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poppingtonic/Testing BLAS.ipynb

Created August 11, 2017 14:38
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Wrapping BLAS/Fortran code in Cython
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Testing BLAS.ipynb
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"<pre class=\"cython line score-16\" onclick='toggleDiv(this)'>+<span class=\"\">08</span>: <span class=\"k\">import</span> <span class=\"nn\">scipy.linalg.blas</span> <span class=\"k\">as</span> <span class=\"nn\">fblas</span></pre>\n",
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"<pre class=\"cython line score-11\" onclick='toggleDiv(this)'>+<span class=\"\">10</span>: <span class=\"n\">REAL</span> <span class=\"o\">=</span> <span class=\"n\">np</span><span class=\"o\">.</span><span class=\"n\">float32</span></pre>\n",
"<pre class='cython code score-11 '> __pyx_t_2 = <span class='pyx_c_api'>__Pyx_GetModuleGlobalName</span>(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 10, __pyx_L1_error)\n",
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"<pre class=\"cython line score-0\">&#xA0;<span class=\"\">12</span>: </pre>\n",
"<pre class=\"cython line score-0\">&#xA0;<span class=\"\">13</span>: <span class=\"k\">cdef</span> <span class=\"kr\">extern</span> <span class=\"k\">from</span> <span class=\"s\">&quot;/home/brian/src/ai.learn/OpenMined/PySonar/notebooks/voidptr.h&quot;</span><span class=\"p\">:</span></pre>\n",
"<pre class=\"cython line score-0\">&#xA0;<span class=\"\">14</span>: <span class=\"n\">void</span><span class=\"o\">*</span> <span class=\"n\">PyCObject_AsVoidPtr</span><span class=\"p\">(</span><span class=\"nb\">object</span> <span class=\"n\">obj</span><span class=\"p\">)</span></pre>\n",
"<pre class=\"cython line score-0\">&#xA0;<span class=\"\">15</span>: </pre>\n",
"<pre class=\"cython line score-0\" onclick='toggleDiv(this)'>+<span class=\"\">16</span>: <span class=\"k\">ctypedef</span> <span class=\"n\">void</span> <span class=\"p\">(</span><span class=\"o\">*</span><span class=\"n\">scopy_ptr</span><span class=\"p\">)</span> <span class=\"p\">(</span><span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">N</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">X</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">incX</span><span class=\"p\">,</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">Y</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">incY</span><span class=\"p\">)</span> <span class=\"k\">nogil</span></pre>\n",
"<pre class='cython code score-0 '>typedef void (*__pyx_t_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_scopy_ptr)(int const *, float const *, int const *, float *, int const *);\n",
"</pre><pre class=\"cython line score-0\" onclick='toggleDiv(this)'>+<span class=\"\">17</span>: <span class=\"k\">ctypedef</span> <span class=\"n\">void</span> <span class=\"p\">(</span><span class=\"o\">*</span><span class=\"n\">saxpy_ptr</span><span class=\"p\">)</span> <span class=\"p\">(</span><span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">N</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">alpha</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">X</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">incX</span><span class=\"p\">,</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">Y</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">incY</span><span class=\"p\">)</span> <span class=\"k\">nogil</span></pre>\n",
"<pre class='cython code score-0 '>typedef void (*__pyx_t_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_saxpy_ptr)(int const *, float const *, float const *, int const *, float *, int const *);\n",
"</pre><pre class=\"cython line score-0\" onclick='toggleDiv(this)'>+<span class=\"\">18</span>: <span class=\"k\">ctypedef</span> <span class=\"nb\">float</span> <span class=\"p\">(</span><span class=\"o\">*</span><span class=\"n\">sdot_ptr</span><span class=\"p\">)</span> <span class=\"p\">(</span><span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">N</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">X</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">incX</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">Y</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">incY</span><span class=\"p\">)</span> <span class=\"k\">nogil</span></pre>\n",
"<pre class='cython code score-0 '>typedef float (*__pyx_t_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_sdot_ptr)(int const *, float const *, int const *, float const *, int const *);\n",
"</pre><pre class=\"cython line score-0\" onclick='toggleDiv(this)'>+<span class=\"\">19</span>: <span class=\"k\">ctypedef</span> <span class=\"n\">double</span> <span class=\"p\">(</span><span class=\"o\">*</span><span class=\"n\">dsdot_ptr</span><span class=\"p\">)</span> <span class=\"p\">(</span><span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">N</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">X</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">incX</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">Y</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">incY</span><span class=\"p\">)</span> <span class=\"k\">nogil</span></pre>\n",
"<pre class='cython code score-0 '>typedef double (*__pyx_t_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_dsdot_ptr)(int const *, float const *, int const *, float const *, int const *);\n",
"</pre><pre class=\"cython line score-0\" onclick='toggleDiv(this)'>+<span class=\"\">20</span>: <span class=\"k\">ctypedef</span> <span class=\"n\">double</span> <span class=\"p\">(</span><span class=\"o\">*</span><span class=\"n\">snrm2_ptr</span><span class=\"p\">)</span> <span class=\"p\">(</span><span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">N</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">X</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">incX</span><span class=\"p\">)</span> <span class=\"k\">nogil</span></pre>\n",
"<pre class='cython code score-0 '>typedef double (*__pyx_t_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_snrm2_ptr)(int const *, float const *, int const *);\n",
"</pre><pre class=\"cython line score-0\">&#xA0;<span class=\"\">21</span>: <span class=\"k\">ctypedef</span> <span class=\"n\">void</span> <span class=\"p\">(</span><span class=\"o\">*</span><span class=\"n\">sscal_ptr</span><span class=\"p\">)</span> <span class=\"p\">(</span><span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">N</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">alpha</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">float</span> <span class=\"o\">*</span><span class=\"n\">X</span><span class=\"p\">,</span> <span class=\"n\">const</span> <span class=\"nb\">int</span> <span class=\"o\">*</span><span class=\"n\">incX</span><span class=\"p\">)</span> <span class=\"k\">nogil</span></pre>\n",
"<pre class=\"cython line score-0\">&#xA0;<span class=\"\">22</span>: </pre>\n",
"<pre class=\"cython line score-9\" onclick='toggleDiv(this)'>+<span class=\"\">23</span>: <span class=\"k\">cdef</span> <span class=\"kt\">scopy_ptr</span> <span class=\"nf\">scopy</span><span class=\"o\">=&lt;</span><span class=\"n\">scopy_ptr</span><span class=\"o\">&gt;</span><span class=\"n\">PyCObject_AsVoidPtr</span><span class=\"p\">(</span><span class=\"n\">fblas</span><span class=\"o\">.</span><span class=\"n\">scopy</span><span class=\"o\">.</span><span class=\"n\">_cpointer</span><span class=\"p\">)</span> <span class=\"c\"># y = x</span></pre>\n",
"<pre class='cython code score-9 '> __pyx_t_1 = <span class='pyx_c_api'>__Pyx_GetModuleGlobalName</span>(__pyx_n_s_fblas); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 23, __pyx_L1_error)\n",
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" __pyx_v_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_scopy = ((__pyx_t_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_scopy_ptr)PyCObject_AsVoidPtr(__pyx_t_1));\n",
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"</pre><pre class=\"cython line score-9\" onclick='toggleDiv(this)'>+<span class=\"\">24</span>: <span class=\"k\">cdef</span> <span class=\"kt\">saxpy_ptr</span> <span class=\"nf\">saxpy</span><span class=\"o\">=&lt;</span><span class=\"n\">saxpy_ptr</span><span class=\"o\">&gt;</span><span class=\"n\">PyCObject_AsVoidPtr</span><span class=\"p\">(</span><span class=\"n\">fblas</span><span class=\"o\">.</span><span class=\"n\">saxpy</span><span class=\"o\">.</span><span class=\"n\">_cpointer</span><span class=\"p\">)</span> <span class=\"c\"># y += alpha * x</span></pre>\n",
"<pre class='cython code score-9 '> __pyx_t_1 = <span class='pyx_c_api'>__Pyx_GetModuleGlobalName</span>(__pyx_n_s_fblas); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 24, __pyx_L1_error)\n",
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" __pyx_t_2 = <span class='pyx_c_api'>__Pyx_PyObject_GetAttrStr</span>(__pyx_t_1, __pyx_n_s_saxpy); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 24, __pyx_L1_error)\n",
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" __pyx_v_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_saxpy = ((__pyx_t_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_saxpy_ptr)PyCObject_AsVoidPtr(__pyx_t_1));\n",
" <span class='pyx_macro_api'>__Pyx_DECREF</span>(__pyx_t_1); __pyx_t_1 = 0;\n",
"</pre><pre class=\"cython line score-9\" onclick='toggleDiv(this)'>+<span class=\"\">25</span>: <span class=\"k\">cdef</span> <span class=\"kt\">sdot_ptr</span> <span class=\"nf\">sdot</span><span class=\"o\">=&lt;</span><span class=\"n\">sdot_ptr</span><span class=\"o\">&gt;</span><span class=\"n\">PyCObject_AsVoidPtr</span><span class=\"p\">(</span><span class=\"n\">fblas</span><span class=\"o\">.</span><span class=\"n\">sdot</span><span class=\"o\">.</span><span class=\"n\">_cpointer</span><span class=\"p\">)</span> <span class=\"c\"># flat = dot(x, y)</span></pre>\n",
"<pre class='cython code score-9 '> __pyx_t_1 = <span class='pyx_c_api'>__Pyx_GetModuleGlobalName</span>(__pyx_n_s_fblas); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 25, __pyx_L1_error)\n",
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" __pyx_v_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_sdot = ((__pyx_t_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_sdot_ptr)PyCObject_AsVoidPtr(__pyx_t_1));\n",
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"</pre><pre class=\"cython line score-9\" onclick='toggleDiv(this)'>+<span class=\"\">26</span>: <span class=\"k\">cdef</span> <span class=\"kt\">dsdot_ptr</span> <span class=\"nf\">dsdot</span><span class=\"o\">=&lt;</span><span class=\"n\">dsdot_ptr</span><span class=\"o\">&gt;</span><span class=\"n\">PyCObject_AsVoidPtr</span><span class=\"p\">(</span><span class=\"n\">fblas</span><span class=\"o\">.</span><span class=\"n\">sdot</span><span class=\"o\">.</span><span class=\"n\">_cpointer</span><span class=\"p\">)</span> <span class=\"c\"># double = dot(x, y)</span></pre>\n",
"<pre class='cython code score-9 '> __pyx_t_1 = <span class='pyx_c_api'>__Pyx_GetModuleGlobalName</span>(__pyx_n_s_fblas); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 26, __pyx_L1_error)\n",
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" __pyx_v_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_dsdot = ((__pyx_t_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_dsdot_ptr)PyCObject_AsVoidPtr(__pyx_t_1));\n",
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"</pre><pre class=\"cython line score-9\" onclick='toggleDiv(this)'>+<span class=\"\">27</span>: <span class=\"k\">cdef</span> <span class=\"kt\">snrm2_ptr</span> <span class=\"nf\">snrm2</span><span class=\"o\">=&lt;</span><span class=\"n\">snrm2_ptr</span><span class=\"o\">&gt;</span><span class=\"n\">PyCObject_AsVoidPtr</span><span class=\"p\">(</span><span class=\"n\">fblas</span><span class=\"o\">.</span><span class=\"n\">snrm2</span><span class=\"o\">.</span><span class=\"n\">_cpointer</span><span class=\"p\">)</span> <span class=\"c\"># sqrt(x^2)</span></pre>\n",
"<pre class='cython code score-9 '> __pyx_t_1 = <span class='pyx_c_api'>__Pyx_GetModuleGlobalName</span>(__pyx_n_s_fblas); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 27, __pyx_L1_error)\n",
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"<pre class='cython code score-9 '> __pyx_t_1 = <span class='pyx_c_api'>__Pyx_GetModuleGlobalName</span>(__pyx_n_s_fblas); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 28, __pyx_L1_error)\n",
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"<pre class=\"cython line score-0\" onclick='toggleDiv(this)'>+<span class=\"\">30</span>: <span class=\"k\">cdef</span> <span class=\"kt\">int</span> <span class=\"nf\">ONE</span> <span class=\"o\">=</span> <span class=\"mf\">1</span></pre>\n",
"<pre class='cython code score-0 '> __pyx_v_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_ONE = 1;\n",
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"<pre class='cython code score-0 '> __pyx_v_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_ONEF = ((__pyx_t_46_cython_magic_9cdd5df9e9ef390fd8f2bcbac58d341e_REAL_t)1.0);\n",
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"<pre class='cython code score-7 '> __pyx_t_1 = <span class='pyx_c_api'>__Pyx_PyInt_As_int</span>(__pyx_v_size); if (unlikely((__pyx_t_1 == (int)-1) &amp;&amp; <span class='py_c_api'>PyErr_Occurred</span>())) __PYX_ERR(0, 34, __pyx_L1_error)\n",
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"<pre class='cython code score-11 '> if (!(likely(((__pyx_v_syn0) == Py_None) || likely(<span class='pyx_c_api'>__Pyx_TypeTest</span>(__pyx_v_syn0, __pyx_ptype_5numpy_ndarray))))) __PYX_ERR(0, 35, __pyx_L1_error)\n",
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"source": [
"%%cython --annotate\n",
"\n",
"import cython\n",
"import numpy as np\n",
"cimport numpy as np\n",
"\n",
"from libc.math cimport exp\n",
"from libc.string cimport memset\n",
"import scipy.linalg.blas as fblas\n",
"\n",
"REAL = np.float32\n",
"ctypedef np.float32_t REAL_t\n",
"\n",
"cdef extern from \"/home/brian/src/ai.learn/OpenMined/PySonar/notebooks/voidptr.h\":\n",
" void* PyCObject_AsVoidPtr(object obj) \n",
"\n",
"ctypedef void (*scopy_ptr) (const int *N, const float *X, const int *incX, float *Y, const int *incY) nogil\n",
"ctypedef void (*saxpy_ptr) (const int *N, const float *alpha, const float *X, const int *incX, float *Y, const int *incY) nogil\n",
"ctypedef float (*sdot_ptr) (const int *N, const float *X, const int *incX, const float *Y, const int *incY) nogil\n",
"ctypedef double (*dsdot_ptr) (const int *N, const float *X, const int *incX, const float *Y, const int *incY) nogil\n",
"ctypedef double (*snrm2_ptr) (const int *N, const float *X, const int *incX) nogil\n",
"ctypedef void (*sscal_ptr) (const int *N, const float *alpha, const float *X, const int *incX) nogil\n",
"\n",
"cdef scopy_ptr scopy=<scopy_ptr>PyCObject_AsVoidPtr(fblas.scopy._cpointer) # y = x\n",
"cdef saxpy_ptr saxpy=<saxpy_ptr>PyCObject_AsVoidPtr(fblas.saxpy._cpointer) # y += alpha * x\n",
"cdef sdot_ptr sdot=<sdot_ptr>PyCObject_AsVoidPtr(fblas.sdot._cpointer) # flat = dot(x, y)\n",
"cdef dsdot_ptr dsdot=<dsdot_ptr>PyCObject_AsVoidPtr(fblas.sdot._cpointer) # double = dot(x, y)\n",
"cdef snrm2_ptr snrm2=<snrm2_ptr>PyCObject_AsVoidPtr(fblas.snrm2._cpointer) # sqrt(x^2)\n",
"cdef sscal_ptr sscal=<sscal_ptr>PyCObject_AsVoidPtr(fblas.sscal._cpointer) # x = alpha * x\n",
"\n",
"cdef int ONE = 1\n",
"cdef REAL_t ONEF = <REAL_t>1.0\n",
"\n",
"def pubDotty(syn0, syn1, size):\n",
" cdef int lSize = size\n",
" f = <REAL_t>dsdot(&lSize, <REAL_t *>(np.PyArray_DATA(syn0)), &ONE, <REAL_t *>(np.PyArray_DATA(syn1)), &ONE)\n",
" return f"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {},
"outputs": [],
"source": [
"np.random.seed(0)\n",
"x = np.zeros(32, dtype='f')\n",
"y = np.zeros(32, dtype='f')\n",
"\n",
"x+=1\n",
"y+=3"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"667 ns ± 22.4 ns per loop (mean ± std. dev. of 7 runs, 1000000 loops each)\n"
]
}
],
"source": [
"%timeit np.dot(x, y)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"189 ns ± 2.12 ns per loop (mean ± std. dev. of 7 runs, 1000000 loops each)\n"
]
}
],
"source": [
"%timeit pubDotty(x, y, len(x))"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"35184380477440.0"
]
},
"execution_count": 34,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pubDotty(x, y, len(x))"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"96.0"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"np.dot(x, y)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.2"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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