2.biocellion_SA_run.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 2. Biocellion Sensitivity Analysis - Run\n",
    "This notebook defines functions to run simulations for the Biocellion ABM models by the CMMC that can be found in github.com/TheCMMC. For more information on the CMMC, visit www.thecmmc.org.  \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import re\n",
    "\n",
    "import pandas as pd\n",
    "import xml.etree.ElementTree as ET\n",
    "\n",
    "from pathlib import Path\n",
    "from datetime import datetime\n",
    "from itertools import chain"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "## User settings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Set this data folder to the place where you cloned the repository https://github.com/TheCMMC/biocellion-data\n",
    "MODEL_FOLDER = Path(\"/home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers\")\n",
    "TOOLS_FOLDER = Path(\"/home/jaroknor/NLeSC/InSilicoMeat/Biocellion/biocellion-tools\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Run biocellion simulations\n",
    "Now that we have sampled the parameters, we can run all simulations for these parameter sets. We need to fill in the paramater values in the correct place in the biocellion files and compile the model. Then run the model and store the results. The output of each run will get a unique time stamp and a parameter file that contains the parameters for that run. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "class Model:\n",
    "    def __init__(self, param_vector, model_folder, output_base_folder, problem, param_info, num_steps=None):\n",
    "        self.param_vector = param_vector\n",
    "        self.model_folder = model_folder\n",
    "        self.output_base_folder = output_base_folder\n",
    "        self.problem = problem\n",
    "        self.param_info = param_info\n",
    "        self.num_steps = num_steps\n",
    "        \n",
    "        self.init_time = None\n",
    "        self.timestamp = None\n",
    "        self.xml = None\n",
    "        self.xml_path = None\n",
    "        self.output_location = None\n",
    "        \n",
    "        self._set_timestamp()\n",
    "        \n",
    "        \n",
    "    def _set_timestamp(self):\n",
    "        self.init_time = datetime.now()\n",
    "        self.timestamp = self.init_time.strftime(\"%Y%m%d-%H%M%S\")\n",
    "\n",
    "\n",
    "    def _prepare_xml(self):\n",
    "        \"\"\"Read original xml file and write to timestamped new file\"\"\"\n",
    "\n",
    "        base_xml_path = self.model_folder / \"run_model.xml\"\n",
    "        self.xml = ET.parse(base_xml_path)\n",
    "        self.xml_path = base_xml_path.with_stem(f\"run_model_{self.timestamp}\")\n",
    "        self.xml.write(self.xml_path)\n",
    "\n",
    "    def _prepare_output_location(self):\n",
    "        \"\"\"Creates new timestamped folder and renames output paths in xml file\"\"\"\n",
    "\n",
    "        self.output_location = self.output_base_folder / f\"output_{self.timestamp}\"\n",
    "        os.mkdir(self.output_location)\n",
    "\n",
    "        #  rename the output paths \n",
    "        root = self.xml.getroot()\n",
    "        for element in chain(root.iter(\"output\"), root.iter(\"stdout\")):\n",
    "            element.set(\"path\", str(self.output_location))\n",
    "        self.xml.write(self.xml_path)\n",
    "        \n",
    "    def _write_simulation_info(self):\n",
    "        param_sample_df = pd.DataFrame([self.param_vector], columns=self.problem[\"names\"])\n",
    "        param_sample_df.to_csv(self.output_location / f\"parameters_{self.timestamp}.csv\")\n",
    "\n",
    "    def _set_num_steps(self):\n",
    "        \"\"\"Creates new timestamped folder and renames output paths in xml file\"\"\"\n",
    "\n",
    "        root = self.xml.getroot()\n",
    "        for element in root.iter(\"time_step\"):\n",
    "            element.set(\"end\", str(self.num_steps))\n",
    "        self.xml.write(self.xml_path)        \n",
    "        \n",
    "\n",
    "    def _enter_parameter(self, index, value):\n",
    "        info = self.param_info.loc[index]\n",
    "        parameter_loc = self.model_folder / info[\"file\"]\n",
    "        param_type, param_name = info[\"type\"], info[\"name\"]\n",
    "        string = f\"const {param_type} {param_name} = .+ ;\" \n",
    "        pattern = re.compile(string)\n",
    "        new_string = f\"const {param_type} {param_name} = {value} ;\"\n",
    "        \n",
    "        with open(parameter_loc, \"r\") as file:\n",
    "            content = file.read()\n",
    "            assert re.search(pattern, content)\n",
    "            content = re.sub(pattern, new_string, content)\n",
    "            \n",
    "        with open(parameter_loc, \"w\") as file:\n",
    "            file.write(content) \n",
    "        \n",
    "        \n",
    "    def prepare(self):\n",
    "        \"\"\"Enters the parameter values and output locations in the right file and place, then compiles the model.\"\"\"\n",
    "\n",
    "        print(f\"Preparing model at {self.init_time}\")\n",
    "        self._prepare_xml()\n",
    "        self._prepare_output_location()\n",
    "        self._write_simulation_info()\n",
    "        if self.num_steps:\n",
    "            self._set_num_steps()\n",
    "        for i, value in enumerate(self.param_vector):\n",
    "            self._enter_parameter(i, value)\n",
    "        print(f\"Output will be collected in: \\n {self.output_location}\")\n",
    "\n",
    "\n",
    "    def build(self):\n",
    "        \"\"\"Builds the model using make, after cleaning up the previous build\"\"\"\n",
    "        print(\"Building the model...\")\n",
    "        cwd = os.getcwd()\n",
    "        os.chdir(self.model_folder)\n",
    "        \n",
    "        os.system(\"make clean\")\n",
    "        os.system(\"make -s\")\n",
    "\n",
    "        os.chdir(cwd)\n",
    "\n",
    "        \n",
    "    def run(self):\n",
    "        print(f\"Starting simulation with {self.xml_path.stem}\")\n",
    "        cwd = os.getcwd()\n",
    "        os.chdir(self.model_folder)\n",
    "        !biocellion {self.xml_path}\n",
    "        os.chdir(cwd)\n",
    "        os.rename(self.xml_path, self.output_location / self.xml_path.name)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Preparing model at 2021-06-21 17:33:00.371283\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output/output_20210621-173300\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210621-173300\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n"
     ]
    }
   ],
   "source": [
    "output_base_folder = MODEL_FOLDER / \"output\"\n",
    "model = Model(param_sample[0], MODEL_FOLDER, output_base_folder, problem, param_info, num_steps=101)\n",
    "model.prepare()\n",
    "model.build()\n",
    "model.run()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "def run_batch(param_vectors, problem, param_info, model_folder, num_steps=101):\n",
    "    # Create the parameter sample file to be able to rerun the same batch\n",
    "    timestamp = datetime.now().strftime(\"%Y%m%d-%H%M%S\")\n",
    "    batch_output_folder = model_folder / f\"output_SA_{timestamp}\"\n",
    "    os.mkdir(batch_output_folder)\n",
    "    param_sample_df = pd.DataFrame(param_vectors, columns=problem[\"names\"])\n",
    "    param_sample_df.to_csv(batch_output_folder / f\"parameter_sample_{timestamp}.csv\")\n",
    "    param_info.to_csv(batch_output_folder / f\"parameter_info_{timestamp}.csv\")\n",
    "    \n",
    "    for i, param_vector in enumerate(param_vectors):\n",
    "        print(f\"Starting run for parameter set {i}\")\n",
    "        model = Model(param_vector, model_folder, batch_output_folder, problem, param_info, num_steps=num_steps)\n",
    "        model.prepare()\n",
    "        model.build()\n",
    "        model.run()\n",
    "        print(\"---------------- \\n\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Starting run for parameter set 0\n",
      "Preparing model at 2021-06-04 17:59:35.226399\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210604-175935\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210604-175935\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.0002 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 1\n",
      "Preparing model at 2021-06-04 18:13:23.076155\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210604-181323\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210604-181323\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.00023 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 2\n",
      "Preparing model at 2021-06-04 18:25:04.626915\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210604-182504\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210604-182504\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000231 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 3\n",
      "Preparing model at 2021-06-04 18:36:41.604051\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210604-183641\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210604-183641\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000578 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 4\n",
      "Preparing model at 2021-06-04 19:19:20.669074\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210604-191920\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210604-191920\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.012444 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 5\n",
      "Preparing model at 2021-06-05 15:03:08.100718\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210605-150308\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210605-150308\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000569 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 6\n",
      "Preparing model at 2021-06-06 04:33:18.888528\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210606-043318\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210606-043318\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.00477 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 7\n",
      "Preparing model at 2021-06-06 14:46:44.749310\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210606-144644\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210606-144644\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.005355 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 8\n",
      "Preparing model at 2021-06-06 21:40:04.350168\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210606-214004\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210606-214004\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000259 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 9\n",
      "Preparing model at 2021-06-06 21:54:47.483392\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210606-215447\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210606-215447\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.001207 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 10\n",
      "Preparing model at 2021-06-07 03:45:15.429289\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210607-034515\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210607-034515\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.003733 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 11\n",
      "Preparing model at 2021-06-07 12:28:04.362802\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210607-122804\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210607-122804\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000274 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 12\n",
      "Preparing model at 2021-06-07 12:43:51.406189\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210607-124351\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210607-124351\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000253 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 13\n",
      "Preparing model at 2021-06-07 13:00:49.754825\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210607-130049\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210607-130049\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000524 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 14\n",
      "Preparing model at 2021-06-07 13:45:18.006102\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210607-134518\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210607-134518\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000255 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 15\n",
      "Preparing model at 2021-06-07 13:59:26.860220\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210607-135926\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210607-135926\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000361 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 16\n",
      "Preparing model at 2021-06-07 14:19:47.242064\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210607-141947\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210607-141947\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000232 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 17\n",
      "Preparing model at 2021-06-07 14:34:29.377119\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210607-143429\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210607-143429\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.001129 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 18\n",
      "Preparing model at 2021-06-07 15:21:19.845072\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210607-152119\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210607-152119\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.0007 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 19\n",
      "Preparing model at 2021-06-07 16:24:22.600794\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210607-162422\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210607-162422\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000229 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 20\n",
      "Preparing model at 2021-06-07 16:38:47.235787\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210607-163847\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210607-163847\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.005594 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 21\n",
      "Preparing model at 2021-06-08 04:05:23.174582\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210608-040523\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210608-040523\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.011238 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 22\n",
      "Preparing model at 2021-06-08 18:54:18.287240\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210608-185418\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210608-185418\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.001205 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 23\n",
      "Preparing model at 2021-06-08 23:02:12.747850\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210608-230212\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210608-230212\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000753 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 24\n",
      "Preparing model at 2021-06-09 01:01:48.625414\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-010148\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-010148\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.001038 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 25\n",
      "Preparing model at 2021-06-09 02:46:12.041049\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-024612\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-024612\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000928 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 26\n",
      "Preparing model at 2021-06-09 04:04:29.687431\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-040429\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-040429\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000233 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 27\n",
      "Preparing model at 2021-06-09 04:18:03.719503\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-041803\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-041803\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000496 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 28\n",
      "Preparing model at 2021-06-09 05:01:18.623184\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-050118\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-050118\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000656 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 29\n",
      "Preparing model at 2021-06-09 07:56:37.025266\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-075637\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-075637\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000827 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 30\n",
      "Preparing model at 2021-06-09 09:14:16.898391\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-091416\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-091416\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000231 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 31\n",
      "Preparing model at 2021-06-09 09:25:55.853048\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-092555\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-092555\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.0002 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 32\n",
      "Preparing model at 2021-06-09 09:40:01.887949\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-094001\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-094001\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000222 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 33\n",
      "Preparing model at 2021-06-09 09:51:22.509227\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-095122\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-095122\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000237 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 34\n",
      "Preparing model at 2021-06-09 10:02:58.454654\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-100258\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-100258\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.0002 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 35\n",
      "Preparing model at 2021-06-09 10:19:14.162589\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-101914\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-101914\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.001368 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 36\n",
      "Preparing model at 2021-06-09 12:20:49.692929\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-122049\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-122049\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.000561 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 37\n",
      "Preparing model at 2021-06-09 14:28:18.728102\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210609-142818\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210609-142818\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.004127 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 38\n",
      "Preparing model at 2021-06-10 06:43:11.941311\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210610-064311\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210610-064311\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n",
      "termination took 0.052921 seconds.\n",
      "Simulation finished.\n",
      "---------------- \n",
      "\n",
      "Starting run for parameter set 39\n",
      "Preparing model at 2021-06-11 10:07:19.934912\n",
      "Output will be collected in: \n",
      " /home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/output_20210604-175935/output_20210611-100719\n",
      "Building the model...\n",
      "Starting simulation with run_model_20210611-100719\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_node_groups\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_nodes_per_group\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"num_sockets_per_node\" (child element of \"system\") will be ignored.\n",
      "WARNING, this binary does not support distributed memory parallelism, and \"load_balance\" (attribute of \"interval\") will be ignored.\n",
      "Reading Velocity_220rpm.txt...  read 291016 points.\n"
     ]
    }
   ],
   "source": [
    "run_batch(param_sample, problem, param_info, MODEL_FOLDER, num_steps=120000)"
   ]
  }
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