diff --git a/README b/README
index 811ae1bf33f84465a8e0e2a9ebaa3dc0f2de485e..b893b418a145f22fc2217e7370b972f91535058a 100644
--- a/README
+++ b/README
@@ -10,8 +10,6 @@ DESCRIPTION
* http://singularity.lbl.gov/
-USAGE
-
STATUS
A work in progress.
@@ -29,6 +27,10 @@ AUTHOR
HPC User Services Group, San Diego Supercomputer Center
University of California, San Diego
+VERSION
+
+ 0.1.2
+
LAST UPDATED
- Thursday, December 20th, 2017
+ Wednesday, February 14th, 2018
diff --git a/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-cpu.def b/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-cpu.def
index 71161c0fa9c501153f01ef6ea82d103cb94cb68e..763713db641c9d19528704335837f8349b9c73d3 100644
--- a/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-cpu.def
+++ b/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-cpu.def
@@ -8,12 +8,11 @@ OSVersion: xenial
AUTHOR_EMAIL mkandes@sdsc.edu
APPLICATION_NAME tensorflow
APPLICATION_VERSION 1.4
- APPLICATION_URL https://www.tensorflow.org/
+ APPLICATION_URL https://www.tensorflow.org
SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.3.2
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
- VERSION 0.0.6
- LAST_UPDATED 20180108
+ LAST_UPDATED 20180214
%setup
@@ -48,29 +47,51 @@ OSVersion: xenial
apt-get -y update && apt-get -y upgrade
+ # Install common packages from 'main'
+ apt-get -y install autoconf
+ apt-get -y install automake
+ apt-get -y install build-essential
+ apt-get -y install libtool
+ apt-get -y install pkg-config
+ apt-get -y install gfortran
+ apt-get -y install zip
+
+ # Make filesystem mount points
mkdir /cvmfs /oasis /projects /scratch
- #echo "deb [arch=amd64] http://storage.googleapis.com/bazel-apt stable jdk1.8" | tee /etc/apt/sources.list.d/bazel.list
- #curl https://bazel.build/bazel-release.pub.gpg | apt-key add -
+ # Build and install from source in /opt
+ cd /opt
+
+ ### Install Bazel using custom APT repository
+ ###apt-get -y install openjdk-8-jdk
+ ###echo "deb [arch=amd64] http://storage.googleapis.com/bazel-apt stable jdk1.8" | tee /etc/apt/sources.list.d/bazel.list
+ ###curl https://bazel.build/bazel-release.pub.gpg | apt-key add -
+ ###apt-get -y update
+ ###apt-get -y install bazel
+ ###apt-get -y upgrade bazel
- apt-get -y update
+ # Install Bazel from Debian Package
apt-get -y install openjdk-8-jdk
- #apt-get -y install bazel
- apt-get -y install expect
- apt-get -y install python-numpy
- apt-get -y install python-dev
- apt-get -y install python-pip
- apt-get -y install python-wheel
apt-get -y install zlib1g-dev
-
wget https://github.com/bazelbuild/bazel/releases/download/0.8.1/bazel_0.8.1-linux-x86_64.deb
dpkg -i bazel_0.8.1-linux-x86_64.deb
+ rm bazel_0.8.1-linux-x86_64.deb
- cd /opt
+ # Install expect to automate responses to TensorFlow build questions
+ apt-get -y install expect
+
+ # Install TensorFlow python dependencies
+ apt-get -y install python-numpy
+ apt-get -y install python-dev
+ apt-get -y install python-pip
+ apt-get -y install python-wheel
+
+ # Download TensorFlow source
git clone https://github.com/tensorflow/tensorflow
cd /opt/tensorflow
git checkout r1.4
+ # Build TensorFlow for python(2)
echo '#!/usr/bin/expect -f' > configure.exp
echo 'spawn ./configure' >> configure.exp
echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> configure.exp
@@ -108,9 +129,85 @@ OSVersion: xenial
bazel-bin/tensorflow/tools/pip_package/build_pip_package /opt/tensorflow_pkg
pip install /opt/tensorflow_pkg/tensorflow-1.4.1-cp27-cp27mu-linux_x86_64.whl
+ rm -rf /opt/tensorflow_pkg
+ rm configure.exp
+
+ # Install TensorFlow python3 dependencies
+ apt-get -y install python3-numpy
+ apt-get -y install python3-dev
+ apt-get -y install python3-pip
+ apt-get -y install python3-wheel
+
+ # Build TensorFlow for python3
+ echo '#!/usr/bin/expect -f' > configure.exp
+ echo 'spawn ./configure' >> configure.exp
+ echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> configure.exp
+ echo 'send "/usr/bin/python3\r"' >> configure.exp
+ echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python3.5/dist-packages\]\r"' >> configure.exp
+ echo 'send "/usr/local/lib/python3.5/dist-packages\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> configure.exp
+ echo 'send "Y\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with OpenCL support? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect ": "' >> configure.exp
+ echo 'send " -march=native\r"' >> configure.exp
+ echo 'expect "> "' >> configure.exp
+
+ chmod +x configure.exp
+ ./configure.exp
+ bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
+ bazel-bin/tensorflow/tools/pip_package/build_pip_package /opt/tensorflow_pkg
+
+ pip3 install /opt/tensorflow_pkg/tensorflow-1.4.1-cp35-cp35m-linux_x86_64.whl
+ rm -rf /opt/tensorflow_pkg
+ rm configure.exp
+
+ # Install common python and python3 packages for data science and
+ # machine learning applications
apt-get -y install python-scipy
-
+ apt-get -y install python-pandas
+ apt-get -y install python-matplotlib
+ apt-get -y install ipython
+ apt-get -y install ipython-notebook
+ apt-get -y install python-sympy
+ apt-get -y install python-nose
+ apt-get -y install python-sklearn
+ apt-get -y install python-mlpy
+ apt-get -y install python-nltk
+ apt-get -y install python-statsmodels
+ apt-get -y install libopencv-dev
+ apt-get -y install python-opencv
+
+ apt-get -y install python3-scipy
+ apt-get -y install python3-pandas
+ apt-get -y install python3-matplotlib
+ apt-get -y install ipython3
+ apt-get -y install ipython3-notebook
+ apt-get -y install python3-sympy
+ apt-get -y install python3-nose
+ apt-get -y install python3-sklearn
+ apt-get -y install python3-nltk
+
+ # Update database for mlocate
+ updatedb
+
%files
%runscript
@@ -118,4 +215,5 @@ OSVersion: xenial
%test
time -p python /opt/tensorflow/tensorflow/examples/tutorials/mnist/mnist_deep.py
+ time -p python3 /opt/tensorflow/tensorflow/examples/tutorials/mnist/mnist_deep.py
diff --git a/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-gpu.def b/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-gpu.def
index 172d61bb537e620b11981a42d34cf2c80e56f4d9..b9a918fd8dca8863663f84d851339e6ac4a273d6 100644
--- a/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-gpu.def
+++ b/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-gpu.def
@@ -8,12 +8,11 @@ OSVersion: xenial
AUTHOR_EMAIL mkandes@sdsc.edu
APPLICATION_NAME tensorflow
APPLICATION_VERSION 1.4
- APPLICATION_URL https://www.tensorflow.org/
+ APPLICATION_URL https://www.tensorflow.org
SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.3.2
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
- VERSION 0.0.5
- LAST_UPDATED 20180108
+ SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
+ LAST_UPDATED 20180214
%setup
@@ -48,12 +47,24 @@ OSVersion: xenial
apt-get -y update && apt-get -y upgrade
+ # Install common packages from 'main'
+ apt-get -y install autoconf
+ apt-get -y install automake
+ apt-get -y install build-essential
+ apt-get -y install libtool
+ apt-get -y install pkg-config
+ apt-get -y install gfortran
+ apt-get -y install zip
+
+ # Make filesystem mount points
mkdir /cvmfs /oasis /projects /scratch
+ # Location of NVIDIA repositories
declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
+ # Install NVIDIA package dependencies
apt-get -y install x11-common
apt-get -y install xserver-xorg-core
apt-get -y install cmake
@@ -87,7 +98,8 @@ OSVersion: xenial
cd /opt
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-367_367.48-0ubuntu1_amd64.deb"
+ # Download NVIDIA drivers, libraries, and packages
+ wget --wait=10 "${CUDA_REPO_URL}/nvidia-367_367.48-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/nvidia-367-dev_367.48-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_367.48-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/libcuda1-367_367.48-0ubuntu1_amd64.deb"
@@ -134,6 +146,7 @@ OSVersion: xenial
wget --wait=10 "${ML_REPO_URL}/libnccl2_2.1.2-1+cuda8.0_amd64.deb"
wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.1.2-1+cuda8.0_amd64.deb"
+ # Install NVIDIA drivers, libraries, and packages
dpkg -i nvidia-367_367.48-0ubuntu1_amd64.deb
dpkg -i nvidia-367-dev_367.48-0ubuntu1_amd64.deb
dpkg -i nvidia-modprobe_367.48-0ubuntu1_amd64.deb
@@ -181,31 +194,109 @@ OSVersion: xenial
dpkg -i libnccl2_2.1.2-1+cuda8.0_amd64.deb
dpkg -i libnccl-dev_2.1.2-1+cuda8.0_amd64.deb
+ rm *.deb
+
+ # Set paths to CUDA binaries and libraries
export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- #echo "deb [arch=amd64] http://storage.googleapis.com/bazel-apt stable jdk1.8" | tee /etc/apt/sources.list.d/bazel.list
- #curl https://bazel.build/bazel-release.pub.gpg | apt-key add -
+ # Build and install from source in /opt
+ cd /opt
+
+ ### Install Bazel using custom APT repository
+ ###apt-get -y install openjdk-8-jdk
+ ###echo "deb [arch=amd64] http://storage.googleapis.com/bazel-apt stable jdk1.8" | tee /etc/apt/sources.list.d/bazel.list
+ ###curl https://bazel.build/bazel-release.pub.gpg | apt-key add -
+ ###apt-get -y update
+ ###apt-get -y install bazel
+ ###apt-get -y upgrade bazel
- apt-get -y update
+ # Install Bazel from Debian Package
apt-get -y install openjdk-8-jdk
- #apt-get -y install bazel
- apt-get -y install expect
- apt-get -y install python-dev
- apt-get -y install python3-numpy
- apt-get -y install python3-dev
- apt-get -y install python3-pip
- apt-get -y install python3-wheel
- apt-get -y install libcupti-dev
apt-get -y install zlib1g-dev
-
wget https://github.com/bazelbuild/bazel/releases/download/0.8.1/bazel_0.8.1-linux-x86_64.deb
dpkg -i bazel_0.8.1-linux-x86_64.deb
+ rm bazel_0.8.1-linux-x86_64.deb
- git clone https://github.com/tensorflow/tensorflow
- cd tensorflow
+ # Install expect to automate responses to TensorFlow build questions
+ apt-get -y install expect
+
+ # Install TensorFlow python dependencies
+ apt-get -y install python-numpy
+ apt-get -y install python-dev
+ apt-get -y install python-pip
+ apt-get -y install python-wheel
+
+ # Download TensorFlow source
+ git clone https://github.com/tensorflow/tensorflow
+ cd /opt/tensorflow
git checkout r1.4
+ # Build TensorFlow for python(2)
+ echo '#!/usr/bin/expect -f' > configure.exp
+ echo 'spawn ./configure' >> configure.exp
+ echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> configure.exp
+ echo 'send "/usr/bin/python\r"' >> configure.exp
+ echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python2.7/dist-packages\]\r"' >> configure.exp
+ echo 'send "/usr/local/lib/python2.7/dist-packages\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> configure.exp
+ echo 'send "Y\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with OpenCL support? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> configure.exp
+ echo 'send "Y\r"' >> configure.exp
+ echo 'expect "Please specify the CUDA SDK version you want to use, e.g. 7.0. \[Leave empty to default to CUDA 8.0\]: "' >> configure.exp
+ echo 'send "8.0\r"' >> configure.exp
+ echo 'expect "Please specify the location where CUDA 8.0 toolkit is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> configure.exp
+ echo 'send "/usr/local/cuda\r"' >> configure.exp
+ echo 'expect "Please specify the cuDNN version you want to use. \[Leave empty to default to cuDNN 6.0\]: "' >> configure.exp
+ echo 'send "6.0.21\r"' >> configure.exp
+ echo 'expect "Please specify the location where cuDNN 6.0.21 library is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> configure.exp
+ echo 'send "/usr/lib/x86_64-linux-gnu\r"' >> configure.exp
+ echo 'expect "Please specify a list of comma-separated Cuda compute capabilities you want to build with.\r"' >> configure.exp
+ echo 'expect "You can find the compute capability of your device at: https://developer.nvidia.com/cuda-gpus.\r"' >> configure.exp
+ echo 'expect "Please note that each additional compute capability significantly increases your build time and binary size. \[Default is: 3.5,5.2\]"' >> configure.exp
+ echo 'send "3.7,6.0\r"' >> configure.exp
+ echo 'expect "Do you want to use clang as CUDA compiler? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect "Please specify which gcc should be used by nvcc as the host compiler. \[Default is /usr/bin/gcc\]: "' >> configure.exp
+ echo 'send "/usr/bin/gcc\r"' >> configure.exp
+ echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> configure.exp
+ echo 'send "N\r"' >> configure.exp
+ echo 'expect ": "' >> configure.exp
+ echo 'send " -march=native\r"' >> configure.exp
+ echo 'expect "> "' >> configure.exp
+
+ chmod +x configure.exp
+ ./configure.exp
+
+ bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
+ bazel-bin/tensorflow/tools/pip_package/build_pip_package /opt/tensorflow_pkg
+
+ pip install /opt/tensorflow_pkg/tensorflow-1.4.1-cp27-cp27mu-linux_x86_64.whl
+
+ rm -rf /opt/tensorflow_pkg
+ rm configure.exp
+
+ # Install TensorFlow python3 dependencies
+ apt-get -y install python3-numpy
+ apt-get -y install python3-dev
+ apt-get -y install python3-pip
+ apt-get -y install python3-wheel
+
+ # Build TensorFlow for python3
echo '#!/usr/bin/expect -f' > configure.exp
echo 'spawn ./configure' >> configure.exp
echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> configure.exp
@@ -260,12 +351,45 @@ OSVersion: xenial
pip3 install /opt/tensorflow_pkg/tensorflow-1.4.1-cp35-cp35m-linux_x86_64.whl
+ rm -rf /opt/tensorflow_pkg
+ rm configure.exp
+
+ # Install common python and python3 packages for data science and
+ # machine learning applications
+ apt-get -y install python-scipy
+ apt-get -y install python-pandas
+ apt-get -y install python-matplotlib
+ apt-get -y install ipython
+ apt-get -y install ipython-notebook
+ apt-get -y install python-sympy
+ apt-get -y install python-nose
+ apt-get -y install python-sklearn
+ apt-get -y install python-mlpy
+ apt-get -y install python-nltk
+ apt-get -y install python-statsmodels
+ apt-get -y install libopencv-dev
+ apt-get -y install python-opencv
+
apt-get -y install python3-scipy
-
+ apt-get -y install python3-pandas
+ apt-get -y install python3-matplotlib
+ apt-get -y install ipython3
+ apt-get -y install ipython3-notebook
+ apt-get -y install python3-sympy
+ apt-get -y install python3-nose
+ apt-get -y install python3-sklearn
+ apt-get -y install python3-nltk
+
+ # Update database for mlocate
+ updatedb
+
%files
%runscript
%test
+ # Test TensorFlow for both python and python3
+ time -p python /opt/tensorflow/tensorflow/examples/tutorials/mnist/mnist_deep.py
time -p python3 /opt/tensorflow/tensorflow/examples/tutorials/mnist/mnist_deep.py
+
diff --git a/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def b/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def
index 1e57a15664df18b8c5ad12ae76bf7b528bc13716..491cd42a90d0404dd61b748f75af6800159fd205 100644
--- a/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def
+++ b/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def
@@ -11,10 +11,9 @@ OSVersion: xenial
APPLICATION_URL https://developer.nvidia.com/cuda-zone
DEVICE_DRIVER_VERSION 367.48
SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.3.1
+ SYSTEM_SINGULARITY_VERSION 2.3.2
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
- VERSION 0.0.2
- LAST_UPDATED 20170831
+ LAST_UPDATED 20180214
%setup
@@ -49,12 +48,24 @@ OSVersion: xenial
apt-get -y update && apt-get -y upgrade
+ # Install common packages from 'main'
+ apt-get -y install autoconf
+ apt-get -y install automake
+ apt-get -y install build-essential
+ apt-get -y install libtool
+ apt-get -y install pkg-config
+ apt-get -y install gfortran
+ apt-get -y install zip
+
+ # Make filesystem mount points
mkdir /cvmfs /oasis /projects /scratch
+ # Location of NVIDIA repositories
declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
+ # Install NVIDIA package dependencies
apt-get -y install x11-common
apt-get -y install xserver-xorg-core
apt-get -y install cmake
@@ -88,6 +99,7 @@ OSVersion: xenial
cd /opt
+ # Download NVIDIA drivers, libraries, and packages
wget --wait=10 "${CUDA_REPO_URL}/nvidia-367_367.48-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/nvidia-367-dev_367.48-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_367.48-0ubuntu1_amd64.deb"
@@ -129,12 +141,13 @@ OSVersion: xenial
wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-8-0_8.0.44-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn5_5.1.10-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn5-dev_5.1.10-1+cuda8.0_amd64.deb"
+ wget --wait=10 "${ML_REPO_URL}/libcudnn6_6.0.21-1+cuda8.0_amd64.deb"
+ wget --wait=10 "${ML_REPO_URL}/libcudnn6-dev_6.0.21-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl1_1.2.3-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_1.2.3-1+cuda8.0_amd64.deb"
+ wget --wait=10 "${ML_REPO_URL}/libnccl2_2.1.2-1+cuda8.0_amd64.deb"
+ wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.1.2-1+cuda8.0_amd64.deb"
+ # Install NVIDIA drivers, libraries, and packages
dpkg -i nvidia-367_367.48-0ubuntu1_amd64.deb
dpkg -i nvidia-367-dev_367.48-0ubuntu1_amd64.deb
dpkg -i nvidia-modprobe_367.48-0ubuntu1_amd64.deb
@@ -176,21 +189,28 @@ OSVersion: xenial
dpkg -i cuda-runtime-8-0_8.0.44-1_amd64.deb
dpkg -i cuda-demo-suite-8-0_8.0.44-1_amd64.deb
- dpkg -i libcudnn5_5.1.10-1+cuda8.0_amd64.deb
- dpkg -i libcudnn5-dev_5.1.10-1+cuda8.0_amd64.deb
+ dpkg -i libcudnn6_6.0.21-1+cuda8.0_amd64.deb
+ dpkg -i libcudnn6-dev_6.0.21-1+cuda8.0_amd64.deb
- dpkg -i libnccl1_1.2.3-1+cuda8.0_amd64.deb
- dpkg -i libnccl-dev_1.2.3-1+cuda8.0_amd64.deb
+ dpkg -i libnccl2_2.1.2-1+cuda8.0_amd64.deb
+ dpkg -i libnccl-dev_2.1.2-1+cuda8.0_amd64.deb
+ rm *.deb
+
+ # Set paths to CUDA binaries and libraries
export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
+ # Update database for mlocate
+ updatedb
+
%files
%runscript
%test
+ # Test if nvcc was installed properly
export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
nvcc --version
diff --git a/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu.def b/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu.def
index 18a39823c85529d4b463a2096b1153a3ff96b438..d6847588274302794a5fd1ecdabbcf0b42f52563 100644
--- a/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu.def
+++ b/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu.def
@@ -10,10 +10,9 @@ OSVersion: xenial
APPLICATION_VERSION none
APPLICATION_URL none
SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.3.1
+ SYSTEM_SINGULARITY_VERSION 2.3.2
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
- VERSION 0.0.5
- LAST_UPDATED 20170811
+ LAST_UPDATED 20180213
%setup
@@ -48,8 +47,24 @@ OSVersion: xenial
apt-get -y update && apt-get -y upgrade
+ # Install common packages from 'main'
+ apt-get -y install autoconf
+ apt-get -y install automake
+ apt-get -y install build-essential
+ apt-get -y install libtool
+ apt-get -y install pkg-config
+ apt-get -y install gfortran
+ apt-get -y install zip
+
+ # Make filesystem mount points
mkdir /cvmfs /oasis /projects /scratch
+ # Build and install from souce in /opt
+ cd /opt
+
+ # Update database for mlocate
+ updatedb
+
%files
%runscript