| ``` | |
| def logC_taylor(x, eps=1e-7, taylor_center=0.5, taylor_radius=0.05): | |
| eps = torch.tensor(eps).type_as(x) | |
| taylor_center = torch.tensor(taylor_center).type_as(x) | |
| taylor_radius = torch.tensor(taylor_radius).type_as(x) | |
| # singular at zero and one, so regularize | |
| mask = x == 0 | |
| x[mask] = x[mask] + eps |
qmaster in /mnt and chown it to you:
sudo mkdir -p /mnt/qmastersudo chown <username> /mnt/qmaster/Volumes diectory (creating it directly in /Volumes causes trouble with unmounting):
| Traceback (most recent call last): | |
| File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/client/session.py", line 1039, in _do_call | |
| return fn(*args) | |
| File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/client/session.py", line 1021, in _run_fn | |
| status, run_metadata) | |
| File "/usr/lib/python3.5/contextlib.py", line 66, in __exit__ | |
| next(self.gen) | |
| File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/framework/errors_impl.py", line 466, in raise_exception_on_not_ok_status | |
| pywrap_tensorflow.TF_GetCode(status)) | |
| tensorflow.python.framework.errors_impl.NotFoundError: Unsuccessful TensorSliceReader constructor: Failed to find any matching files for ./checkpoints/BEGAN_64_64_0001.tfmod |
These instructions assume an ssh client at least as recent as OpenSSH 7.3, otherwise the ProxyJump will fail.
~/.ssh/config file (change rorydm to your own username):Host tartarus
HostName n70
ProxyJump qmaster
User rorydm
LocalForward 8888 localhost:9999
| # install matching nvidia drivers on AWS | |
| # from https://stradajl.readthedocs.io/en/latest/tutorial/ | |
| # really should rebuild genomics container on top of nvidia-docker | |
| # ---------------------------------------------------------------- | |
| # First update the system and install build-essential: | |
| sudo apt-get update && sudo apt-get upgrade | |
| sudo apt-get install build-essential |
| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "execution_count": 1, | |
| "metadata": { | |
| "collapsed": true | |
| }, | |
| "outputs": [], | |
| "source": [ |
| # clone repo | |
| git clone https://github.com/andersx/fragbuilder | |
| # add to path, wherever you put it | |
| export PYTHONPATH="${HOME}/git-repos/fragbuilder":$PYTHONPATH | |
| # install openbabel dependency | |
| git clone git://github.com/openbabel/openbabel.git | |
| cd openbabel | |
| mkdir build |
| install anaconda | |
| add channel to conda config: | |
| conda config --add channels http://conda.binstar.org/omnia | |
| conda install openmm | |
| conda install openmmtools |
| How to install the MMTK python package | |
| On Mac (10.10) | |
| install anaconda | |
| create an environment with anaconda specifically for MMTK (needs numpy<1.9): | |
| - conda create -n mmtk numpy=1.8.2 | |
| active that environment | |
| - source activate mmtk | |
| install netcdf and cython: |