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Update Pylith-plot-test.ipynb
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@chongjh11
chongjh11 committed Jun 6, 2024
1 parent 8d44500 commit add054e
Showing 1 changed file with 17 additions and 7 deletions.
24 changes: 17 additions & 7 deletions Pylith-plot-test.ipynb
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"cell_type": "code",
"execution_count": 1,
"id": "4981e2d8",
"metadata": {},
"metadata": {
"metadata": {}
},
"outputs": [],
"source": [
"import pandas as pd\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import h5py \n"
"import h5py \n",
"\n",
"# This script was running in Jupyter Notebook\n",
"print('Setup complete')"
]
},
{
Expand All @@ -20,20 +25,25 @@
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'h5py' is not defined",
"ename": "OSError",
"evalue": "Unable to open file (unable to open file: name = '/output/step02_interseismic-groundsurf.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;31mOSError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-2-85bcbaa21aea>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0mfilename\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'/output/step02_interseismic-groundsurf.h5'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0;32mwith\u001b[0m \u001b[0mh5py\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mFile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"r\"\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 5\u001b[0m \u001b[0;31m# Print all root level object names (aka keys)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6\u001b[0m \u001b[0;31m# these can be group or dataset names\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mNameError\u001b[0m: name 'h5py' is not defined"
"\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/h5py/_hl/files.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, **kwds)\u001b[0m\n\u001b[1;32m 404\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mphil\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 405\u001b[0m \u001b[0mfapl\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmake_fapl\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdriver\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlibver\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrdcc_nslots\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrdcc_nbytes\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrdcc_w0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 406\u001b[0;31m fid = make_fid(name, mode, userblock_size,\n\u001b[0m\u001b[1;32m 407\u001b[0m \u001b[0mfapl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfcpl\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmake_fcpl\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtrack_order\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mtrack_order\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 408\u001b[0m swmr=swmr)\n",
"\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/h5py/_hl/files.py\u001b[0m in \u001b[0;36mmake_fid\u001b[0;34m(name, mode, userblock_size, fapl, fcpl, swmr)\u001b[0m\n\u001b[1;32m 171\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mswmr\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mswmr_support\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 172\u001b[0m \u001b[0mflags\u001b[0m \u001b[0;34m|=\u001b[0m \u001b[0mh5f\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mACC_SWMR_READ\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 173\u001b[0;31m \u001b[0mfid\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mh5f\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mflags\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfapl\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mfapl\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 174\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0mmode\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'r+'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 175\u001b[0m \u001b[0mfid\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mh5f\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mh5f\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mACC_RDWR\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfapl\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mfapl\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32mh5py/_objects.pyx\u001b[0m in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mh5py/_objects.pyx\u001b[0m in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mh5py/h5f.pyx\u001b[0m in \u001b[0;36mh5py.h5f.open\u001b[0;34m()\u001b[0m\n",
"\u001b[0;31mOSError\u001b[0m: Unable to open file (unable to open file: name = '/output/step02_interseismic-groundsurf.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)"
]
}
],
"source": [
"# import the file\n",
"filename = '/output/step02_interseismic-groundsurf.h5'\n",
"filename = './output/step02_interseismic-groundsurf.h5'\n",
"\n",
"with h5py.File(filename, \"r\") as f:\n",
" # Print all root level object names (aka keys) \n",
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