├── LICENSE ├── README.md ├── build.sh ├── links.sh ├── sherlock.sh ├── tensorflow.sh ├── tf-gpu.def └── tf.def /LICENSE: -------------------------------------------------------------------------------- 1 | Apache License 2 | Version 2.0, January 2004 3 | http://www.apache.org/licenses/ 4 | 5 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 6 | 7 | 1. Definitions. 8 | 9 | "License" shall mean the terms and conditions for use, reproduction, 10 | and distribution as defined by Sections 1 through 9 of this document. 11 | 12 | "Licensor" shall mean the copyright owner or entity authorized by 13 | the copyright owner that is granting the License. 14 | 15 | "Legal Entity" shall mean the union of the acting entity and all 16 | other entities that control, are controlled by, or are under common 17 | control with that entity. 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My 6 | personal machine was MacOS, so I first installed virtualbox, vagrant, and 7 | vagrant-manager. Then I create an ubuntu 14.04 VM using vagrant, and installed 8 | singualrity 2.2 on it. See instructions here 9 | http://singularity.lbl.gov/install-mac. Finally, I installed yum via `sudo 10 | apt-get install yum`. 11 | 12 | ## NVIDIA, CUDA 13 | 14 | Get cuda and nvidia *.run scripts matching those currently on sherlock. As of 15 | 2-21-17, these were cuda 8.0, and nvidia drivers 375.26 . The CUDA driver was 16 | obtained from https://developer.nvidia.com/cuda-downloads, under the linux 17 | centOS 6 downloads for cuda 8. The NVIDIA driver was obtained from 18 | http://www.nvidia.com/Download/driverResults.aspx/112992/en-us. Place the two 19 | *.run scripts within this directory. 20 | 21 | ## cuDNN 22 | 23 | The cuDNN version downloaded was cuDNN 8.0 v5.1, which was obtained from 24 | https://developer.nvidia.com/rdp/cudnn-download, under cuDNN 8.0 v5.1 Library for Linux. 25 | Place the resulting .tar file within this directory. 26 | 27 | # Usage 28 | 29 | From this directory, simply run `sh build.sh`, and then move the resulting 30 | tf-gpu.img onto sherlock (it is 4GB so it may take a while). You will then be 31 | able to run python with the latest version of GPU-enabled tensorflow by running 32 | `module load singularity` and then `singularity run tf-gpu.img`. 33 | 34 | You can confirm you have access to a GPU by running 35 | ``` 36 | import tensorflow as tf 37 | tf.Session(config=tf.ConfigProto(log_device_placement=True)) 38 | ``` 39 | 40 | # Origin 41 | 42 | Adapted from Jianxiong Dong's scripts at 43 | https://github.com/jdongca2003/Tensorflow-singularity-container-with-GPU-support 44 | , as well as Igor and Tru Huynh's advice on the singularity google group at 45 | https://groups.google.com/a/lbl.gov/forum/#!topic/singularity/CezfXNjLGe0 . For 46 | use on Stanford sherlock cluster, which runs CentOS 6.7. 47 | -------------------------------------------------------------------------------- /build.sh: -------------------------------------------------------------------------------- 1 | IMG="tf-gpu.img" 2 | DEF="tf-gpu.def" 3 | sudo rm -f $IMG 4 | sudo singularity create -s 4000 $IMG 5 | sudo singularity bootstrap $IMG $DEF 6 | sudo singularity exec -B `pwd`:/mnt -w $IMG sh /mnt/tensorflow.sh 7 | sudo singularity exec -B `pwd`:/mnt -w $IMG sh /mnt/sherlock.sh 8 | -------------------------------------------------------------------------------- /links.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/bash 2 | 3 | dir=/usr/local/NVIDIA-Linux-x86_64-$1 4 | 5 | cd $dir 6 | 7 | ln -s libcuda.so.$1 libcuda.so 8 | ln -s libEGL.so.$1 libEGL.so 9 | ln -s libGLESv1_CM.so.$1 libGLESv1_CM.so 10 | ln -s libGLESv2.so.$1 libGLESv2.so 11 | ln -s libGL.so.$1 libGL.so 12 | ln -s libglx.so.$1 libglx.so 13 | ln -s libnvcuvid.so.$1 libnvcuvid.so 14 | ln -s libnvidia-cfg.so.$1 libnvidia-cfg.so 15 | ln -s libnvidia-compiler.so.$1 libnvidia-compiler.so 16 | ln -s libnvidia-eglcore.so.$1 libnvidia-eglcore.so 17 | ln -s libnvidia-encode.so.$1 libnvidia-encode.so 18 | ln -s libnvidia-fbc.so.$1 libnvidia-fbc.so 19 | ln -s libnvidia-glcore.so.$1 libnvidia-glcore.so 20 | ln -s libnvidia-glsi.so.$1 libnvidia-glsi.so 21 | ln -s libnvidia-gtk2.so.$1 libnvidia-gtk2.so 22 | ln -s libnvidia-gtk3.so.$1 libnvidia-gtk3.so 23 | ln -s libnvidia-ifr.so.$1 libnvidia-ifr.so 24 | ln -s libnvidia-ml.so.$1 libnvidia-ml.so 25 | ln -s libnvidia-ml.so.$1 libnvidia-ml.so.1 26 | ln -s libnvidia-opencl.so.$1 libnvidia-opencl.so 27 | ln -s libnvidia-tls.so.$1 libnvidia-tls.so 28 | ln -s libnvidia-wfb.so.$1 libnvidia-wfb.so 29 | ln -s libvdpau_nvidia.so.$1 libvdpau_nvidia.so 30 | ln -s libvdpau.so.$1 libvdpau.so 31 | ln -s libvdpau_trace.so.$1 libvdpau_trace.so 32 | ln -s libcuda.so.$1 libcuda.so.1 33 | -------------------------------------------------------------------------------- /sherlock.sh: -------------------------------------------------------------------------------- 1 | # Because sherlock doesn't enable singularity overlay, we must create these 2 | # before moving container to sherlock. 3 | mkdir -p /share/PI 4 | mkdir -p /scratch 5 | mkdir -p /local-scratch 6 | -------------------------------------------------------------------------------- /tensorflow.sh: -------------------------------------------------------------------------------- 1 | driver_version=375.26 2 | cuda="cuda-linux64-rel-8.0.44-21122537.run" 3 | cudnn="cudnn-8.0-linux-x64-v5.1.tar" 4 | sh /mnt/NVIDIA-Linux-x86_64-$driver_version.run -x 5 | mv NVIDIA-Linux-x86_64-$driver_version /usr/local/ 6 | sh /mnt/links.sh $driver_version 7 | 8 | sh /mnt/$cuda --toolkit --noprompt 9 | tar xvf /mnt/$cudnn -C /usr/local 10 | 11 | driver_path=/usr/local/NVIDIA-Linux-x86_64-$driver_version 12 | echo " " >> /environment 13 | echo "LD_LIBRARY_PATH=/usr/local/cuda/lib64:/usr/local/cuda/extras/CUPTI/lib64:$driver_path:$LD_LIBRARY_PATH" >> /environment 14 | echo "PATH=$driver_path:\$PATH" >> /environment 15 | echo "export PATH LD_LIBRARY_PATH" >> /environment 16 | 17 | export LC_ALL=C 18 | pip install --no-cache-dir tensorflow-gpu==0.12.1 19 | -------------------------------------------------------------------------------- /tf-gpu.def: -------------------------------------------------------------------------------- 1 | # Copyright (c) 2015-2016, Gregory M. Kurtzer. All rights reserved. 2 | # 3 | # "Singularity" Copyright (c) 2016, The Regents of the University of California, 4 | # through Lawrence Berkeley National Laboratory (subject to receipt of any 5 | # required approvals from the U.S. Dept. of Energy). All rights reserved. 6 | 7 | BootStrap: docker 8 | From: library/ubuntu:trusty 9 | IncludeCmd: yes 10 | 11 | %runscript 12 | exec /usr/bin/python "$@" 13 | 14 | %post 15 | apt-get update && apt-get -y upgrade 16 | apt-get -y install vim \ 17 | python-pip 18 | -------------------------------------------------------------------------------- /tf.def: -------------------------------------------------------------------------------- 1 | Bootstrap: docker 2 | From: tensorflow/tensorflow:latest 3 | IncludeCmd: yes 4 | 5 | %runscript 6 | exec /usr/bin/python "$@" 7 | 8 | %post 9 | apt-get update && apt-get -y upgrade 10 | --------------------------------------------------------------------------------