caffe installation: gcc error namespace "std" has no member "isnan"

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I'm trying to install (py)caffe on ubuntu 17.10

However when I do make all I get the following error:

./include/caffe/common.hpp(84): error: namespace "std" has no member "isnan"

./include/caffe/common.hpp(85): error: namespace "std" has no member "isinf"

2 errors detected in the compilation of "/tmp/tmpxft_00004921_00000000-19_nesterov_solver.compute_61.cpp1.ii".
Makefile:594: recipe for target '.build_release/cuda/src/caffe/solvers/nesterov_solver.o' failed

or when I use cmake instead

/home/thijser/caffe/include/caffe/common.hpp(84): error: namespace "std" has no member "isnan"

/home/thijser/caffe/include/caffe/common.hpp(85): error: namespace "std" has no member "isinf"

2 errors detected in the compilation of "/tmp/tmpxft_00004e32_00000000-7_math_functions.cpp1.ii".
CMake Error at cuda_compile_1_generated_math_functions.cu.o.Release.cmake:282 (message):
  Error generating file
  /home/thijser/caffe/build/src/caffe/CMakeFiles/cuda_compile_1.dir/util/./cuda_compile_1_generated_math_functions.cu.o

Note that I'm not just going for sudo apt-get install caffe as doing so does not also install pycaffe, any solution that also installs pycaffe is also valid. I understand that isnan in std likely comes via boost or that this somehow involves a discrepancy between c++ versions? I'm not much of a c++ expert so I'm not sure how that works, I use gcc4.9 for this as nvcc doesn't like later versions of gcc. I know that caffe works on other people's machines and on a older version of ubuntu I had installed so that suggests it's all a configuration issue.

Anybody know how to fix this?

edit using verbose mode on cmake I was able to find out that it doing the following as it happened 

/usr/bin/cmake -E remove /home/thijser/caffe/build/src/caffe/CMakeFiles/cuda_compile_1.dir/util/cuda_compile_1_generated_math_functions.cu.o.depend.tmp /home/thijser/caffe/build/src/caffe/CMakeFiles/cuda_compile_1.dir/util/cuda_compile_1_generated_math_functions.cu.o.NVCC-depend
-- Generating /home/thijser/caffe/build/src/caffe/CMakeFiles/cuda_compile_1.dir/util/./cuda_compile_1_generated_math_functions.cu.o
/usr/bin/nvcc /home/thijser/caffe/src/caffe/util/math_functions.cu -c -o /home/thijser/caffe/build/src/caffe/CMakeFiles/cuda_compile_1.dir/util/./cuda_compile_1_generated_math_functions.cu.o -ccbin /usr/bin/cc -m64 -DCAFFE_VERSION=1.0.0 -Xcompiler ,\"-fPIC\",\"-Wall\",\"-Wno-sign-compare\",\"-Wno-uninitialized\",\"-O3\",\"-DNDEBUG\" -gencode arch=compute_61,code=sm_61 -Xcudafe --diag_suppress=cc_clobber_ignored -Xcudafe --diag_suppress=integer_sign_change -Xcudafe --diag_suppress=useless_using_declaration -Xcudafe --diag_suppress=set_but_not_used -DUSE_LMDB -DUSE_LEVELDB -DUSE_OPENCV -DWITH_PYTHON_LAYER -Xcompiler -fPIC -DNVCC -I/home/thijser/caffe/include -I/home/thijser/caffe/src -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/opencv -I/usr/include/x86_64-linux-gnu -I/usr/include/python2.7 -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/home/thijser/caffe/build/include -I/home/thijser/caffe/build
/home/thijser/caffe/include/caffe/common.hpp(84): error: namespace "std" has no member "isnan"

/home/thijser/caffe/include/caffe/common.hpp(85): error: namespace "std" has no member "isinf"

testing against the following code: https://ideone.com/Yxvt5m

$ gcc -std=c++11 test.cpp which is the same as g++ test.cpp gave me

test.cpp: In function ‘int main()’:
test.cpp:7:15: error: ‘__builtin_isnan’ is not a member of ‘std’
       cout << std::isnan(42.0) << std::isinf(42.0);
               ^
test.cpp:7:15: note: suggested alternative:
<built-in>: note:   ‘__builtin_isnan’
test.cpp:7:35: error: ‘__builtin_isinf_sign’ is not a member of ‘std’
       cout << std::isnan(42.0) << std::isinf(42.0);
                                   ^
test.cpp:7:35: note: suggested alternative:
<built-in>: note:   ‘__builtin_isinf_sign’

suggesting an configuration issue on my machine, however clang++ test.cpp did not give any error suggesting that maybe we could use that to install caffe?

$ gcc --version

gcc (Ubuntu 4.8.5-4ubuntu6) 4.8.5
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$gcc -xc++ -E -v -

Using built-in specs.
COLLECT_GCC=gcc
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.5-4ubuntu6' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.8.5 (Ubuntu 4.8.5-4ubuntu6) 
COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'
 /usr/lib/gcc/x86_64-linux-gnu/4.8/cc1plus -E -quiet -v -imultiarch x86_64-linux-gnu -D_GNU_SOURCE - -mtune=generic -march=x86-64 -fstack-protector -Wformat -Wformat-security
ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/4.8"
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
 /usr/include/c++/4.8
 /usr/include/x86_64-linux-gnu/c++/4.8
 /usr/include/c++/4.8/backward
 /usr/lib/gcc/x86_64-linux-gnu/4.8/include
 /usr/local/include
 /usr/lib/gcc/x86_64-linux-gnu/4.8/include-fixed
 /usr/include/x86_64-linux-gnu
 /usr/include
End of search list.

Edit: thanks to @EliahKagan 's suggestions in the askubuntu chat I found that adding in the line CXXFLAGS += g++ -D_GLIBCXX_USE_C99_MATH -std=c++11 to the makefile solves this issue, however it inimitably throws the next error of 

thijser@AI-core-Regain:~/caffe/build$ make all
[  0%] Building CXX object src/caffe/CMakeFiles/caffeproto.dir/__/__/include/caffe/proto/caffe.pb.cc.o
In file included from /home/thijser/caffe/build/include/caffe/proto/caffe.pb.cc:5:
/home/thijser/caffe/build/include/caffe/proto/caffe.pb.h:7:10: fatal error: 
      'string' file not found
#include <string>
         ^~~~~~~~

1 error generated.

caffe nvcc ubuntu gcc c++
3 Answers

After a long and detailed discussion with several of the people on the chat.askubuntu.com room @EliahKagan found out that there is a python3-caffe-cuda package which allows on to import caffe in python3. Note that this won't solve this issue for anyone in the future who has python2 but for me it works. In other words sudo apt-get install caffe and then using python3 rather then python2.7 worked for me.

Also note that we found that the underlying issue appears to be that gcc/g++ isn't finding the standard libraries (std) however it seems that clang and later version of gcc (gcc7)can find these libraries however these do not work with the current version of nvcc.

user_19300110

I am pretty sure you should set the right C++ standard. std::isnan is part of C++11 and newer GCCs use this version by default. Older ones still default to C++98.

user_27990370
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