PreparePartition.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "62972a57-1983-4b8b-b635-60d0886fc2ef",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/lborge01/virtualenvironments/basicP3/lib/python3.11/site-packages/MDAnalysis/topology/TPRParser.py:161: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13\n",
      "  import xdrlib\n"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "sys.path.append('/local/lborge01/Martini_Partition_Source/')\n",
    "from funcs import *\n",
    "import MDAnalysis as md\n",
    "import subprocess\n",
    "import os\n",
    "import numpy as np\n",
    "from collections import Counter\n",
    "from multiprocessing import Process\n",
    "from tqdm import tqdm\n",
    "main_dir = os.getcwd()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "071f8f02-3f75-45e0-89c2-853c551df04e",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "solvents             = ['water', \n",
    "                        'octanol-water_74-26', \n",
    "                        'hexadecane', \n",
    "                        'chloroform']\n",
    "\n",
    "reps                 = [1, 2, 3,]# 4, 5]\n",
    "\n",
    "mols = [\n",
    "    ['Test', '/local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/CG_WAT/initial_CG.itp', '/local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro'],\n",
    "       ]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "443d3e39-2f04-4395-b7e5-dba2599a8383",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/lborge01/virtualenvironments/basicP3/lib/python3.11/site-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/CG_WAT/initial_CG.itp. Skipping this file.\n",
      "  warnings.warn('No coordinate reader found for {}. Skipping '\n",
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/water.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/1/water/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed -151289857\n",
      "Try 1 success (now 904 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Replaced 1 residues (1 atoms)\n",
      "Writing generated configuration to ./Partitions/Test/1/water/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/1/water/system.gro to ./Partitions/Test/1/water/#system.gro.1#\n",
      "\n",
      "Output configuration contains 903 atoms in 898 residues\n",
      "\n",
      "GROMACS reminds you: \"We All Get the Flu, We All Get Aids\" (LIVE)\n",
      "\n",
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/octanol-water_74-26.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/1/octanol-water_74-26/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed -34083617\n",
      "Try 1 success (now 1337 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Replaced 2 residues (6 atoms)\n",
      "Writing generated configuration to ./Partitions/Test/1/octanol-water_74-26/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/1/octanol-water_74-26/system.gro to ./Partitions/Test/1/octanol-water_74-26/#system.gro.1#\n",
      "\n",
      "Output configuration contains 1331 atoms in 468 residues\n",
      "\n",
      "GROMACS reminds you: \"We All Get the Flu, We All Get Aids\" (LIVE)\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n",
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n",
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/hexadecane.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/1/hexadecane/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed -1073764493\n",
      "Try 1 success (now 1246 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Replaced 5 residues (20 atoms)\n",
      "Writing generated configuration to ./Partitions/Test/1/hexadecane/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/1/hexadecane/system.gro to ./Partitions/Test/1/hexadecane/#system.gro.1#\n",
      "\n",
      "Output configuration contains 1226 atoms in 306 residues\n",
      "\n",
      "GROMACS reminds you: \"We All Get the Flu, We All Get Aids\" (LIVE)\n",
      "\n",
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/chloroform.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/1/chloroform/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed -1964507459\n",
      "Try 1 success (now 904 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Replaced 2 residues (2 atoms)\n",
      "Writing generated configuration to ./Partitions/Test/1/chloroform/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/1/chloroform/system.gro to ./Partitions/Test/1/chloroform/#system.gro.1#\n",
      "\n",
      "Output configuration contains 902 atoms in 897 residues\n",
      "\n",
      "GROMACS reminds you: \"We All Get the Flu, We All Get Aids\" (LIVE)\n",
      "\n",
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/water.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/2/water/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed -786449\n",
      "Try 1 success (now 904 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Replaced 1 residues (1 atoms)\n",
      "Writing generated configuration to ./Partitions/Test/2/water/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/2/water/system.gro to ./Partitions/Test/2/water/#system.gro.1#\n",
      "\n",
      "Output configuration contains 903 atoms in 898 residues\n",
      "\n",
      "GROMACS reminds you: \"We All Get the Flu, We All Get Aids\" (LIVE)\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n",
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n",
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/octanol-water_74-26.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/2/octanol-water_74-26/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed -1350571585\n",
      "Try 1 success (now 1337 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Replaced 2 residues (6 atoms)\n",
      "Writing generated configuration to ./Partitions/Test/2/octanol-water_74-26/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/2/octanol-water_74-26/system.gro to ./Partitions/Test/2/octanol-water_74-26/#system.gro.1#\n",
      "\n",
      "Output configuration contains 1331 atoms in 468 residues\n",
      "\n",
      "GROMACS reminds you: \"We All Get the Flu, We All Get Aids\" (LIVE)\n",
      "\n",
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/hexadecane.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/2/hexadecane/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed -279113668\n",
      "Try 1 success (now 1246 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Replaced 1 residues (4 atoms)\n",
      "Writing generated configuration to ./Partitions/Test/2/hexadecane/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/2/hexadecane/system.gro to ./Partitions/Test/2/hexadecane/#system.gro.1#\n",
      "\n",
      "Output configuration contains 1242 atoms in 310 residues\n",
      "\n",
      "GROMACS reminds you: \"We All Get the Flu, We All Get Aids\" (LIVE)\n",
      "\n",
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/chloroform.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/2/chloroform/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed 234815486\n",
      "Try 1 success (now 904 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Writing generated configuration to ./Partitions/Test/2/chloroform/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/2/chloroform/system.gro to ./Partitions/Test/2/chloroform/#system.gro.1#\n",
      "\n",
      "Output configuration contains 904 atoms in 899 residues\n",
      "\n",
      "GROMACS reminds you: \"Contemplating answers that could break my bonds.\" (Peter Hammill)\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n",
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n",
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/water.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/3/water/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed -8528545\n",
      "Try 1 success (now 904 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Replaced 1 residues (1 atoms)\n",
      "Writing generated configuration to ./Partitions/Test/3/water/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/3/water/system.gro to ./Partitions/Test/3/water/#system.gro.1#\n",
      "\n",
      "Output configuration contains 903 atoms in 898 residues\n",
      "\n",
      "GROMACS reminds you: \"Contemplating answers that could break my bonds.\" (Peter Hammill)\n",
      "\n",
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/octanol-water_74-26.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/3/octanol-water_74-26/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed -1107447831\n",
      "Try 1 success (now 1337 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Replaced 1 residues (3 atoms)\n",
      "Writing generated configuration to ./Partitions/Test/3/octanol-water_74-26/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/3/octanol-water_74-26/system.gro to ./Partitions/Test/3/octanol-water_74-26/#system.gro.1#\n",
      "\n",
      "Output configuration contains 1334 atoms in 469 residues\n",
      "\n",
      "GROMACS reminds you: \"Contemplating answers that could break my bonds.\" (Peter Hammill)\n",
      "\n",
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/hexadecane.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/3/hexadecane/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed 2130051039\n",
      "Try 1 success (now 1246 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Replaced 3 residues (12 atoms)\n",
      "Writing generated configuration to ./Partitions/Test/3/hexadecane/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/3/hexadecane/system.gro to ./Partitions/Test/3/hexadecane/#system.gro.1#\n",
      "\n",
      "Output configuration contains 1234 atoms in 308 residues\n",
      "\n",
      "GROMACS reminds you: \"Contemplating answers that could break my bonds.\" (Peter Hammill)\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n",
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n",
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx insert-molecules uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "                 :-) GROMACS - gmx insert-molecules, 2023.4 (-:\n",
      "\n",
      "Executable:   /projects/DAMM/gromacs/avx2256/gromacs-2023.4/bin/gmx\n",
      "Data prefix:  /projects/DAMM/gromacs/avx2256/gromacs-2023.4\n",
      "Working dir:  /local/lborge01/LNP/PartitionTesting/Test\n",
      "Command line:\n",
      "  gmx insert-molecules -f /local/lborge01/Martini_Partition_Source//solvents/chloroform.gro -ci /local/lborge01/LNP/LNP_Param/2ndOrder/Fragment_H7P/cg_good.gro -o ./Partitions/Test/3/chloroform/system.gro -nmol 1 -try 100000 -replace 'not resname UNK'\n",
      "\n",
      "Reading solute configuration\n",
      "Initialising inter-atomic distances...\n",
      "Using random seed -293607898\n",
      "Try 1 success (now 904 atoms)!\n",
      "\n",
      "Added 1 molecules (out of 1 requested)\n",
      "Replaced 2 residues (2 atoms)\n",
      "Writing generated configuration to ./Partitions/Test/3/chloroform/system.gro\n",
      "\n",
      "Back Off! I just backed up ./Partitions/Test/3/chloroform/system.gro to ./Partitions/Test/3/chloroform/#system.gro.1#\n",
      "\n",
      "Output configuration contains 902 atoms in 897 residues\n",
      "\n",
      "GROMACS reminds you: \"Contemplating answers that could break my bonds.\" (Peter Hammill)\n",
      "\n"
     ]
    }
   ],
   "source": [
    "##\n",
    "## Prepare directory structure and data\n",
    "##\n",
    "for mol in mols:\n",
    "    molname, cg_itp, cg_inputstructure = mol\n",
    "    prepare_partition_setup(molname, cg_itp, cg_inputstructure, solvents, reps)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "dca3868f-1ee6-43db-bfbb-715d2fd84b91",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "0it [00:00, ?it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running Test. (1/1)\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "0it [00:10, ?it/s]Process Process-7:\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "Process Process-11:\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "Process Process-14:\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "Process Process-31:\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "Process Process-33:\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "Process Process-18:\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "\n",
      "Process Process-6:\n",
      "\n",
      "KeyboardInterrupt\n",
      "\n",
      "Process Process-22:\n",
      "Process Process-35:\n",
      "Process Process-15:\n",
      "Process Process-12:\n",
      "Process Process-19:\n",
      "Process Process-26:\n",
      "Process Process-34:\n",
      "Process Process-24:\n",
      "Process Process-20:\n",
      "Process Process-13:\n",
      "Process Process-16:\n",
      "Process Process-9:\n",
      "Process Process-2:\n",
      "Process Process-27:\n",
      "Process Process-21:\n",
      "Process Process-5:\n",
      "Process Process-23:\n",
      "Process Process-28:\n",
      "Process Process-36:\n",
      "Process Process-10:\n",
      "Process Process-17:\n",
      "Process Process-4:\n",
      "Process Process-25:\n",
      "Process Process-29:\n",
      "Process Process-30:\n",
      "Process Process-8:\n",
      "Process Process-3:\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "KeyboardInterrupt\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "KeyboardInterrupt\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "KeyboardInterrupt\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "Traceback (most recent call last):\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "KeyboardInterrupt\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "Traceback (most recent call last):\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Process Process-32:\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "Process Process-1:\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "Traceback (most recent call last):\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1262, in wait\n",
      "    return self._wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1997, in _wait\n",
      "    (pid, sts) = self._try_wait(0)\n",
      "                 ^^^^^^^^^^^^^^^^^\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1955, in _try_wait\n",
      "    (pid, sts) = os.waitpid(self.pid, wait_flags)\n",
      "                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "Traceback (most recent call last):\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "Traceback (most recent call last):\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 314, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/usr/lib/python3.11/multiprocessing/process.py\", line 108, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/local/lborge01/Martini_Partition_Source/funcs.py\", line 77, in staterunmd\n",
      "    subprocess.call(f\"gmx mdrun -deffnm rel -v -nt 1 -pin on -pinoffset {offset} -pme cpu -pmefft cpu -bonded cpu -update cpu -nb cpu\",\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 391, in call\n",
      "    return p.wait(timeout=timeout)\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1275, in wait\n",
      "    self._wait(timeout=sigint_timeout)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "  File \"/usr/lib/python3.11/subprocess.py\", line 1991, in _wait\n",
      "    time.sleep(delay)\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n"
     ]
    }
   ],
   "source": [
    "##\n",
    "## Run the partitions!\n",
    "##\n",
    "for idx, mol in tqdm(enumerate(mols)):\n",
    "    molname, cg_itp, cg_inputstructure = mol\n",
    "    print(f'Running {molname}. ({idx+1}/{len(mols)})')\n",
    "    run_partitions_locally(molname, np.unique(md.Universe(cg_itp).atoms.resnames)[0],\n",
    "                           reps, solvents)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4459da58-f28d-4453-9961-ac3063a8d86c",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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