{"status":"SUCCEEDED","exception":null,"skipReason":null,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m=================================================== Set up storage ==================================================\u001b[0m\n\n\u001b[0;36m========================================== Downloading COMBINE/OMEX 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    421      0 --:--:-- --:--:-- --:--:--   422\n\r100  777k  100  777k    0     0  1646k      0 --:--:-- --:--:-- --:--:-- 1646k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX 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 log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (24.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/rawLog.txt\nCompleted 3.4 KiB/3.4 KiB (50.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/reports.h5 (deflated 60%)\n  adding: outputs/Smith1980_HypothalamicRegulation.sedml/ (stored 0%)\n  adding: outputs/Smith1980_HypothalamicRegulation.sedml/plot_1_task1.pdf (deflated 25%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 33.0 KiB/33.0 KiB (432.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/outputs/reports.h5\nCompleted 25.9 KiB/52.3 KiB (317.7 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/output.zip\nCompleted 25.9 KiB/52.3 KiB (317.7 KiB/s) with 3 file(s) remaining\rCompleted 36.0 KiB/52.3 KiB (337.6 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/outputs/plots.zip\nCompleted 36.0 KiB/52.3 KiB (337.6 KiB/s) with 2 file(s) remaining\rCompleted 49.7 KiB/52.3 KiB (449.0 KiB/s) with 2 file(s) remaining\rupload: outputs/Smith1980_HypothalamicRegulation.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/outputs/Smith1980_HypothalamicRegulation.sedml/plot_1_task1.pdf\nCompleted 49.7 KiB/52.3 KiB (449.0 KiB/s) with 1 file(s) remaining\rCompleted 52.3 KiB/52.3 KiB (394.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/MODEL7898438988-biopax2.owl  \n  inflating: contents/MODEL7898438988-biopax3.owl  \n  inflating: contents/MODEL7898438988-matlab.m  \n  inflating: contents/MODEL7898438988-octave.m  \n  inflating: contents/MODEL7898438988.m  \n  inflating: contents/MODEL7898438988.ode  \n  inflating: contents/MODEL7898438988.pdf  \n  inflating: contents/MODEL7898438988.png  \n  inflating: contents/MODEL7898438988.svg  \n  inflating: contents/MODEL7898438988_url.xml  \n  inflating: contents/Smith1980_HypothalamicRegulation-biopax2.owl  \n  inflating: contents/Smith1980_HypothalamicRegulation-biopax3.owl  \n  inflating: contents/Smith1980_HypothalamicRegulation-matlab.m  \n  inflating: contents/Smith1980_HypothalamicRegulation-octave.m  \n  inflating: contents/Smith1980_HypothalamicRegulation.cps  \n  inflating: contents/Smith1980_HypothalamicRegulation.ode  \n  inflating: contents/Smith1980_HypothalamicRegulation.sedml  \n  inflating: contents/Smith1980_HypothalamicRegulation.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 2.7 KiB/997.4 KiB (35.3 KiB/s) with 22 file(s) remaining\rupload: contents/MODEL7898438988-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/MODEL7898438988-biopax3.owl\nCompleted 2.7 KiB/997.4 KiB (35.3 KiB/s) with 21 file(s) remaining\rCompleted 5.9 KiB/997.4 KiB (49.4 KiB/s) with 21 file(s) remaining\rupload: contents/MODEL7898438988-matlab.m to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/MODEL7898438988-matlab.m\nCompleted 5.9 KiB/997.4 KiB (49.4 KiB/s) with 20 file(s) remaining\rCompleted 9.2 KiB/997.4 KiB (66.8 KiB/s) with 20 file(s) remaining\rupload: contents/MODEL7898438988-octave.m to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/MODEL7898438988-octave.m\nCompleted 9.2 KiB/997.4 KiB (66.8 KiB/s) with 19 file(s) remaining\rCompleted 18.1 KiB/997.4 KiB (127.9 KiB/s) with 19 file(s) remaining\rupload: contents/MODEL7898438988_url.xml to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/MODEL7898438988_url.xml\nCompleted 18.1 KiB/997.4 KiB (127.9 KiB/s) with 18 file(s) remaining\rCompleted 19.0 KiB/997.4 KiB (131.8 KiB/s) with 18 file(s) remaining\rupload: contents/MODEL7898438988.svg to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/MODEL7898438988.svg\nCompleted 19.0 KiB/997.4 KiB (131.8 KiB/s) with 17 file(s) remaining\rCompleted 79.0 KiB/997.4 KiB (542.3 KiB/s) with 17 file(s) remaining\rupload: contents/Smith1980_HypothalamicRegulation.cps to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/Smith1980_HypothalamicRegulation.cps\nCompleted 79.0 KiB/997.4 KiB (542.3 KiB/s) with 16 file(s) remaining\rCompleted 88.0 KiB/997.4 KiB (554.6 KiB/s) with 16 file(s) remaining\rupload: contents/Smith1980_HypothalamicRegulation-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/Smith1980_HypothalamicRegulation-biopax2.owl\nCompleted 88.0 KiB/997.4 KiB (554.6 KiB/s) with 15 file(s) remaining\rCompleted 100.0 KiB/997.4 KiB (618.1 KiB/s) with 15 file(s) remaining\rupload: contents/Smith1980_HypothalamicRegulation-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/Smith1980_HypothalamicRegulation-biopax3.owl\nCompleted 100.0 KiB/997.4 KiB (618.1 KiB/s) with 14 file(s) remaining\rCompleted 104.8 KiB/997.4 KiB (569.1 KiB/s) with 14 file(s) remaining\rupload: contents/Smith1980_HypothalamicRegulation-octave.m to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/Smith1980_HypothalamicRegulation-octave.m\nCompleted 104.8 KiB/997.4 KiB (569.1 KiB/s) with 13 file(s) remaining\rCompleted 108.2 KiB/997.4 KiB (571.5 KiB/s) with 13 file(s) remaining\rupload: contents/Smith1980_HypothalamicRegulation.ode to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/Smith1980_HypothalamicRegulation.ode\nCompleted 108.2 KiB/997.4 KiB (571.5 KiB/s) with 12 file(s) remaining\rCompleted 364.2 KiB/997.4 KiB (1.8 MiB/s) with 12 file(s) remaining  \rCompleted 620.2 KiB/997.4 KiB (3.1 MiB/s) with 12 file(s) remaining  \rCompleted 625.0 KiB/997.4 KiB (3.0 MiB/s) with 12 file(s) remaining  \rupload: contents/Smith1980_HypothalamicRegulation-matlab.m to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/Smith1980_HypothalamicRegulation-matlab.m\nCompleted 625.0 KiB/997.4 KiB (3.0 MiB/s) with 11 file(s) remaining\rCompleted 625.6 KiB/997.4 KiB (3.0 MiB/s) with 11 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/curation_notes.txt\nCompleted 625.6 KiB/997.4 KiB (3.0 MiB/s) with 10 file(s) remaining\rCompleted 628.3 KiB/997.4 KiB (2.9 MiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/manifest.xml\nCompleted 628.3 KiB/997.4 KiB (2.9 MiB/s) with 9 file(s) remaining\rCompleted 632.5 KiB/997.4 KiB (2.8 MiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/metadata.rdf\nCompleted 632.5 KiB/997.4 KiB (2.8 MiB/s) with 8 file(s) remaining\rCompleted 644.6 KiB/997.4 KiB (2.9 MiB/s) with 8 file(s) remaining\rupload: contents/Smith1980_HypothalamicRegulation.sedml to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/Smith1980_HypothalamicRegulation.sedml\nCompleted 644.6 KiB/997.4 KiB (2.9 MiB/s) with 7 file(s) remaining\rCompleted 684.6 KiB/997.4 KiB (2.9 MiB/s) with 7 file(s) remaining\rupload: contents/Smith1980_HypothalamicRegulation.xml to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/Smith1980_HypothalamicRegulation.xml\nCompleted 684.6 KiB/997.4 KiB (2.9 MiB/s) with 6 file(s) remaining\rCompleted 852.7 KiB/997.4 KiB (3.3 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/curation_image.png\nCompleted 852.7 KiB/997.4 KiB (3.3 MiB/s) with 5 file(s) remaining\rCompleted 857.8 KiB/997.4 KiB (3.3 MiB/s) with 5 file(s) remaining\rupload: contents/MODEL7898438988.png to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/MODEL7898438988.png\nCompleted 857.8 KiB/997.4 KiB (3.3 MiB/s) with 4 file(s) remaining\rCompleted 859.4 KiB/997.4 KiB (3.1 MiB/s) with 4 file(s) remaining\rupload: contents/MODEL7898438988.ode to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/MODEL7898438988.ode\nCompleted 859.4 KiB/997.4 KiB (3.1 MiB/s) with 3 file(s) remaining\rCompleted 992.3 KiB/997.4 KiB (3.5 MiB/s) with 3 file(s) remaining\rupload: contents/MODEL7898438988.pdf to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/MODEL7898438988.pdf\nCompleted 992.3 KiB/997.4 KiB (3.5 MiB/s) with 2 file(s) remaining\rCompleted 994.9 KiB/997.4 KiB (3.4 MiB/s) with 2 file(s) remaining\rupload: contents/MODEL7898438988-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/MODEL7898438988-biopax2.owl\nCompleted 994.9 KiB/997.4 KiB (3.4 MiB/s) with 1 file(s) remaining\rCompleted 997.4 KiB/997.4 KiB (3.2 MiB/s) with 1 file(s) remaining\rupload: contents/MODEL7898438988.m to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/contents/MODEL7898438988.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 11.3 KiB/11.3 KiB (118.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6c195afd5df175f181/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Smith1980_HypothalamicRegulation.sedml\ncreating dataset /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1, shape: (20, 101), type: float64\ndataset created, uuid: d-7b83d865-69167fae-2ea3-ccef07-d3dc2b, chunk_size: (20, 101)\ncreating dataset /Smith1980_HypothalamicRegulation.sedml/plot_1_task1, shape: (6, 101), type: float64\ndataset created, uuid: d-7b83d865-69167fae-b886-1df2d6-2916ef, chunk_size: (6, 101)\ncreating attribute combineArchiveLocation in /Smith1980_HypothalamicRegulation.sedml\ncreating attribute uri in /Smith1980_HypothalamicRegulation.sedml\ncreating attribute _type in /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1\ncreating attribute uri in /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1\ncreating attribute _type in /Smith1980_HypothalamicRegulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Smith1980_HypothalamicRegulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Smith1980_HypothalamicRegulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Smith1980_HypothalamicRegulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Smith1980_HypothalamicRegulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Smith1980_HypothalamicRegulation.sedml/plot_1_task1\ncreating attribute sedmlId in /Smith1980_HypothalamicRegulation.sedml/plot_1_task1\ncreating attribute sedmlName in /Smith1980_HypothalamicRegulation.sedml/plot_1_task1\ncreating attribute uri in /Smith1980_HypothalamicRegulation.sedml/plot_1_task1\ncreate_links: /\ngot link: Smith1980_HypothalamicRegulation.sedml\ncreate_links: /Smith1980_HypothalamicRegulation.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1 to tgt: /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1, shape: (20, 101), type: float64\niterating over chunks for /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 20, 1), slice(0, 101, 1))\ndone with dataload for /Smith1980_HypothalamicRegulation.sedml/autogen_report_for_task1\nwrite_dataset src: /Smith1980_HypothalamicRegulation.sedml/plot_1_task1 to tgt: /Smith1980_HypothalamicRegulation.sedml/plot_1_task1, shape: (6, 101), type: float64\niterating over chunks for /Smith1980_HypothalamicRegulation.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 101, 1))\ndone with dataload for /Smith1980_HypothalamicRegulation.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b6c195afd5df175f181\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nCreate thumbnails from the images specified in the manifest ... succeeded.\nPost thumbnails to the API ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.28785,"sedDocuments":[{"location":"Smith1980_HypothalamicRegulation.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  Smith1980_HypothalamicRegulation.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 20 data sets\r\n    Plots (1):\r\n      plot_1_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: Smith1980_HypothalamicRegulation.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":0.831955,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.226343,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.40783,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"},{"id":"p1_curve_4_task1","status":"SUCCEEDED"},{"id":"p1_curve_5_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.069463,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_L","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_H","status":"SUCCEEDED"},{"id":"autogen_task1_h","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_b1","status":"SUCCEEDED"},{"id":"autogen_task1_g1","status":"SUCCEEDED"},{"id":"autogen_task1_b2","status":"SUCCEEDED"},{"id":"autogen_task1_g2","status":"SUCCEEDED"},{"id":"autogen_task1_b3","status":"SUCCEEDED"},{"id":"autogen_task1_Compartment","status":"SUCCEEDED"},{"id":"autogen_task1_LH_formation","status":"SUCCEEDED"},{"id":"autogen_task1_T_formation","status":"SUCCEEDED"},{"id":"autogen_task1_R_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_LH_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_T_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_R_formation","status":"SUCCEEDED"}]}]}]}