eric496 / linux_settings

Install ubuntu 16.04, CUDA 8.0 and CUDNN 5.0

1. install ubuntu 16.04 without GPU

2. download CUDA 8.0

3. $sudo apt-get update

4. shut down and plug in GPU

5. start and press "esc" to grub2 window

6. hightlight "Ubuntu" and press "e" to edit: add "nomodeset" after "ro" (with a trailing space) in the "linux" line, then press f10 to start

7. sudo chvt 1

8. $sudo service lightdm stop

9. $sudo bash cuda_8.0.44_linux.run

10. $sudo service lightdm start

11. install cuDNN 5.0

    $cd cudnn_foler

    $sudo cp -P include/cudnn.h /usr/include

    $sudo cp -P lib64/libcudnn* /usr/lib/x86_64-linux-gnu/

    $sudo chmod a+r /usr/lib/x86_64-linux-gnu/libcudnn*

12. add PATH to ~/.bashrc

    $export PATH="/usr/local/cuda-8.0/bin:$PATH"

    $export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64:$LD_LIBRARY_PATH"

    $sudo ldconfig /usr/local/cuda-8.0/lib64

Install Anaconda

$bash Anaconda.sh

Install OpenBLAS

$sudo apt-get install gfortran

$git clone https://github.com/xianyi/OpenBLAS

$cd OpenBLAS

$make FC=gfortran

$sudo make PREFIX=/usr/local install

error: "cannot find -lgfortran"

solution: $sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/libgfortran.so

Create Conda virtual environment for all machine learning libraries

$conda create -n mlenv python=2.7

$source activate mlenv

Install TensorFlow

(mlenv)$ conda install -c conda-forge tensorflow

Install Theano

1. $sudo apt-get install python-numpy python-scipy python-dev python-pip python-nose g++ libopenblas-dev git

2. $pip install --upgrade --no-deps git+git://github.com/Theano/Theano.git

3. downgrade g++ to 4.9 (5.3 or later version is not compatible)

   $sudo apt-get install g++-4.9

   $sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 20

   $sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 10

   $sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 20

   $sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-5 10

   $sudo update-alternatives --install /usr/bin/cc cc /usr/bin/gcc 30

   $sudo update-alternatives --set cc /usr/bin/gcc

   $sudo update-alternatives --install /usr/bin/c++ c++ /usr/bin/g++ 30

   $sudo update-alternatives --set c++ /usr/bin/g++

4. work around a glibc bug

   echo -e "\n[nvcc]\nflags=-D_FORCE_INLINES\n" >> ~/.theanorc

5. add the following to ~/.theanorc

    [global]

        floatX = float32

        device = gpu

    [nvcc]

        flags=-D_FORCE_INLINES

        fastmath = True

    [lib]

        cnmem = 0.9

If we want to use one GPU to train multiple small nets, we need to remove the line cnmem=0.9, otherwise we get a theano error (since 90% of the GPU memory is allocated to the first net)

Install Keras

1. $git clone https://github.com/fchollet/keras.git

2. $cd keras; $sudo python setup.py install

Install Torch

1. $git clone https://github.com/torch/distro.git ~/torch --recursive

2. $cd ~/torch; bash install-deps;

3. $ ./install.sh

4. $source ~/.bashrc

Install iTorch

1. $luarocks install lzmq

2. $git clone https://github.com/facebook/iTorch.git

3. $cd iTorch; luarocks make;

Install Caffe

Refer to this but before 'make all' and 'make test', modify the Makefile.config:

INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/include/hdf5/serial/

LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib /usr/lib/x86_64-linux-gnu/hdf5/serial/

Install Mxnet

1. $sudo apt-get update

2. $sudo apt-get install -y build-essential git libatlas-base-dev libopencv-dev

3. $git clone --recursive https://github.com/dmlc/mxnet

4. $vim mxnet/make/config.mk

5. change these lines:

   ADD_LDFLAGS = -I/usr/local/openblas/lib

   ADD_CFLAGS = -I/usr/local/openblas/include

   USE_CUDA = 1

   USE_CUDNN = 1

   USE_CUDA_PATH = /usr/local/cuda-8.0

   USE_BLAS = openblas

6. $cd mxnet; make -j4

7. $cd mxnet/python; python setup.py install

Other libraries

1. opencv: $conda install -c conda-forge opencv
2. sklearn update $conda update scikit-learn
3. seaborn $conda install seaborn

Other settings

Blank screen error

1. $sudo /usr/bin/
2. $gnome-terminal
3. $ccsm
4. "Enable Unity Desktop" - For any conflict, just disable the settings in "General"

Fish settings

$set fish env var:

$set -U fish_user_paths $fish_user_paths my_path

for example: set -U fisher_user_paths $fish_user_paths ~/anaconda2/bin/

Disable "system program problem detected" dialog

1. $sudo rm /var/crash/*
2. $vim /etc/default/apport
3. change "enable=1" to "enable=0"
4. $sudo service apport stop
5. $sudo reboot

Store git credentials

1. $git config credential.helper store
2. $git push http://example.com/repo.git
3. Username:
4. Password:

Matlab launch failure (halting on the start logo)

1. $sudo chown username -R ~/.matlab

2. $sudo apt-get install matlab-support