* Saved developmental notebooks to devise/test the "lmod_python_fix.py".
These were done on Wahab with legacy (lmod-based) Python suite.
Sigs:
# -rw-r--r-- 1 wpurwant users 56588 2020-06-09 17:35 debug_ipython_start_1.ipynb
# -rw-r--r-- 1 wpurwant users 20395 2020-06-09 17:34 debug_ipython_start_2.ipynb
# -rw-r--r-- 1 wpurwant users 21965 2020-06-09 19:20 debug_ipython_start_3.ipynb
# -rw-r--r-- 1 wpurwant users 10717 2020-06-09 19:23 debug_ipython_start_4_vanilla.ipynb
# -rw-r--r-- 1 wpurwant users 37041 2020-06-09 19:59 debug_ipython_start_5.ipynb
# b061fbc819806bc18d48287a9654bcc5 debug_ipython_start_1.ipynb
# bc262fc0d3cd290da1f46a242a6fcccb debug_ipython_start_2.ipynb
# 5f289c909e967096712b3196a19979b7 debug_ipython_start_3.ipynb
# b5f0cd9251e325b0c7e0222ba4cfc037 debug_ipython_start_4_vanilla.ipynb
# abc440a885da0872d5bc215adfc3edd7 debug_ipython_start_5.ipynb
This commit is contained in:
Wirawan Purwanto
@@ -0,0 +1,415 @@
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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Examine & fix jupyter / ipython start file\n",
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"\n",
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"Date: 2020-06-09\n",
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"\n",
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"Purpose: Try to examine the outcome of *my* fix to `~/.ipython/profile_default/startup/000-odurc-lmod.py` + the handmade \"module\" command (mine: `lmod_python_fix1.py`).\n",
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"\n",
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"Test-4: this is what happens if we revert to \"vanilla\" module command without changing sys.path.\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"<function env_modules_python.module(command, *arguments)>"
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]
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},
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"execution_count": 1,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"module"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"'/shared/apps/common/lmod/current/init/env_modules_python.py'"
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]
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},
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"execution_count": 2,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"module.__code__.co_filename"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"module??"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"'/tmp/tmp.JtRbow9G3w'"
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]
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},
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"execution_count": 4,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"import os\n",
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"\n",
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"xlibpath = os.environ.get(\"LMOD_MANUAL_LD_LIBRARY_PATH\")\n",
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"xlibpath"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"['/home/wpurwant/Testbeds/jupyter/wahab_jupyter_start',\n",
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" '/shared/apps/common/lmod/scripts/init',\n",
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" '',\n",
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" '/shared/apps/auto/py-jupyter/1.1.4-gcc-7.3.0-cxdz/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-numpy/1.16.3-gcc-7.3.0-mdow/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-six/1.12.0-gcc-7.3.0-ay7a/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-jinja2/2.10-gcc-7.3.0-usre/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-babel/2.6.0-gcc-7.3.0-be4y/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-pytz/2018.4-gcc-7.3.0-wqdr/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-markupsafe/1.0-gcc-7.3.0-biyo/lib/python3.7/site-packages',\n",
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" '/shared/apps/common/python/3.7.3-wqal/lib/python37.zip',\n",
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" '/shared/apps/common/python/3.7.3-wqal/lib/python3.7',\n",
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" '/shared/apps/common/python/3.7.3-wqal/lib/python3.7/lib-dynload',\n",
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" '/home/wpurwant/.local/lib/python3.7/site-packages',\n",
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" '/shared/apps/common/python/3.7.3-wqal/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-jupyter/1.1.4-gcc-7.3.0-cxdz/lib/python3.7/site-packages/IPython/extensions',\n",
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" '/home/wpurwant/.ipython',\n",
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" '/home/wpurwant/Testbeds/jupyter/wahab_jupyter_start',\n",
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" '/shared/apps/common/lmod/current/init']"
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]
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},
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"import sys\n",
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"sys.path"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"['/shared/apps/common/lmod/scripts/init',\n",
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" '/shared/apps/auto/py-jupyter/1.1.4-gcc-7.3.0-cxdz/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-numpy/1.16.3-gcc-7.3.0-mdow/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-six/1.12.0-gcc-7.3.0-ay7a/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-jinja2/2.10-gcc-7.3.0-usre/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-babel/2.6.0-gcc-7.3.0-be4y/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-pytz/2018.4-gcc-7.3.0-wqdr/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-markupsafe/1.0-gcc-7.3.0-biyo/lib/python3.7/site-packages']"
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]
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},
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"execution_count": 7,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"os.environ['PYTHONPATH'].split(\":\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"total 0\r\n"
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]
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}
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],
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"source": [
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"ls -l $xlibpath"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"Currently Loaded Modules:\n",
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" 1) python/3.7.3 5) py-jinja2/2.10 9) py-jupyter/1.1.4\n",
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" 2) py-markupsafe/1.0 6) py-six/1.12.0 10) texlive/2020\n",
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" 3) py-pytz/2018.4 7) intel-mkl/2019.4.243\n",
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" 4) py-babel/2.6.0 8) py-numpy/1.16.3\n",
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"\n",
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" \n",
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"\n",
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"\n"
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]
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}
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],
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"source": [
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"module(\"list\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"total 0\r\n"
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]
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}
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],
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"source": [
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"ls -l $xlibpath"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"['/home/wpurwant/Testbeds/jupyter/wahab_jupyter_start',\n",
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" '/shared/apps/common/lmod/scripts/init',\n",
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" '',\n",
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" '/shared/apps/auto/py-jupyter/1.1.4-gcc-7.3.0-cxdz/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-numpy/1.16.3-gcc-7.3.0-mdow/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-six/1.12.0-gcc-7.3.0-ay7a/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-jinja2/2.10-gcc-7.3.0-usre/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-babel/2.6.0-gcc-7.3.0-be4y/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-pytz/2018.4-gcc-7.3.0-wqdr/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-markupsafe/1.0-gcc-7.3.0-biyo/lib/python3.7/site-packages',\n",
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" '/shared/apps/common/python/3.7.3-wqal/lib/python37.zip',\n",
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" '/shared/apps/common/python/3.7.3-wqal/lib/python3.7',\n",
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" '/shared/apps/common/python/3.7.3-wqal/lib/python3.7/lib-dynload',\n",
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" '/home/wpurwant/.local/lib/python3.7/site-packages',\n",
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" '/shared/apps/common/python/3.7.3-wqal/lib/python3.7/site-packages',\n",
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" '/shared/apps/auto/py-jupyter/1.1.4-gcc-7.3.0-cxdz/lib/python3.7/site-packages/IPython/extensions',\n",
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" '/home/wpurwant/.ipython',\n",
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" '/home/wpurwant/Testbeds/jupyter/wahab_jupyter_start',\n",
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" '/shared/apps/common/lmod/current/init']"
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]
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},
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"execution_count": 12,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"import sys\n",
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"sys.path"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"total 0\r\n"
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]
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}
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],
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"source": [
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"ls -l $xlibpath"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"<function env_modules_python.module(command, *arguments)>"
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]
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},
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"execution_count": 14,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"module"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 15,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"Currently Loaded Modules:\n",
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" 1) python/3.7.3 5) py-jinja2/2.10 9) py-jupyter/1.1.4\n",
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" 2) py-markupsafe/1.0 6) py-six/1.12.0 10) texlive/2020\n",
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" 3) py-pytz/2018.4 7) intel-mkl/2019.4.243\n",
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" 4) py-babel/2.6.0 8) py-numpy/1.16.3\n",
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"\n",
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" \n",
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"\n",
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"\n"
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]
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}
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],
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"source": [
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"module(\"list\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 16,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"total 0\r\n"
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]
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}
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],
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"source": [
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"ls -l $xlibpath"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 17,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"The following have been reloaded with a version change:\n",
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" 1) py-pytz/2018.4 => py-pytz/2019.3\n",
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"\n",
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"\n"
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]
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}
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],
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"source": [
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"module(\"load\", \"py-pandas\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 18,
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"metadata": {},
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"outputs": [],
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"source": [
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"import numpy"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 19,
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"metadata": {},
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"outputs": [
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{
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"ename": "ModuleNotFoundError",
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"evalue": "No module named 'pandas'",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
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"\u001b[0;32m<ipython-input-19-38d4b0363d82>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mpandas\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
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"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'pandas'"
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]
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}
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],
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"source": [
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"import pandas"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## ERROR!\n",
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"\n",
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"The running python cannot find pandas."
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.3"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}
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