diff --git a/README.md b/README.md index ac2a07e..459e94b 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,4 @@ -MBARJournalClub -=============== +MSMBuilder3 Design and Python API +================================= + +You can view the slides here: http://rawgit.com/kyleabeauchamp/MSMBuilderTalk/master/index.html diff --git a/notebook/Benchmark.html b/notebook/Benchmark.html deleted file mode 100644 index 3c926ad..0000000 --- a/notebook/Benchmark.html +++ /dev/null @@ -1,1777 +0,0 @@ - - - - - -Notebook - - - - - - - - - - - - - - - - - - - - - - -
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from pymbar.mbar_solvers import logsumexp
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n, m = (10000, 2000)
-x = np.random.normal(size=(n, m))
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%time L = logsumexp(x, axis=1, use_numexpr=False)
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-CPU times: user 399 ms, sys: 17.4 ms, total: 416 ms
-Wall time: 415 ms
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%time L = logsumexp(x, axis=1, use_numexpr=True)
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-CPU times: user 237 ms, sys: 69.9 ms, total: 307 ms
-Wall time: 79.8 ms
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- - diff --git a/notebook/Benchmarking logsumexp.ipynb b/notebook/Benchmarking logsumexp.ipynb deleted file mode 100644 index 947b296..0000000 --- a/notebook/Benchmarking logsumexp.ipynb +++ /dev/null @@ -1,96 +0,0 @@ -{ - "metadata": { - "name": "", - "signature": "sha256:2356219076881dd6da0e16f563e1f1df1cdea267199d06ca55196b08aaa1bfc0" - }, - "nbformat": 3, - "nbformat_minor": 0, - "worksheets": [ - { - "cells": [ - { - "cell_type": "code", - "collapsed": false, - "input": [ - "from pymbar.mbar_solvers import logsumexp\n", - "import numpy as np" - ], - "language": "python", - "metadata": {}, - "outputs": [], - "prompt_number": 1 - }, - { - "cell_type": "code", - "collapsed": false, - "input": [ - "n, m = (10000, 2000)\n", - "x = np.random.normal(size=(n, m))" - ], - "language": "python", - "metadata": {}, - "outputs": [], - "prompt_number": 17 - }, - { - "cell_type": "code", - "collapsed": false, - "input": [ - "%time L = logsumexp(x, axis=1, use_numexpr=False)" - ], - "language": "python", - "metadata": {}, - "outputs": [ - { - "output_type": "stream", - "stream": "stdout", - "text": [ - "CPU times: user 416 ms, sys: 17.7 ms, total: 433 ms\n", - "Wall time: 432 ms\n" - ] - } - ], - "prompt_number": 18 - }, - { - "cell_type": "code", - "collapsed": false, - "input": [ - "%time L = logsumexp(x, axis=1, use_numexpr=True)" - ], - "language": "python", - "metadata": {}, - "outputs": [ - { - "output_type": "stream", - "stream": "stdout", - "text": [ - "CPU times: user 254 ms, sys: 66.7 ms, total: 321 ms\n", - "Wall time: 81.2 ms\n" - ] - } - ], - "prompt_number": 19 - }, - { - "cell_type": "code", - "collapsed": false, - "input": [], - "language": "python", - "metadata": {}, - "outputs": [], - "prompt_number": 15 - }, - { - "cell_type": "code", - "collapsed": false, - "input": [], - "language": "python", - "metadata": {}, - "outputs": [] - } - ], - "metadata": {} - } - ] -} \ No newline at end of file