100,10)\r\n\r\nMOLECULE PARAMETERS\r\n 3 molecule lists:\r\n  rlist, flist, unassignedlist\r\n 2 species defined:\r\n rabbit:\r\n  solution: difc=100, rms step=0.447214, list=rlist, number=1000\r\n  solution: color= 1,0,0, display size= 2\r\n fox:\r\n  solution: difc=100, rms step=0.447214, list=flist, number=1000\r\n  solution: color= 0,0.5,0, display size= 3\r\n Overall spatial resolution: 0.447214\r\n\r\nSURFACE PARAMETERS\r\n No internal surfaces\r\n\r\nRUNTIME COMMAND INTERPRETER\r\n No output files\r\n No output data tables\r\n No commands\r\n\r\nVIRTUAL BOX PARAMETERS\r\n 2352 boxes\r\n Number of boxes on each side: 28 28 3\r\n Requested molecules per box: 1\r\n Box dimensions:  7.14286 7.14286 6.66667\r\n Box volumes: 340.136\r\n Molecules per box= 0.85034\r\n\r\nORDER 0 REACTION PARAMETERS\r\n No reactions of order 0\r\n\r\nORDER 1 REACTION PARAMETERS\r\n 2 reactions defined\r\n Reactive molecule lists: rlist flist\r\n Reactants, sorted by molecule species:\r\n  rabbit : r1\r\n  fox : r3\r\n Reaction details:\r\n  Reaction r1: rabbit -> rabbit + rabbit\r\n   requested and actual rate constants: 10, 10\r\n   characteristic time: 0.1\r\n   conditional reaction probability per time step: 0.00995017\r\n   unbinding radius: 0\r\n  Reaction r3: fox -> 0\r\n   requested and actual rate constants: 10, 10\r\n   characteristic time: 0.1\r\n   conditional reaction probability per time step: 0.00995017\r\n\r\nORDER 2 REACTION PARAMETERS\r\n 1 reactions defined\r\n Reactive molecule lists: flist+rlist rlist+flist\r\n Reactants, sorted by molecule species:\r\n  rabbit+fox : r2\r\n Reaction details:\r\n  Reaction r2: rabbit + fox -> fox + fox\r\n   requested and actual rate constants: 8000, 8000.09\r\n   characteristic time: 0.199998\r\n   binding radius: 3.55359\r\n   unbinding radius: 0\r\n\r\nRULES:\r\n none\r\n\r\nPARAMETER CHECK\r\n WARNING: reactive volume of rabbit is 23.4963 % of total volume\r\n WARNING: reactive volume of fox is 23.4963 % of total volume\r\n WARNING: total reactive volume is a large fraction of total volume\r\n No errors\r\n 3 total warnings\r\n\r\nSimulating\r\nLibsmoldyn notification from smolRunSim: Simulation complete\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":6.165167,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  simulation.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 3 data sets\r\n    Plots (1):\r\n      Figure: 2 curves\r\n\r\nExecuting SED-ML file 1: simulation.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `Figure`\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `Figure` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"simulation.sedml"}],"duration":6.643309,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m============================================ Downloading COMBINE archive ============================================\u001b[0m\n  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n                                 Dload  Upload   Total   Spent    Left  Speed\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    470      0 --:--:-- --:--:-- --:--:--   471\n\r100 18714  100 18714    0     0  46507      0 --:--:-- --:--:-- --:--:-- 46507\n\n\u001b[0;36m============================================= Executing COMBINE archive =============================================\u001b[0m\nINFO:    Using cached SIF image\n \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 2 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 2\n      Skipped: 0\n      Failed: 0\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 1 SED documents:\n  SED documents (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Tasks (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Outputs (2):\n    Succeeded: 2\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /simulation.sedml\ncreating dataset /simulation.sedml/Figure, shape: (3, 2001), type: float64\ndataset created, uuid: d-58ddb6d8-d0609822-3ed2-d50bbe-15af10, chunk_size: (3, 2001)\ncreating dataset /simulation.sedml/report, shape: (3, 2001), type: float64\ndataset created, uuid: d-58ddb6d8-d0609822-a12b-86a6f8-d77842, chunk_size: (3, 2001)\ncreating attribute combineArchiveLocation in /simulation.sedml\ncreating attribute uri in /simulation.sedml\ncreating attribute _type in /simulation.sedml/Figure\ncreating attribute sedmlDataSetDataTypes in /simulation.sedml/Figure\ncreating attribute sedmlDataSetIds in /simulation.sedml/Figure\ncreating attribute sedmlDataSetLabels in /simulation.sedml/Figure\ncreating attribute sedmlDataSetNames in /simulation.sedml/Figure\ncreating attribute sedmlDataSetShapes in /simulation.sedml/Figure\ncreating attribute sedmlId in /simulation.sedml/Figure\ncreating attribute sedmlName in /simulation.sedml/Figure\ncreating attribute uri in /simulation.sedml/Figure\ncreating attribute _type in /simulation.sedml/report\ncreating attribute sedmlDataSetDataTypes in /simulation.sedml/report\ncreating attribute sedmlDataSetIds in /simulation.sedml/report\ncreating attribute sedmlDataSetLabels in /simulation.sedml/report\ncreating attribute sedmlDataSetNames in /simulation.sedml/report\ncreating attribute sedmlDataSetShapes in /simulation.sedml/report\ncreating attribute sedmlId in /simulation.sedml/report\ncreating attribute uri in /simulation.sedml/report\ncreate_links: /\ngot link: simulation.sedml\ncreate_links: /simulation.sedml\ngot link: Figure\ngot link: report\nwrite_dataset src: /simulation.sedml/Figure to tgt: /simulation.sedml/Figure, shape: (3, 2001), type: float64\niterating over chunks for /simulation.sedml/Figure\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 2001, 1))\ndone with dataload for /simulation.sedml/Figure\nwrite_dataset src: /simulation.sedml/report to tgt: /simulation.sedml/report, shape: (3, 2001), type: float64\niterating over chunks for /simulation.sedml/report\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 2001, 1))\ndone with dataload for /simulation.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/61fea4933c41b662ca49b3d8\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/simulation.sedml/ (stored 0%)\n  adding: outputs/simulation.sedml/Figure.pdf (deflated 16%)\n  adding: outputs/log.yml (deflated 64%)\n  adding: outputs/reports.h5 (deflated 69%)\n  adding: rawLog.txt (deflated 76%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 35.9 KiB/75.5 KiB (471.7 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/61fea4933c41b662ca49b3d8/output.zip\nCompleted 35.9 KiB/75.5 KiB (471.7 KiB/s) with 3 file(s) remaining\rCompleted 52.0 KiB/75.5 KiB (440.9 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/61fea4933c41b662ca49b3d8/outputs/plots.zip\nCompleted 52.0 KiB/75.5 KiB (440.9 KiB/s) with 2 file(s) remaining\rCompleted 71.4 KiB/75.5 KiB (416.3 KiB/s) with 2 file(s) remaining\rupload: outputs/simulation.sedml/Figure.pdf to s3://files.biosimulations.org/simulations/61fea4933c41b662ca49b3d8/outputs/simulation.sedml/Figure.pdf\nCompleted 71.4 KiB/75.5 KiB (416.3 KiB/s) with 1 file(s) remaining\rCompleted 75.5 KiB/75.5 KiB (411.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/61fea4933c41b662ca49b3d8/rawLog.txt\nCompleted 50.9 KiB/50.9 KiB (615.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/61fea4933c41b662ca49b3d8/outputs/reports.h5\nCompleted 5.5 KiB/5.5 KiB (71.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/61fea4933c41b662ca49b3d8/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\n\u001b[0;32mPost the Metadata to the API.....Succeeded\nProcess the Metadata in the combine archive.....Succeeded\nPost thumbnails to the API.....Succeeded\nCreate thumbnails from the images specified in the manifest.....Succeeded\nRead the manifest and post the files to the API.....Succeeded\nExtract the files in the combine archive.....Succeeded\nProcess the manifest file in the combine archive.....Succeeded\nPost the SED-ML file to the API.....Succeeded\nProcess the SED-ML file in the combine archive.....Succeeded\nPost the logs to the API.....Succeeded\nRetrieve the logs of the simulation run.....Succeeded\nProcess and upload the outputs of the simulation run.....Succeeded\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}