<commit_before>{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Automated Post Processing Quick Start\n",
    "\n",
    "\n",
    "\n",
    "This utility has been designed with the goal of being as simple to use as possible, but there are a number of configuration options that must be set before the first run. You will need to collect a few nessesary pieces of information. This document will assume you're running on the acme1.llnl.gov server, but the only thing that would be different if running elsewhere would be paths. All this information will need to be written to the run configuration file run.cfg.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup\n",
    "\n",
    "#### The model run directory on the compute machine. \n",
    "\n",
    "This is the output directory for the model on the HPC facility. An example would be the 20170313.beta1_2 run by <NAME> on Edison:\n",
    "\n",
    "    /scratch2/scratchdirs/golaz/ACME_simulations/20170313.beta1_02.A_WCYCL1850S.ne30_oECv3_ICG.edison/run\n",
    "\n",
    "This path should be written to the run.cfg under \n",
    "* [transfer] source_path = /remote/model/path/run"
   ]
  },
  {
   "cell_type": "markdown",<commit_msg>Updates instructions<commit_after>{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Automated Post Processing Quick Start\n",
    "\n",
    "\n",
    "\n",
    "This utility has been designed with the goal of being as simple to use as possible, but there are a number of configuration options that must be set before the first run. You will need to collect a few nessesary pieces of information. This document will assume you're running on the acme1.llnl.gov server, but the only thing that would be different if running elsewhere would be paths. All this information will need to be written to the run configuration file run.cfg.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup\n",
    "\n",
    "### First time setup keys\n",
    "\n",
    "The keys you need to change before running the first time are:\n",
    "\n",
    "1. [transfer] source_path\n",
    "2. [global] output_path = /your/output/path\n",
    "3. [global] input_path = /your/input/path\n",
    "4. [global] simulation_end_year = SOMENUMBER\n",
    "5. [global] set_frequency = [LIST, OF, NUMBERS]\n",
    "6. [global] run_id = YOUR_RUN_ID\n",
    "7. [monitor] compute_username = YOUR_EDISON_USERNAME\n",
    "8. [monitor] compute_password = <PASSWORD> (optional)\n",
    "9. [transfer] processing_username = YOU_ACME1_USERNAME\n",
    "10. [transfer] processing_password = <PASSWORD> (optional)\n",
    "11. [transfer] globus_username = YOUR_GLOBUS_USERNAME\n",
    "12. [transfer] globus_password = YOUR_GLOBUS_PASSWORD (optional)\n",
    "\n",
    "Once these are set, only the input/output paths and run_id need to be changed for each subsequent run.\n",
    "\n",
    "#### The model run directory on the compute machine. \n",
    "\n",
    "This is the output directory for the model on the HPC facility. An example would be the 20170313.beta1_2 run by <NAME> on Edison:\n",
    "\n",
    "    /scratch2/scratchdirs/golaz/ACME_simulations/20170313.beta1_02.A_WCYCL1850S.ne30_oECv3_ICG.edison/run\n",
    "\n",
    "This path should be written to the run.cfg under \n",
    "* [transfer] source_path = /remote/model/path/run"
   ]
  },
  {
   "cell_type": "markdown",
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