Skip to content
Snippets Groups Projects
Commit 646cf8a6 authored by Marty Kandes's avatar Marty Kandes
Browse files

naked-singularity-v0.9.3 :: updated pytorch-cpu.def and pytorch-gpu.def 

to PyTorch v1.4.0; both builds utilize OpenMPI v3.1.4; CUDA 10 is used
in pytorch-gpu.def; also made some minor updates to Ubuntu definition
files
parent 3c85cc34
No related branches found
No related tags found
No related merge requests found
Expand all Show whitespace changes
Inline Side-by-side
Showing
with 429 additions and 396 deletions
definition-files/comet/pytorch/pytorch-cpu.def
+ 102
− 106
View file @ 646cf8a6
Bootstrap: debootstrap Bootstrap: debootstrap
MirrorURL: http://us.archive.ubuntu.com/ubuntu MirrorURL: http://us.archive.ubuntu.com/ubuntu
OSVersion: xenial OSVersion: bionic
%labels %labels
APPLICATION_NAME pytorch APPLICATION_NAME pytorch
APPLICATION_VERSION 1.2.0 APPLICATION_VERSION 1.4.0
APPLICATION_URL http://pytorch.org/ APPLICATION_URL http://pytorch.org
SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_VERSION 2.6.1
SINGULARITY_IMAGE_SIZE 16384 SINGULARITY_IMAGE_SIZE 16384
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20191015 LAST_UPDATED 20200225
%setup %setup
...@@ -27,8 +24,8 @@ OSVersion: xenial ...@@ -27,8 +24,8 @@ OSVersion: xenial
export LC_ALL=C export LC_ALL=C
# Set paths to OpenMPI binaries and libraries # Set paths to OpenMPI binaries and libraries
export PATH="/opt/openmpi-1.8.4/bin:${PATH}" export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}" export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
# Set default miniconda environment # Set default miniconda environment
export PATH="/opt/miniconda3/bin:${PATH}" export PATH="/opt/miniconda3/bin:${PATH}"
...@@ -72,26 +69,18 @@ OSVersion: xenial ...@@ -72,26 +69,18 @@ OSVersion: xenial
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install gfortran
apt-get -y install pkg-config apt-get -y install pkg-config
apt-get -y install wget apt-get -y install wget
apt-get -y install gfortran
apt-get -y install zip apt-get -y install zip
# Install expect to automate responses for interactive build questions # Install expect to automate responses for interactive build questions
apt-get -y install expect apt-get -y install expect
# Make filesystem mount points
mkdir /cvmfs /oasis /projects /scratch
# Use /tmp to store temporary files within the container during the # Use /tmp to store temporary files within the container during the
# bootstraping process # bootstraping process
cd /tmp cd /tmp
# Install miniconda2
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
chmod +x Miniconda2-latest-Linux-x86_64.sh
./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
# Install miniconda3 # Install miniconda3
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh chmod +x Miniconda3-latest-Linux-x86_64.sh
...@@ -131,19 +120,44 @@ OSVersion: xenial ...@@ -131,19 +120,44 @@ OSVersion: xenial
apt-get -y install zlib1g-dev apt-get -y install zlib1g-dev
# Download, build, and install OpenMPI # Download, build, and install OpenMPI
wget https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.4.tar.gz wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
tar -xzvf openmpi-1.8.4.tar.gz tar -xzvf openmpi-3.1.4.tar.gz
cd openmpi-1.8.4 cd openmpi-3.1.4
./configure --prefix=/opt/openmpi-1.8.4 ./configure --prefix=/opt/openmpi-3.1.4
make all install make all install
# Set paths to OpenMPI binaries and libraries # Set paths to OpenMPI binaries and libraries
export PATH="/opt/openmpi-1.8.4/bin:${PATH}" export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}" export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
# Install PyTorch dependencies for python(2) # Setup conda environment
export PATH="/opt/miniconda2/bin:${PATH}" export PATH="/opt/miniconda3/bin:${PATH}"
export CMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"} export CMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"}
# Install common python packages
conda install -y jupyterlab
conda install -y numpy
conda install -y matplotlib
conda install -y pandas
conda install -y plotly
conda install -y scipy
conda install -y scikit-learn
conda install -y scikit-image
conda install -y seaborn
conda install -y statsmodels
conda install -y opencv
# Install GPU-accelerated python packages
conda install -y numba
# Install additional python packages
conda install -y astropy
conda install -y biopython
conda install -y h5py
conda install -y nltk
conda install -y sympy
# Install PyTorch dependencies
conda install -y numpy conda install -y numpy
conda install -y ninja conda install -y ninja
conda install -y pyyaml conda install -y pyyaml
...@@ -152,115 +166,97 @@ OSVersion: xenial ...@@ -152,115 +166,97 @@ OSVersion: xenial
conda install -y setuptools conda install -y setuptools
conda install -y cmake conda install -y cmake
conda install -y cffi conda install -y cffi
conda install -y typing
conda install -y mkldnn -c mingfeima
conda install -y future
# Install common python packages for data science and machine
# learning applications
conda install -y pandas
conda install -y matplotlib
conda install -y ipython
conda install -y jupyter
conda install -y sympy
conda install -y nose
conda install -y scikit-learn
conda install -y scikit-image
conda install -y nltk
conda install -y statsmodels
conda install -y opencv
cd /opt cd /opt
# Download, build, and install PyTorch for python(2) # Download, build, and install PyTorch
git clone --recursive https://github.com/pytorch/pytorch
cd pytorch
git checkout v1.4.0
git submodule sync
git submodule update --init --recursive
export CC='mpicc' export CC='mpicc'
export CXX='mpicxx' export CXX='mpicxx'
export CFLAGS='-march=haswell -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mmovbe -maes -mno-sha -mpclmul -mpopcnt -mabm -mno-lwp -mfma -mno-fma4 -mno-xop -mbmi -mbmi2 -mno-tbm -mavx -mavx2 -msse4.2 -msse4.1 -mlzcnt -mno-rtm -mno-hle -mrdrnd -mf16c -mfsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=haswell' export CFLAGS='-mtune=generic'
export USE_OPENMP=1
export BLAS='MKL'
export USE_FBGEMM=1
export USE_MKLDNN=1
export USE_NNPACK=1 export USE_NNPACK=1
export USE_NUMPY=1
export USE_QNNPACK=1 export USE_QNNPACK=1
export USE_MKLDNN=1
export USE_DISTRIBUTED=1 export USE_DISTRIBUTED=1
export USE_GLOO=1
export USE_GLOO_IBVERBS=1
export USE_IBVERBS=1 export USE_IBVERBS=1
export USE_GLOO=1
export USE_MPI=1 export USE_MPI=1
export USE_C10D_MPI=1 export USE_C10D_MPI=1
export USE_NCCL=0
export USE_SYSTEM_NCCL=0
export NCCL_INCLUDE_DIR='/usr/include'
export USE_OPENMP=1
export ATEN_THREADING='OMP'
export MKL_THREADING='OMP'
export TORCH_CUDA_ARCH_LIST='NONE'
export USE_CUDA=0 export USE_CUDA=0
export USE_CUDNN=0 export USE_CUDNN=0
export USE_NCCL=0
export USE_FFMPEG=0
export USE_OPENCV=1 export USE_OPENCV=1
export USE_FBGEMM=0
export TORCH_CUDA_ARCH_LIST="NONE"
git clone --recursive https://github.com/pytorch/pytorch
cd /opt/pytorch
git checkout v1.2.0
git submodule sync
git submodule update --init
python setup.py install python setup.py install
# Download and install PyTorch Vision package for python(2) # Download and install vision package for PyTorch
git clone https://github.com/pytorch/vision.git git clone https://github.com/pytorch/vision.git
cd /opt/pytorch/vision cd vision
git checkout v0.3.0 git checkout v0.5.0
python setup.py install python setup.py install
# Install PyTorch dependencies for python3 cd ../
export PATH="/opt/miniconda3/bin:${PATH}"
export CMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"}
conda install -y numpy
conda install -y ninja
conda install -y pyyaml
conda install -y mkl
conda install -y mkl-include
conda install -y setuptools
conda install -y cmake
conda install -y cffi
conda install -y typing
conda install -y mkldnn -c mingfeima
conda install -y future
# Install common python3 packages for data science and machine # Download and install text package for PyTorch
# learning applications git clone https://github.com/pytorch/text.git
conda install -y pandas cd text
conda install -y matplotlib git checkout 0.5.0
conda install -y ipython
conda install -y jupyter
conda install -y sympy
conda install -y nose
conda install -y scikit-learn
conda install -y scikit-image
conda install -y nltk
conda install -y statsmodels
conda install -y opencv
# Download, build, and install PyTorch for python3
cd /opt/pytorch
python setup.py clean --all
python setup.py install python setup.py install
# Download and install PyTorch Vision package for python3 cd ../
cd /opt/pytorch/vision
python setup.py clean --all # Download and install audio package for PyTorch
git clone https://github.com/pytorch/audio.git
cd audio
git checkout v0.4.0
python setup.py install python setup.py install
# Download the PyTorch examples repository cd ../
cd /opt/pytorch
# Download examples for PyTorch
git clone https://github.com/pytorch/examples.git git clone https://github.com/pytorch/examples.git
cd /opt
# Install fastai for PyTorch
git clone https://github.com/fastai/fastai
cd fastai
git checkout 1.0.60
tools/run-after-git-clone
pip install -e ".[dev]"
# Clean up /tmp directory
cd /tmp
rm Miniconda3-latest-Linux-x86_64.sh
rm *.deb
rm -rf openmpi-3.1.4*
# Update database for mlocate # Update database for mlocate
updatedb updatedb
%files %files
%runscript %runscript
echo " "
echo " __________________ __ _______________ "
echo " -----/ ____/ __ \/ |/ / ____/_ __/ "
echo " --/ / / / / / /|_/ / __/ / / "
echo " / /___/ /_/ / / / / /___ / / "
echo " \____/\____/_/ /_/_____/ /_/ "
echo " "
%test %test
definition-files/comet/pytorch/pytorch-gpu.def
+ 308
− 254
View file @ 646cf8a6
This diff is collapsed.
definition-files/comet/ubuntu/ubuntu-cuda-openmpi.def
+ 1
− 17
View file @ 646cf8a6
...@@ -14,7 +14,7 @@ OSVersion: bionic ...@@ -14,7 +14,7 @@ OSVersion: bionic
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20200211 LAST_UPDATED 20200225
%setup %setup
...@@ -26,7 +26,6 @@ OSVersion: bionic ...@@ -26,7 +26,6 @@ OSVersion: bionic
# Set paths to CUDA binaries and libraries # Set paths to CUDA binaries and libraries
export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}" export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}" export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
# Set paths to OpenMPI binaries and libraries # Set paths to OpenMPI binaries and libraries
export PATH="/opt/openmpi-3.1.4/bin:${PATH}" export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
...@@ -337,24 +336,9 @@ OSVersion: bionic ...@@ -337,24 +336,9 @@ OSVersion: bionic
dpkg -i python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb dpkg -i python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb
dpkg -i python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb dpkg -i python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb
# Fixing some path-related issues associated with deb-based install of libcudnn and libnccl ...
mv /usr/lib/x86_64-linux-gnu/libcudnn_static.a /usr/local/cuda-10.1/lib64/libcudnn_static.a
mv /usr/lib/x86_64-linux-gnu/libcudnn_static_v7.a /usr/local/cuda-10.1/lib64/libcudnn_static_v7.a
mv /usr/lib/x86_64-linux-gnu/libcudnn.so.7.6.5 /usr/local/cuda-10.1/lib64/libcudnn.so.7.6.5
ln -s /usr/local/cuda-10.1/lib64/libcudnn.so.7.6.5 /usr/local/cuda-10.1/lib64/libcudnn.so.7
ln -s /usr/local/cuda-10.1/lib64/libcudnn.so.7 /usr/local/cuda-10.1/lib64/libcudnn.so
mv /usr/lib/x86_64-linux-gnu/libnccl_static.a /usr/local/cuda-10.1/lib64/libnccl_static.a
mv /usr/lib/x86_64-linux-gnu/libnccl.so.2.5.6 /usr/local/cuda-10.1/lib64/libnccl.so.2.5.6
ln -s /usr/local/cuda-10.1/lib64/libnccl.so.2.5.6 /usr/local/cuda-10.1/lib64/libnccl.so.2
ln -s /usr/local/cuda-10.1/lib64/libnccl.so.2 /usr/local/cuda-10.1/lib64/libnccl.so
mv /usr/include/nccl.h /usr/local/cuda-10.1/include/nccl.h
ln -s /usr/local/cuda-10.1/lib64 /usr/local/cuda-10.1/lib
mv /usr/share/doc/libnccl2/NCCL-SLA.txt.gz /usr/local/cuda-10.1/NCCL-SLA.txt
# Set paths to CUDA binaries and libraries # Set paths to CUDA binaries and libraries
export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}" export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}" export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
# Install basic drivers for user space access to Ethernet, RDMA, # Install basic drivers for user space access to Ethernet, RDMA,
# and Infiniband. See https://community.mellanox.com/docs/DOC-2431 # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
......
definition-files/comet/ubuntu/ubuntu-cuda.def
+ 6
− 17
View file @ 646cf8a6
...@@ -14,7 +14,7 @@ OSVersion: bionic ...@@ -14,7 +14,7 @@ OSVersion: bionic
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20200210 LAST_UPDATED 20200225
%setup %setup
...@@ -26,7 +26,6 @@ OSVersion: bionic ...@@ -26,7 +26,6 @@ OSVersion: bionic
# Set paths to CUDA binaries and libraries # Set paths to CUDA binaries and libraries
export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}" export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}" export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
# Set default miniconda environment # Set default miniconda environment
export PATH="/opt/miniconda3/bin:${PATH}" export PATH="/opt/miniconda3/bin:${PATH}"
...@@ -333,24 +332,14 @@ OSVersion: bionic ...@@ -333,24 +332,14 @@ OSVersion: bionic
dpkg -i python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb dpkg -i python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb
dpkg -i python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb dpkg -i python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb
# Fixing some path-related issues associated with deb-based install of libcudnn and libnccl ...
mv /usr/lib/x86_64-linux-gnu/libcudnn_static.a /usr/local/cuda-10.1/lib64/libcudnn_static.a
mv /usr/lib/x86_64-linux-gnu/libcudnn_static_v7.a /usr/local/cuda-10.1/lib64/libcudnn_static_v7.a
mv /usr/lib/x86_64-linux-gnu/libcudnn.so.7.6.5 /usr/local/cuda-10.1/lib64/libcudnn.so.7.6.5
ln -s /usr/local/cuda-10.1/lib64/libcudnn.so.7.6.5 /usr/local/cuda-10.1/lib64/libcudnn.so.7
ln -s /usr/local/cuda-10.1/lib64/libcudnn.so.7 /usr/local/cuda-10.1/lib64/libcudnn.so
mv /usr/lib/x86_64-linux-gnu/libnccl_static.a /usr/local/cuda-10.1/lib64/libnccl_static.a
mv /usr/lib/x86_64-linux-gnu/libnccl.so.2.5.6 /usr/local/cuda-10.1/lib64/libnccl.so.2.5.6
ln -s /usr/local/cuda-10.1/lib64/libnccl.so.2.5.6 /usr/local/cuda-10.1/lib64/libnccl.so.2
ln -s /usr/local/cuda-10.1/lib64/libnccl.so.2 /usr/local/cuda-10.1/lib64/libnccl.so
mv /usr/include/nccl.h /usr/local/cuda-10.1/include/nccl.h
ln -s /usr/local/cuda-10.1/lib64 /usr/local/cuda-10.1/lib
mv /usr/share/doc/libnccl2/NCCL-SLA.txt.gz /usr/local/cuda-10.1/NCCL-SLA.txt
# Set paths to CUDA binaries and libraries # Set paths to CUDA binaries and libraries
export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}" export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}" export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
# Clean up /tmp directory
cd /tmp
rm Miniconda3-latest-Linux-x86_64.sh
rm *.deb
# Update database for mlocate # Update database for mlocate
updatedb updatedb
......
definition-files/comet/ubuntu/ubuntu-openmpi.def
+ 7
− 1
View file @ 646cf8a6
...@@ -14,7 +14,7 @@ OSVersion: bionic ...@@ -14,7 +14,7 @@ OSVersion: bionic
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20200213 LAST_UPDATED 20200225
%setup %setup
...@@ -130,6 +130,12 @@ OSVersion: bionic ...@@ -130,6 +130,12 @@ OSVersion: bionic
export PATH="/opt/openmpi-3.1.4/bin:${PATH}" export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}" export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
# Clean up /tmp directory
cd /tmp
rm Miniconda3-latest-Linux-x86_64.sh
rm *.deb
rm -rf openmpi-3.1.4*
# Update database for mlocate # Update database for mlocate
updatedb updatedb
......
definition-files/comet/ubuntu/ubuntu.def
+ 5
− 1
View file @ 646cf8a6
...@@ -14,7 +14,7 @@ OSVersion: bionic ...@@ -14,7 +14,7 @@ OSVersion: bionic
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20200210 LAST_UPDATED 20200225
%setup %setup
...@@ -82,6 +82,10 @@ OSVersion: bionic ...@@ -82,6 +82,10 @@ OSVersion: bionic
chmod +x Miniconda3-latest-Linux-x86_64.sh chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3 ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
# Clean up /tmp directory
cd /tmp
rm Miniconda3-latest-Linux-x86_64.sh
# Update database for mlocate # Update database for mlocate
updatedb updatedb
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment