Open philastrophist opened 5 years ago
AstroVPK
commented
5 years ago Can you describe the problems that you're experiencing with the installation process? Let me know what platform you've working on and cut & paste any error messages that you're running across.... Thanks!
philastrophist
commented
5 years ago Yes, I'm attempting to install all of the various dependencies. A few of them fail so I've had to install them using conda or apt-get instead of from source. The main one I'm struggling with at the moment is carmcmc. I get the error message below. If you want to see exactly what I've done. The Dockerfile I'm writing is below as well. Thanks for the help! Your code would be really useful right now!
Dockerfile
FROM ubuntu
SHELL ["/bin/bash", "-c"]
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ENV PATH /opt/conda/bin:$PATH
ENV TINI_VERSION v0.16.1
RUN apt-get update --fix-missing && \
apt-get install -y wget bzip2 ca-certificates curl git build-essential cmake libgtk2.0-common \
libpango-1.0.0 libasound2-dev xserver-xorg cpio && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda && \
rm ~/miniconda.sh && \
/opt/conda/bin/conda clean -tipsy && \
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc
ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
RUN chmod +x /usr/bin/tini
COPY parallel_studio_xe_2019_update5_cluster_edition_online.tgz .
COPY mysilent.cfg .
RUN echo "ACTIVATION_SERIAL_NUMBER=$SERIAL_NUMBER" && echo "ACTIVATION_SERIAL_NUMBER=$SERIAL_NUMBER" >> mysilent.cfg
RUN tar -xvzf parallel_studio_xe_2019_update5_cluster_edition_online.tgz && \
cd parallel_studio_xe_2019_update5_cluster_edition_online && \
./install.sh --silent ../mysilent.cfg --cli-mode && \
echo "source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64" >> ~/.bashrc
RUN cd ~
#COPY l_mkl_2019.5.281_online.tgz .
#RUN tar -xvzf l_mkl_2019.5.281_online.tgz -C mkl && cd mkl
RUN conda install mkl
RUN wget https://github.com/stevengj/nlopt/archive/v2.6.1.tar.gz -O nlopt.tar.gz
RUN tar -xvzf nlopt.tar.gz && cd nlopt-2.6.1/ && cmake . && make && make install && ldconfig && cd ..
RUN conda update --all && conda install cython future pytest
RUN conda install numpy matplotlib scipy
RUN pip install gatspy multi_key_dict fitsio==0.9.8
# carma_pack
# RUN wget http://sourceforge.net/projects/boost/files/boost/1.54.0/boost_1_54_0.tar.bz2 && tar --bzip2 -xf boost_1_54_0.tar.bz2
# RUN cd boost_1_54_0 && ./bootstrap.sh && sed -i 's/explicit yield_sources ;/explicit allocator_sources ;/g' libs/coroutine/build/Jamfile.v2
# RUN cd boost_1_54_0 && ./b2 install
RUN wget http://sourceforge.net/projects/arma/files/armadillo-9.700.3.tar.xz && \
tar -xf armadillo-9.700.3.tar.xz && cd armadillo-9.700.3 && \
cmake -DCMAKE_INSTALL_PREFIX=/opt/armadillo -DBOOST_ROOT=$BOOST_DIR/ . && \
make install && cd ~
RUN apt-get update && apt-get install -y libboost-all-dev
RUN echo "export ARMADILLO_DIR=/opt/armadillo" >> ~/.bashrc
ENV ARMADILLO_DIR "/opt/armadillo"
RUN echo "export LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}" >> ~/.bashrc
ENV LD_LIBRARY_PATH "/usr/local/lib:${LD_LIBRARY_PATH}"
RUN echo "export LD_LIBRARY_PATH=/opt/armadillo/lib:${LD_LIBRARY_PATH}" >> ~/.bashrc
ENV LD_LIBRARY_PATH "/opt/armadillo/lib:${LD_LIBRARY_PATH}"
RUN echo "export BOOST_DIR=/usr/local" >> ~/.bashrc
ENV BOOST_DIR "/usr/local"
ENV NUMPY_DIR "/opt/conda"
RUN git clone https://github.com/brandonckelly/carma_pack.git
RUN cd carma_pack/src/ && pip install .
RUN pip install acor
RUN git clone https://github.com/AstroVPK/kali.git && cd kali && source ./bin/setup.sh && python setup.py build_ext
RUN echo "source ~/kali/bin/setup.sh" >> ~/.bashrc
RUN pytest tests && cd ~
ENTRYPOINT [ "/usr/bin/tini", "--" ]
CMD [ "/bin/bash" ]
Error message
Processing /carma_pack/src
Building wheels for collected packages: carmcmc
Building wheel for carmcmc (setup.py): started
Building wheel for carmcmc (setup.py): still running...
Building wheel for carmcmc (setup.py): finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /opt/conda/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-ORR7mJ/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-ORR7mJ/setup.py'"'"';f=getattr
(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-veJ52d --python-
tag cp27
cwd: /tmp/pip-req-build-ORR7mJ/
Complete output (296 lines):
non-existing path in '.': '/usr/lib64'
non-existing path in '.': '/usr/lib64'
non-existing path in '.': 'examples'
running bdist_wheel
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building library "carmcmc" sources
building extension "carmcmc._carmcmc" sources
building data_files sources
build_src: building npy-pkg config files
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
building 'carmcmc' library
compiling C++ sources
C compiler: g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC
creating build
creating build/temp.linux-x86_64-2.7
compile options: '-I/opt/conda/include -I/usr/local/include -I/opt/armadillo/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/python
2.7/site-packages/numpy/core/include -c'
extra options: '-O3 -std=c++0x'
g++: ./kfilter.cpp
g++: ./proposals.cpp
./kfilter.cpp: In member function ‘virtual std::pair<double, double> KalmanFilter1::Predict(double)’:
./kfilter.cpp:88:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<ipredict; i++) {
~^~~~~~~~~
./kfilter.cpp:124:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=ipredict+1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./kfilter.cpp: In member function ‘virtual void KalmanFilterp::Reset()’:
./kfilter.cpp:147:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=2; i<p_; i++) {
~^~~
./kfilter.cpp:165:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<p_; i++) {
~^~~
./kfilter.cpp:166:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=i; j<p_; j++) {
~^~~
./kfilter.cpp: In member function ‘virtual std::pair<double, double> KalmanFilterp::Predict(double)’:
./kfilter.cpp:232:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<ipredict; i++) {
~^~~~~~~~~
./kfilter.cpp:275:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=ipredict+1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./kfilter.cpp:10:0:
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:256:56: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time.n_elem; i++) {
~^~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:369:62: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++: ./random.cpp
./random.cpp: In member function ‘arma::vec RandomGenerator::normal(arma::mat)’:
./random.cpp:99:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<z.n_elem; i++) {
~^~~~~~~~~
g++: ./carpack.cpp
g++: ./carmcmc.cpp
./carpack.cpp: In member function ‘virtual arma::vec CARp::SetStartingValue(arma::vec)’:
./carpack.cpp:236:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (init.n_elem != (p_+3)) {
~~~~~~~~~~~~^~~~~~~~~
./carpack.cpp: In member function ‘arma::vec CARp::StartingAR()’:
./carpack.cpp:279:46: warning: ‘typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), const arma::Op<T1, arma::op_sort_vec> >::result arma::sort(const T1&
, arma::uword) [with T1 = arma::Col<double>; typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), const arma::Op<T1, arma::op_sort_vec> >::result = const a
rma::Op<arma::Col<double>, arma::op_sort_vec>; arma::uword = long long unsigned int]’ is deprecated [-Wdeprecated-declarations]
lorentz_cent = arma::sort(lorentz_cent, 1);
^
In file included from /opt/armadillo/include/armadillo:462:0,
from ./carpack.cpp:17:
/opt/armadillo/include/armadillo_bits/fn_sort.hpp:74:1: note: declared here
sort
^~~~
./carpack.cpp: In member function ‘virtual bool CARp::CheckPriorBounds(arma::vec)’:
./carpack.cpp:355:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<lorentz_cent.n_elem; i++) {
~^~~~~~~~~~~~~~~~~~~~
./carpack.cpp: In member function ‘double CARp::Variance(arma::cx_vec, arma::vec, double, double)’:
./carpack.cpp:384:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int k=0; k<alpha_roots.n_elem; k++) {
~^~~~~~~~~~~~~~~~~~~
./carpack.cpp:387:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int l=0; l<alpha_roots.n_elem; l++) {
~^~~~~~~~~~~~~~~~~~~
./carpack.cpp: In member function ‘virtual arma::vec CARMA::SetStartingValue(arma::vec)’:
./carpack.cpp:481:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (init.n_elem != (p_+q_+3)) {
~~~~~~~~~~~~^~~~~~~~~~~~
./carpack.cpp: In member function ‘virtual arma::vec ZCARMA::SetStartingValue(arma::vec)’:
./carpack.cpp:648:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (init.n_elem != (p_+4)) {
~~~~~~~~~~~~^~~~~~~~~
./carpack.cpp: In function ‘arma::vec polycoefs(arma::cx_vec)’:
./carpack.cpp:749:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<roots.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carpack.cpp:23:
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:256:56: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time.n_elem; i++) {
~^~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:369:62: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:
./carpack.cpp:78:23: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./carpack.cpp:23:0:
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./carpack.cpp:90:36: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carpack.cpp:23:
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:
./carpack.cpp:218:27: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./carpack.cpp:23:0:
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./carpack.cpp:220:42: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::basic
_string<char>]’:
./carpack.cpp:756:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<value_.n_elem; i++) {
~^~~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
./carpack.cpp:756:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
./carmcmc.cpp: In function ‘std::shared_ptr<CAR1> RunCar1Sampler(int, int, std::vector<double>, std::vector<double>, std::vector<double>, int, const std::vector<double>&)’:
./carmcmc.cpp:43:9: warning: unused variable ‘report_iter’ [-Wunused-variable]
int report_iter = burnin + thin * sample_size;
^~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carmcmc.cpp:27:
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:256:56: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time.n_elem; i++) {
~^~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:369:62: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from ./carmcmc.cpp:27:0:
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::basic
_string<char>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<value_.n_elem; i++) {
~^~~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<value_.n_elem; i++) {
~^~~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘void CARMA_Base<OmegaType>::Save(arma::vec&) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/steps.hpp:344:13: required from ‘void ExchangeStep<ParValueType, ParameterType>::DoStep() [with ParValueType = arma::Col<double>; ParameterType = CARp]’
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carmcmc.cpp:27:
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:
./include/carpack.hpp:155:13: required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’
./carmcmc.cpp:177:1: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:
./include/carpack.hpp:155:13: required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’
./carmcmc.cpp:177:1: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++: ./steps.cpp
g++: ./samplers.cpp
./steps.cpp: In member function ‘virtual void AdaptiveMetro::DoStep()’:
./steps.cpp:66:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<old_value.n_rows; i++) {
~^~~~~~~~~~~~~~~~~
./steps.cpp: In function ‘void CholUpdateR1(arma::mat&, arma::vec&, bool)’:
./steps.cpp:118:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int k=0; k<L.n_rows; k++) {
~^~~~~~~~~
./steps.cpp:123:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (k < L.n_rows-1) {
~~^~~~~~~~~~~~
./samplers.cpp: In member function ‘void Sampler::Iterate(int, bool)’:
./samplers.cpp:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < steps_.size(); ++i) {
~~^~~~~~~~~~~~~~~
./samplers.cpp:49:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < steps_.size(); ++i) {
~~^~~~~~~~~~~~~~~
./samplers.cpp: In member function ‘void Sampler::Run(arma::vec)’:
./samplers.cpp:76:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool useInit = (init.n_elem == npar);
~~~~~~~~~~~~^~~~~~~
ar: adding 7 object files to build/temp.linux-x86_64-2.7/libcarmcmc.a
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
updating extension 'carmcmc._carmcmc' libraries from ['boost_python', 'boost_filesystem', 'boost_system', 'armadillo', 'carmcmc'] to ['boost_python', 'boost_filesystem', 'boost_system', 'armadillo
', 'carmcmc', 'boost_python', 'boost_filesystem', 'boost_system', 'armadillo']
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'carmcmc._carmcmc' extension
compiling C++ sources
C compiler: g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC
compile options: '-I/opt/conda/include -I/usr/local/include -I/opt/armadillo/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/python
2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c'
extra options: '-O3 -std=c++0x'
g++: ./boost_python_wrapper.cpp
g++: ./carmcmc.cpp
./boost_python_wrapper.cpp:12:10: fatal error: boost/python/numeric.hpp: No such file or directory
#include <boost/python/numeric.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: Command "g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/opt/conda/include -I/usr/local/include -I/opt/armadill
o/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c ./boos
t_python_wrapper.cpp -o build/temp.linux-x86_64-2.7/boost_python_wrapper.o -MMD -MF build/temp.linux-x86_64-2.7/boost_python_wrapper.o.d -O3 -std=c++0x" failed with exit status 1
./carmcmc.cpp: In function ‘std::shared_ptr<CAR1> RunCar1Sampler(int, int, std::vector<double>, std::vector<double>, std::vector<double>, int, const std::vector<double>&)’:
./carmcmc.cpp:43:9: warning: unused variable ‘report_iter’ [-Wunused-variable]
int report_iter = burnin + thin * sample_size;
^~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carmcmc.cpp:27:
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:256:56: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time.n_elem; i++) {
~^~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:369:62: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from ./carmcmc.cpp:27:0:
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::basic
_string<char>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<value_.n_elem; i++) {
~^~~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<value_.n_elem; i++) {
~^~~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘void CARMA_Base<OmegaType>::Save(arma::vec&) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/steps.hpp:344:13: required from ‘void ExchangeStep<ParValueType, ParameterType>::DoStep() [with ParValueType = arma::Col<double>; ParameterType = CARp]’
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carmcmc.cpp:27:
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:
./include/carpack.hpp:155:13: required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’
./carmcmc.cpp:177:1: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:
./include/carpack.hpp:155:13: required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’
./carmcmc.cpp:177:1: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
----------------------------------------
ERROR: Failed building wheel for carmcmc
Running setup.py clean for carmcmc
Failed to build carmcmc
Installing collected packages: carmcmc
Running setup.py install for carmcmc: started
Running setup.py install for carmcmc: still running...
Running setup.py install for carmcmc: finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /opt/conda/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-ORR7mJ/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-ORR7mJ/setup.py'"'"';f=getat
tr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-QfigSn/inst
all-record.txt --single-version-externally-managed --compile
cwd: /tmp/pip-req-build-ORR7mJ/
Complete output (296 lines):
non-existing path in '.': '/usr/lib64'
non-existing path in '.': '/usr/lib64'
non-existing path in '.': 'examples'
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building library "carmcmc" sources
building extension "carmcmc._carmcmc" sources
building data_files sources
build_src: building npy-pkg config files
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
building 'carmcmc' library
compiling C++ sources
C compiler: g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC
creating build
creating build/temp.linux-x86_64-2.7
compile options: '-I/opt/conda/include -I/usr/local/include -I/opt/armadillo/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/pyth
on2.7/site-packages/numpy/core/include -c'
extra options: '-O3 -std=c++0x'
g++: ./proposals.cpp
g++: ./kfilter.cpp
./kfilter.cpp: In member function ‘virtual std::pair<double, double> KalmanFilter1::Predict(double)’:
./kfilter.cpp:88:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<ipredict; i++) {
~^~~~~~~~~
./kfilter.cpp:124:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=ipredict+1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./kfilter.cpp: In member function ‘virtual void KalmanFilterp::Reset()’:
./kfilter.cpp:147:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=2; i<p_; i++) {
~^~~
./kfilter.cpp:165:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<p_; i++) {
~^~~
./kfilter.cpp:166:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=i; j<p_; j++) {
~^~~
./kfilter.cpp: In member function ‘virtual std::pair<double, double> KalmanFilterp::Predict(double)’:
./kfilter.cpp:232:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<ipredict; i++) {
~^~~~~~~~~
./kfilter.cpp:275:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=ipredict+1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./kfilter.cpp:10:0:
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:256:56: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time.n_elem; i++) {
~^~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:369:62: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++: ./random.cpp
./random.cpp: In member function ‘arma::vec RandomGenerator::normal(arma::mat)’:
./random.cpp:99:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<z.n_elem; i++) {
~^~~~~~~~~
g++: ./carpack.cpp
g++: ./carmcmc.cpp
./carpack.cpp: In member function ‘virtual arma::vec CARp::SetStartingValue(arma::vec)’:
./carpack.cpp:236:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (init.n_elem != (p_+3)) {
~~~~~~~~~~~~^~~~~~~~~
./carpack.cpp: In member function ‘arma::vec CARp::StartingAR()’:
./carpack.cpp:279:46: warning: ‘typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), const arma::Op<T1, arma::op_sort_vec> >::result arma::sort(const T
1&, arma::uword) [with T1 = arma::Col<double>; typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), const arma::Op<T1, arma::op_sort_vec> >::result = const
arma::Op<arma::Col<double>, arma::op_sort_vec>; arma::uword = long long unsigned int]’ is deprecated [-Wdeprecated-declarations]
lorentz_cent = arma::sort(lorentz_cent, 1);
^
In file included from /opt/armadillo/include/armadillo:462:0,
from ./carpack.cpp:17:
/opt/armadillo/include/armadillo_bits/fn_sort.hpp:74:1: note: declared here
sort
^~~~
./carpack.cpp: In member function ‘virtual bool CARp::CheckPriorBounds(arma::vec)’:
./carpack.cpp:355:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<lorentz_cent.n_elem; i++) {
~^~~~~~~~~~~~~~~~~~~~
./carpack.cpp: In member function ‘double CARp::Variance(arma::cx_vec, arma::vec, double, double)’:
./carpack.cpp:384:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int k=0; k<alpha_roots.n_elem; k++) {
~^~~~~~~~~~~~~~~~~~~
./carpack.cpp:387:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int l=0; l<alpha_roots.n_elem; l++) {
~^~~~~~~~~~~~~~~~~~~
./carpack.cpp: In member function ‘virtual arma::vec CARMA::SetStartingValue(arma::vec)’:
./carpack.cpp:481:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (init.n_elem != (p_+q_+3)) {
~~~~~~~~~~~~^~~~~~~~~~~~
./carpack.cpp: In member function ‘virtual arma::vec ZCARMA::SetStartingValue(arma::vec)’:
./carpack.cpp:648:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (init.n_elem != (p_+4)) {
~~~~~~~~~~~~^~~~~~~~~
./carpack.cpp: In function ‘arma::vec polycoefs(arma::cx_vec)’:
./carpack.cpp:749:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<roots.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carpack.cpp:23:
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:256:56: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time.n_elem; i++) {
~^~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:369:62: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:
./carpack.cpp:78:23: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./carpack.cpp:23:0:
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./carpack.cpp:90:36: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carpack.cpp:23:
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:
./carpack.cpp:218:27: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./carpack.cpp:23:0:
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./carpack.cpp:220:42: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::bas
ic_string<char>]’:
./carpack.cpp:756:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<value_.n_elem; i++) {
~^~~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
./carpack.cpp:756:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
./carmcmc.cpp: In function ‘std::shared_ptr<CAR1> RunCar1Sampler(int, int, std::vector<double>, std::vector<double>, std::vector<double>, int, const std::vector<double>&)’:
./carmcmc.cpp:43:9: warning: unused variable ‘report_iter’ [-Wunused-variable]
int report_iter = burnin + thin * sample_size;
^~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carmcmc.cpp:27:
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:256:56: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time.n_elem; i++) {
~^~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:369:62: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from ./carmcmc.cpp:27:0:
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::bas
ic_string<char>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<value_.n_elem; i++) {
~^~~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<value_.n_elem; i++) {
~^~~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘void CARMA_Base<OmegaType>::Save(arma::vec&) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/steps.hpp:344:13: required from ‘void ExchangeStep<ParValueType, ParameterType>::DoStep() [with ParValueType = arma::Col<double>; ParameterType = CARp]’
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carmcmc.cpp:27:
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:
./include/carpack.hpp:155:13: required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’
./carmcmc.cpp:177:1: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:
./include/carpack.hpp:155:13: required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’
./carmcmc.cpp:177:1: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++: ./steps.cpp
g++: ./samplers.cpp
./steps.cpp: In member function ‘virtual void AdaptiveMetro::DoStep()’:
./steps.cpp:66:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<old_value.n_rows; i++) {
~^~~~~~~~~~~~~~~~~
./steps.cpp: In function ‘void CholUpdateR1(arma::mat&, arma::vec&, bool)’:
./steps.cpp:118:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int k=0; k<L.n_rows; k++) {
~^~~~~~~~~
./steps.cpp:123:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (k < L.n_rows-1) {
~~^~~~~~~~~~~~
./samplers.cpp: In member function ‘void Sampler::Iterate(int, bool)’:
./samplers.cpp:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < steps_.size(); ++i) {
~~^~~~~~~~~~~~~~~
./samplers.cpp:49:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < steps_.size(); ++i) {
~~^~~~~~~~~~~~~~~
./samplers.cpp: In member function ‘void Sampler::Run(arma::vec)’:
./samplers.cpp:76:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool useInit = (init.n_elem == npar);
~~~~~~~~~~~~^~~~~~~
ar: adding 7 object files to build/temp.linux-x86_64-2.7/libcarmcmc.a
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
updating extension 'carmcmc._carmcmc' libraries from ['boost_python', 'boost_filesystem', 'boost_system', 'armadillo', 'carmcmc'] to ['boost_python', 'boost_filesystem', 'boost_system', 'armadil
lo', 'carmcmc', 'boost_python', 'boost_filesystem', 'boost_system', 'armadillo']
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'carmcmc._carmcmc' extension
compiling C++ sources
C compiler: g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC
compile options: '-I/opt/conda/include -I/usr/local/include -I/opt/armadillo/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/pyth
on2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c'
extra options: '-O3 -std=c++0x'
g++: ./boost_python_wrapper.cpp
g++: ./carmcmc.cpp
./boost_python_wrapper.cpp:12:10: fatal error: boost/python/numeric.hpp: No such file or directory
#include <boost/python/numeric.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: Command "g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/opt/conda/include -I/usr/local/include -I/opt/armadi
llo/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c ./bo
ost_python_wrapper.cpp -o build/temp.linux-x86_64-2.7/boost_python_wrapper.o -MMD -MF build/temp.linux-x86_64-2.7/boost_python_wrapper.o.d -O3 -std=c++0x" failed with exit status 1
./carmcmc.cpp: In function ‘std::shared_ptr<CAR1> RunCar1Sampler(int, int, std::vector<double>, std::vector<double>, std::vector<double>, int, const std::vector<double>&)’:
./carmcmc.cpp:43:9: warning: unused variable ‘report_iter’ [-Wunused-variable]
int report_iter = burnin + thin * sample_size;
^~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carmcmc.cpp:27:
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:256:56: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time.n_elem; i++) {
~^~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/kfilter.hpp:369:62: required from here
./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from ./carmcmc.cpp:27:0:
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::bas
ic_string<char>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<value_.n_elem; i++) {
~^~~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<value_.n_elem; i++) {
~^~~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/carpack.hpp: In instantiation of ‘void CARMA_Base<OmegaType>::Save(arma::vec&) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:
./include/steps.hpp:344:13: required from ‘void ExchangeStep<ParValueType, ParameterType>::DoStep() [with ParValueType = arma::Col<double>; ParameterType = CARp]’
./carmcmc.cpp:177:1: required from here
./include/carpack.hpp:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
In file included from ./include/carpack.hpp:24:0,
from ./carmcmc.cpp:27:
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:
./include/carpack.hpp:155:13: required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’
./carmcmc.cpp:177:1: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1; i<time_.n_elem; i++) {
~^~~~~~~~~~~~~
./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:
./include/carpack.hpp:155:13: required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’
./carmcmc.cpp:177:1: required from here
./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/conda/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-ORR7mJ/setup.py'"'"'; __file__='"'"'/tmp/pip-req-b
uild-ORR7mJ/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --r
ecord /tmp/pip-record-QfigSn/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
The command '/bin/bash -c cd carma_pack/src/ && pip install .' returned a non-zero code: 1 carmcmc is a package written by Brandon Kelly (https://arxiv.org/abs/1402.5978) and outside my control. It is included here purely to allowusers to compare results returned by his code to this package. It is completely optional and you can safely skip it.
philastrophist
commented
5 years ago Ok, cool. I've skipped that. But now I get the below. I'm not even sure where the error is....
Cloning into 'kali'...
notice: kali tools have been set up.
/opt/conda/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /kali/src/CARMATask_cython.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/opt/conda/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /kali/src/MBHBTask_cython.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/opt/conda/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /kali/src/rand.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Compiling /kali/src/rand.pyx because it changed.
Compiling /kali/src/CARMATask_cython.pyx because it changed.
Compiling /kali/src/MBHBTask_cython.pyx because it changed.
[1/3] Cythonizing /kali/src/CARMATask_cython.pyx
[2/3] Cythonizing /kali/src/MBHBTask_cython.pyx
[3/3] Cythonizing /kali/src/rand.pyx
running build_ext
building 'rand' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/kali
creating build/temp.linux-x86_64-2.7/kali/src
g++ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/kali/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c /kali/src/rand.cpp -o build/temp.linux-x86_64-2.7/kali/src/rand.o -O3 -std=c++11 -I$MKLROOT/include -limf -fopenmp -fopenmp-simd
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:0,
from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /kali/src/rand.cpp:658:
/opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^~~~~~~
g++ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/kali/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c /kali/src/rdrand.cpp -o build/temp.linux-x86_64-2.7/kali/src/rdrand.o -O3 -std=c++11 -I$MKLROOT/include -limf -fopenmp -fopenmp-simd
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
g++ -pthread -shared -B /opt/conda/compiler_compat -L/opt/conda/lib -Wl,-rpath=/opt/conda/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/kali/src/rand.o build/temp.linux-x86_64-2.7/kali/src/rdrand.o -L$MKLROOT/lib/inte -L/opt/conda/lib -Wl,-R$MKLROOT/lib/inte -lpython2.7 -o lib/rand.so -L$MKLROOT/lib/intel64 -lmkl_rt -lpthread -lm -ldl -lgomp -lnlopt
building 'LCTools_cython' extension
g++ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/kali/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c /kali/src/LCTools_cython.cpp -o build/temp.linux-x86_64-2.7/kali/src/LCTools_cython.o -O3 -std=c++11 -I$MKLROOT/include -limf -fopenmp -fopenmp-simd
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:0,
from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /kali/src/LCTools_cython.cpp:339:
/opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^~~~~~~
In file included from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:21:0,
from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /kali/src/LCTools_cython.cpp:339:
/opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
_import_array(void)
^~~~~~~~~~~~~
g++ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/kali/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c /kali/src/LC.cpp -o build/temp.linux-x86_64-2.7/kali/src/LC.o -O3 -std=c++11 -I$MKLROOT/include -limf -fopenmp -fopenmp-simd
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
/kali/src/LC.cpp:13:10: fatal error: mkl.h: No such file or directory
#include <mkl.h>
^~~~~~~
compilation terminated.
error: command 'g++' failed with exit status 1
Here's the error - /kali/src/LC.cpp:13:10: fatal error: mkl.h: No such file or directory You're missing MKL - either it isn't installed or the headers are not in one of the standard places. Generally speaking, MKL is a great library to use if you're on an Intel platform. Everything still works on AMD platforms but other libraries exist that potentially faster.
philastrophist
commented
5 years ago Thanks! I added a call to compilevars.sh and it appears to stop that message.
Ok this is relevant to your package now, running python setup.py build_ext gives me a new message:
DOCKERFILE
FROM ubuntu
SHELL ["/bin/bash", "-c"]
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ENV PATH /opt/conda/bin:$PATH
ENV TINI_VERSION v0.16.1
RUN apt-get update --fix-missing && \
apt-get install -y wget bzip2 ca-certificates curl git build-essential cmake libgtk2.0-common \
libpango-1.0.0 libasound2-dev xserver-xorg cpio && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda && \
rm ~/miniconda.sh && \
/opt/conda/bin/conda clean -tipsy && \
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc
ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
RUN chmod +x /usr/bin/tini
COPY parallel_studio_xe_2019_update5_cluster_edition_online.tgz .
COPY mysilent.cfg .
RUN echo "ACTIVATION_SERIAL_NUMBER=$SERIAL_NUMBER" && echo "ACTIVATION_SERIAL_NUMBER=$SERIAL_NUMBER" >> mysilent.cfg
RUN tar -xvzf parallel_studio_xe_2019_update5_cluster_edition_online.tgz && \
cd parallel_studio_xe_2019_update5_cluster_edition_online && \
./install.sh --silent ../mysilent.cfg --cli-mode && \
echo "source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64" >> ~/.bashrc
RUN cd ~
RUN conda install mkl
RUN wget https://github.com/stevengj/nlopt/archive/v2.6.1.tar.gz -O nlopt.tar.gz
RUN tar -xvzf nlopt.tar.gz && cd nlopt-2.6.1/ && cmake . && make && make install && ldconfig && cd ..
RUN conda update --all && conda install cython future pytest
RUN conda install numpy matplotlib scipy
RUN pip install gatspy multi_key_dict fitsio==0.9.8
# carma_pack
# RUN wget http://sourceforge.net/projects/boost/files/boost/1.54.0/boost_1_54_0.tar.bz2 && tar --bzip2 -xf boost_1_54_0.tar.bz2
# RUN cd boost_1_54_0 && ./bootstrap.sh && sed -i 's/explicit yield_sources ;/explicit allocator_sources ;/g' libs/coroutine/build/Jamfile.v2
# RUN cd boost_1_54_0 && ./b2 install
RUN wget http://sourceforge.net/projects/arma/files/armadillo-9.700.3.tar.xz && \
tar -xf armadillo-9.700.3.tar.xz && cd armadillo-9.700.3 && \
cmake -DCMAKE_INSTALL_PREFIX=/opt/armadillo -DBOOST_ROOT=$BOOST_DIR/ . && \
make install && cd ~
RUN apt-get update && apt-get install -y libboost-all-dev
RUN echo "export ARMADILLO_DIR=/opt/armadillo" >> ~/.bashrc
ENV ARMADILLO_DIR "/opt/armadillo"
RUN echo "export LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}" >> ~/.bashrc
ENV LD_LIBRARY_PATH "/usr/local/lib:${LD_LIBRARY_PATH}"
RUN echo "export LD_LIBRARY_PATH=/opt/armadillo/lib:${LD_LIBRARY_PATH}" >> ~/.bashrc
ENV LD_LIBRARY_PATH "/opt/armadillo/lib:${LD_LIBRARY_PATH}"
RUN echo "export BOOST_DIR=/usr/local" >> ~/.bashrc
ENV BOOST_DIR "/usr/local"
ENV NUMPY_DIR "/opt/conda"
# COPY l_mkl_2019.5.281_online.tgz .
# RUN tar -xvzf l_mkl_2019.5.281_online.tgz && cd l_mkl_2019.5.281_online && ls
# RUN git clone https://github.com/brandonckelly/carma_pack.git
# RUN cd carma_pack/src/ && pip install .
RUN pip install acor
RUN echo "source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64" >> ~/.bashrc
RUN echo "source /opt/intel/mkl/bin/mklvars.sh intel64" >> ~/.bashrc
RUN git clone https://github.com/AstroVPK/kali.git
ENV GXX_INCLUDE "/usr/lib/gcc/x86_64-pc-linux-gnu/6.4.1/include/c++"
RUN source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64 && \
source /opt/intel/mkl/bin/mklvars.sh intel64 && \
cd kali && source ./bin/setup.sh && python setup.py build_ext
RUN echo "source ~/kali/bin/setup.sh" >> ~/.bashrc
RUN pytest tests && cd ~
ENTRYPOINT [ "/usr/bin/tini", "--" ]
CMD [ "/bin/bash" ]ERROR MESSAGE
Compiling /kali/src/rand.pyx because it changed.
Compiling /kali/src/CARMATask_cython.pyx because it changed.
Compiling /kali/src/MBHBTask_cython.pyx because it changed.
[1/3] Cythonizing /kali/src/CARMATask_cython.pyx
[2/3] Cythonizing /kali/src/MBHBTask_cython.pyx
[3/3] Cythonizing /kali/src/rand.pyx
running build_ext
building 'rand' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/kali
creating build/temp.linux-x86_64-2.7/kali/src
icpc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/kali/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c /kali/src/rand.cpp -o build/temp.linux-x86_64-2.7/kali/src/rand.o -O3 -xHost -ip -parallel -funroll-loops -fno-alias -fno-fnalias -fargument-noalias -fstrict-aliasing -ansi-alias -fno-stack-protector-all -Wall -gxx-name=g++-4.8 -std=c++11 -falign-functions -I$MKLROOT/include -limf -qopenmp -qopenmp-simd -qopt-report=5 -qopt-report-phase=all
icpc: error #10417: Problem setting up the Intel(R) Compiler compilation environment. Requires 'install path' setting gathered from 'g++-4.8'
error: command 'icpc' failed with exit status 1
The command '/bin/bash -c source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64 && source /opt/intel/mkl/bin/mklvars.sh intel64 && cd kali && source ./bin/setup.sh && python setup.py build_ext' returned a non-zero code: 1I see that there is a branch for the Dockerfile, but it is a bit out of date now. I'll try it out and see what happens.
The installation process is horrendously complicated and I can't seem to get it right. Can you put a working Dockerfile up there? Thanks!