SimEx_Test.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
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   "outputs": [],
   "source": [
    "from SimEx import *\n",
    "from os.path import isfile, isdir\n",
    "from os import getcwd, listdir\n",
    "import inspect\n",
    "from subprocess import Popen, call, PIPE\n",
    "from ipywidgets import widgets\n",
    "from IPython.display import display"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "#sig = inspect.signature(PhotonBeamParameters.__init__)\n",
    "#sig.parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "beam = PhotonBeamParameters(\n",
    "    photon_energy = 4972.0*electronvolt,  # photon energy in eV\n",
    "    beam_diameter_fwhm=1.3e-7*meter,         # focus diameter in m\n",
    "    pulse_energy=0.45e-3*joule,                   # pulse energy in J\n",
    "    photon_energy_relative_bandwidth=0.003, # relative bandwidth dE/E\n",
    "    divergence=0.0*radian,                         # Beam divergence in rad\n",
    "    photon_energy_spectrum_type='tophat',   # Spectrum type. Acceptable values are \"tophat\", \"SASE\", and \"twocolor\")\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Checking presence of 5udc.pdb. Will query from PDB if not found in $PWD.\n",
      "Sample path is set to 5udc.pdb.\n"
     ]
    }
   ],
   "source": [
    "parameters = CrystFELPhotonDiffractorParameters(\n",
    "    sample='5udc.pdb',                    # Looks up pdb file in cwd, if not found, queries from RCSB pdb mirror.\n",
    "    uniform_rotation=True,                # Apply random rotation\n",
    "    number_of_diffraction_patterns=1,     #\n",
    "    powder=False,                         # Set to True to create a virtual powder diffraction pattern (unested) \n",
    "    intensities_file=None,                # File that contains reflection intensities. If set to none, use uniform intensity distribution\n",
    "    crystal_size_range=[1e-7,1e-7],       # Range ([min,max]) in units of metres of crystal size.\n",
    "    poissonize=False,                     # Set to True to add Poisson noise.\n",
    "    number_of_background_photons=0,       # Change number to add uniformly distributed background photons.\n",
    "    suppress_fringes=False,               # Set to True to suppress side maxima between reflection peaks.\n",
    "    beam_parameters=beam,                 # Beam parameters object from above\n",
    "    detector_geometry='simple.geom',      # External file that contains the detector geometry in CrystFEL notation.\n",
    "    )\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "False"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "parameters.use_gpu"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "if not isfile('simple.geom'):\n",
    "    xfile = !wget https://raw.githubusercontent.com/eucall-software/simex_platform/develop/Tests/python/unittest/TestFiles/simple.geom"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from SimEx.Utilities.EntityChecks import checkAndSetInstance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "diffractor = CrystFELPhotonDiffractor(\n",
    "    parameters=parameters,      \n",
    "    output_path=\"xstal_diffr\")  # Output will go to a new dir \"xstal_diffr/\" in the current directory.'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "dfile = 'diffractor.dill'\n",
    "diffractor.dumpToFile(dfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/home/reppinjo/xstal_diffr'"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "diffractor.output_path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "def submitSLURM():\n",
    "    batch_template = '''#!/bin/sh\n",
    "    #SBATCH --partition={0}   \n",
    "    #SBATCH --time={1}       \n",
    "    #SBATCH --nodes={2}\n",
    "    #SBATCH --output={3}/crystfel_%A.out\n",
    "\n",
    "    export MODULEPATH=$MODULEPATH:$HOME/simex_dev_workshop/modulefiles\n",
    "    module load python3/3.4\n",
    "    module load simex\n",
    "\n",
    "    mpirun -np {4} python3 $HOME/simex_platform/Sources/python/SimEx/Calculators/CrystFELPhotonDiffractor.py {5}\n",
    "    '''\n",
    "\n",
    "    partition = 'maxwell'\n",
    "    time = '00:10:00'\n",
    "    nnodes = 1\n",
    "    ntask = 24\n",
    "    final_script = batch_template.format(partition, time, nnodes, getcwd(), ntask, dfile)\n",
    "\n",
    "    fname = 'batch.sh'\n",
    "    with open(fname,'w') as ffile:\n",
    "        ffile.write(final_script)\n",
    "\n",
    "    slurm = Popen(['sbatch',fname], stdout=PIPE)\n",
    "    print(slurm.stdout.read().strip().decode('utf-8'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
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   "outputs": [
    {
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       "model_id": "96482fde7bdb4e9d9c3cc280c7b7d2d9",
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       "version_minor": 0
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      "text/plain": [
       "Button(description='Submit to SLURM', style=ButtonStyle())"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Submitted batch job 977270\n"
     ]
    }
   ],
   "source": [
    "w = widgets.Button(description='Submit to SLURM')\n",
    "w.on_click(lambda b: submitSLURM())\n",
    "display(w)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)\r\n",
      "            977268   maxwell     bash reppinjo  R       3:57      1 max-wn060\r\n"
     ]
    }
   ],
   "source": [
    "!squeue -u reppinjo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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