1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
|
#!/bin/bash
# Build script for Linux distribution, for use in automated packaging.
# Note that this must be run from outside the checked-out openmm/ directory.
#
# For Docker build
#
# Fix hbb issues.
# If statements needed because multiple Python versions are built in same docker image.
if [ ! -e /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux ]; then
ln -s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/ /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux
fi
if [ ! -e /opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/x86_64-redhat-linux ]; then
ln -s /opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/x86_64-CentOS-linux/ /opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/x86_64-redhat-linux
fi
# Clang paths
export CLANG_PREFIX="/opt/clang"
export PATH=$PATH:$CLANG_PREFIX/bin
# enable devtoolset-2
# will return an error return code because of python 3.x incompatible code, but this error is inconsequential
#source /opt/rh/devtoolset-2/enable || true
export PATH=/opt/rh/devtoolset-2/root/usr/bin${PATH:+:${PATH}}
export MANPATH=/opt/rh/devtoolset-2/root/usr/share/man:$MANPATH
export INFOPATH=/opt/rh/devtoolset-2/root/usr/share/info${INFOPATH:+:${INFOPATH}}
export PCP_DIR=/opt/rh/devtoolset-2/root
# Some perl Ext::MakeMaker versions install things under /usr/lib/perl5
# even though the system otherwise would go to /usr/lib64/perl5.
export PERL5LIB=/opt/rh/devtoolset-2/root//usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi:/opt/rh/devtoolset-2/root/usr/lib/perl5:/opt/rh/devtoolset-2/root//usr/lib/perl5/vendor_perl/5.8.8${PERL5LIB:+:${PERL5LIB}}
# bz847911 workaround:
# we need to evaluate rpm's installed run-time % { _libdir }, not rpmbuild time
# or else /etc/ld.so.conf.d files?
rpmlibdir=`rpm --eval "%{_libdir}"`
# bz1017604: On 64-bit hosts, we should include also the 32-bit library path.
if [ "$rpmlibdir" != "${rpmlibdir/lib64/}" ]; then
rpmlibdir32=":/opt/rh/devtoolset-2/root${rpmlibdir/lib64/lib}"
fi
export LD_LIBRARY_PATH=/opt/rh/devtoolset-2/root$rpmlibdir$rpmlibdir32${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
# duplicate python site.py logic for sitepackages
pythonvers=`python -c 'import sys; print(sys.version[:3])'`
export PYTHONPATH=/opt/rh/devtoolset-2/root/usr/lib64/python$pythonvers/site-packages:/opt/rh/devtoolset-2/root/usr/lib/python$pythonvers/site-packages${PYTHONPATH:+:${PYTHONPATH}}
# CFLAGS
export MINIMAL_CFLAGS="-g -O3"
export CFLAGS="$MINIMAL_CFLAGS"
export CXXFLAGS="$MINIMAL_CFLAGS"
export LDFLAGS="$LDPATHFLAGS"
# Set relative workspace path.
export WORKSPACE=`pwd`
# Add conda binaries to path.
PATH=$WORKSPACE/miniconda/bin:$PATH
INSTALL=`pwd`/install
if [ -e $INSTALL ]; then
rm -rf $INSTALL
fi
CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$INSTALL"
# Don't build tests
CMAKE_FLAGS+=" -DBUILD_TESTING=OFF"
# Use clang 3.8.1 inside omnia-build-box docker image
CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=$CLANG_PREFIX/bin/clang -DCMAKE_CXX_COMPILER=$CLANG_PREFIX/bin/clang++"
# Ensure we build a release
CMAKE_FLAGS+=" -DCMAKE_BUILD_TYPE=Release"
# setting the rpath so that libOpenMMPME.so finds the right libfftw3
#CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
# Use NVIDIA CUDA 8.0
CMAKE_FLAGS+=" -DCUDA_CUDART_LIBRARY=/usr/local/cuda-8.0/lib64/libcudart.so"
CMAKE_FLAGS+=" -DCUDA_NVCC_EXECUTABLE=/usr/local/cuda-8.0/bin/nvcc"
CMAKE_FLAGS+=" -DCUDA_SDK_ROOT_DIR=/usr/local/cuda-8.0/"
CMAKE_FLAGS+=" -DCUDA_TOOLKIT_INCLUDE=/usr/local/cuda-8.0/include"
CMAKE_FLAGS+=" -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-8.0/"
# Use AMD APP SDK 3.0
CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=/opt/AMDAPPSDK-3.0/include/"
CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so"
# Generate API docs
CMAKE_FLAGS+=" -DOPENMM_GENERATE_API_DOCS=ON"
# Set location for FFTW3
PREFIX="$WORKSPACE/miniconda"
CMAKE_FLAGS+=" -DFFTW_INCLUDES=$PREFIX/include"
CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.so"
CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.so"
# Necessary to find GL headers
CMAKE_FLAGS+=" -DCMAKE_CXX_FLAGS_RELEASE=-I/usr/include/nvidia/"
# Build in subdirectory.
if [ -e build ]; then
rm -rf build
fi
mkdir build
cd build
cmake ../openmm $CMAKE_FLAGS
make -j4 all install
export CFLAGS="$MINIMAL_CFLAGS"
export CXXFLAGS="$MINIMAL_CFLAGS"
export LDFLAGS="$LDPATHFLAGS"
make -j4 PythonInstall C++ApiDocs PythonApiDocs sphinxpdf
# Install.
make install
cd ..
|
