Caffe: Error with GCC 6.x

[dakatapetrov]

I get fatal error: stdlib.h: No such file or directory when compiling:

PROTOC src/caffe/proto/caffe.proto
CXX src/caffe/solver.cpp
CXX src/caffe/data_transformer.cpp
CXX src/caffe/data_reader.cpp
CXX src/caffe/blob.cpp
CXX src/caffe/util/sampler.cpp
CXX src/caffe/util/math_functions.cpp
CXX src/caffe/util/io.cpp
In file included from /usr/include/boost/config/platform/linux.hpp:15:0,
                 from /usr/include/boost/config.hpp:57,
                 from /usr/include/boost/thread/detail/platform.hpp:14,
                 from /usr/include/boost/thread/thread_only.hpp:12,
                 from /usr/include/boost/thread/thread.hpp:12,
                 from /usr/include/boost/thread.hpp:13,
                 from src/caffe/data_reader.cpp:1:
/usr/include/c++/6.2.1/cstdlib:75:25: fatal error: stdlib.h: No such file or directory
 #include_next <stdlib.h>
                         ^
compilation terminated.
In file included from /usr/include/c++/6.2.1/bits/stl_algo.h:59:0,
                 from /usr/include/c++/6.2.1/algorithm:62,
                 from src/caffe/util/sampler.cpp:1:
/usr/include/c++/6.2.1/cstdlib:75:25: fatal error: stdlib.h: No such file or directory
 #include_next <stdlib.h>
                         ^
compilation terminated.
make: *** [Makefile:576: .build_release/src/caffe/util/sampler.o] Error 1
make: *** Waiting for unfinished jobs....
make: *** [Makefile:576: .build_release/src/caffe/data_reader.o] Error 1
In file included from /usr/include/c++/6.2.1/bits/stl_algo.h:59:0,
                 from /usr/include/c++/6.2.1/algorithm:62,
                 from /usr/include/opencv2/core/base.hpp:53,
                 from /usr/include/opencv2/core.hpp:54,
                 from /usr/include/opencv2/core/core.hpp:48,
                 from src/caffe/data_transformer.cpp:2:
/usr/include/c++/6.2.1/cstdlib:75:25: fatal error: stdlib.h: No such file or directory
 #include_next <stdlib.h>
                         ^
compilation terminated.
make: *** [Makefile:576: .build_release/src/caffe/data_transformer.o] Error 1
In file included from /usr/include/c++/6.2.1/bits/stl_algo.h:59:0,
                 from /usr/include/c++/6.2.1/algorithm:62,
                 from ./include/caffe/blob.hpp:4,
                 from src/caffe/blob.cpp:4:
/usr/include/c++/6.2.1/cstdlib:75:25: fatal error: stdlib.h: No such file or directory
 #include_next <stdlib.h>
                         ^
compilation terminated.
make: *** [Makefile:576: .build_release/src/caffe/blob.o] Error 1
In file included from /usr/include/boost/config/platform/linux.hpp:15:0,
                 from /usr/include/boost/config.hpp:57,
                 from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:26,
                 from /usr/include/boost/math/special_functions/next.hpp:13,
                 from src/caffe/util/math_functions.cpp:1:
/usr/include/c++/6.2.1/cstdlib:75:25: fatal error: stdlib.h: No such file or directory
 #include_next <stdlib.h>
                         ^
compilation terminated.
make: *** [Makefile:576: .build_release/src/caffe/util/math_functions.o] Error 1
In file included from /usr/include/c++/6.2.1/ext/string_conversions.h:41:0,
                 from /usr/include/c++/6.2.1/bits/basic_string.h:5402,
                 from /usr/include/c++/6.2.1/string:52,
                 from /usr/include/c++/6.2.1/stdexcept:39,
                 from /usr/include/c++/6.2.1/array:39,
                 from /usr/include/c++/6.2.1/tuple:39,
                 from /usr/include/c++/6.2.1/bits/stl_map.h:63,
                 from /usr/include/c++/6.2.1/map:61,
                 from src/caffe/solver.cpp:3:
/usr/include/c++/6.2.1/cstdlib:75:25: fatal error: stdlib.h: No such file or directory
 #include_next <stdlib.h>
                         ^
compilation terminated.
make: *** [Makefile:576: .build_release/src/caffe/solver.o] Error 1
In file included from /usr/include/c++/6.2.1/bits/stl_algo.h:59:0,
                 from /usr/include/c++/6.2.1/algorithm:62,
                 from /usr/include/boost/algorithm/string/classification.hpp:14,
                 from src/caffe/util/io.cpp:1:
/usr/include/c++/6.2.1/cstdlib:75:25: fatal error: stdlib.h: No such file or directory
 #include_next <stdlib.h>
                         ^
compilation terminated.
make: *** [Makefile:576: .build_release/src/caffe/util/io.o] Error 1

Environment:

• Arch Linux 64
• GCC 6.2.1

I have no issues compiling the master caffe branch.

[youngwanLEE]

Why don't you try to compile by gcc version 5 ?

[dakatapetrov]

Now I get another error:

CXX/LD -o .build_release/tools/net_speed_benchmark.bin
.build_release/tools/create_label_map.o: In function `main':
create_label_map.cpp:(.text.startup+0x204): undefined reference to `caffe::LabelMap::LabelMap()'
create_label_map.cpp:(.text.startup+0x216): undefined reference to `caffe::ReadLabelFileToLabelMap(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, caffe::LabelMap*)'
create_label_map.cpp:(.text.startup+0x22e): undefined reference to `caffe::LabelMap::~LabelMap()'
create_label_map.cpp:(.text.startup+0x2e0): undefined reference to `caffe::LabelMap::~LabelMap()'
collect2: error: ld returned 1 exit status
make: *** [Makefile:620: .build_release/tools/create_label_map.bin] Error 1
make: *** Waiting for unfinished jobs....
.build_release/tools/convert_annoset.o: In function `main':
convert_annoset.cpp:(.text.startup+0xbef): undefined reference to `caffe::AnnotatedDatum::AnnotatedDatum()'
convert_annoset.cpp:(.text.startup+0x1478): undefined reference to `caffe::LabelMap::LabelMap()'
convert_annoset.cpp:(.text.startup+0x14a1): undefined reference to `caffe::MapNameToLabel(caffe::LabelMap const&, bool, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, int> > >*)'
convert_annoset.cpp:(.text.startup+0x187e): undefined reference to `caffe::ReadImageToDatum(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, int, int, int, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, caffe::Datum*)'
convert_annoset.cpp:(.text.startup+0x1a22): undefined reference to `caffe::LabelMap::~LabelMap()'
convert_annoset.cpp:(.text.startup+0x1b1d): undefined reference to `caffe::AnnotatedDatum::~AnnotatedDatum()'
convert_annoset.cpp:(.text.startup+0x1df0): undefined reference to `caffe::ReadRichImageToAnnotatedDatum(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, int, int, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, caffe::AnnotatedDatum_AnnotationType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, int> > > const&, caffe::AnnotatedDatum*)'
convert_annoset.cpp:(.text.startup+0x2141): undefined reference to `caffe::AnnotatedDatum::~AnnotatedDatum()'
convert_annoset.cpp:(.text.startup+0x226a): undefined reference to `caffe::LabelMap::~LabelMap()'
collect2: error: ld returned 1 exit status
make: *** [Makefile:619: .build_release/tools/convert_annoset.bin] Error 1
.build_release/tools/get_image_size.o: In function `main':
get_image_size.cpp:(.text.startup+0x6ca): undefined reference to `caffe::GetImageSize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int*, int*)'
collect2: error: ld returned 1 exit status
make: *** [Makefile:619: .build_release/tools/get_image_size.bin] Error 1

Probably because other dependencies are built with gcc 6. Looking at similar issues in the caffe repo, they suggest to use cmake, but it gives errors as well

[gaoshoufenmu]

In the file Makefile.config, add /usr/include/c++/7 and /usr/include /usr/local/include for INCLUDE_DIRS so that the compiler can find the file stdlib.h, and notice that 7 in first path represents the main version of g++.

[Totemi1324]

I face a similar issue, but I'm not able to compile with any C++/GNU version (I tried 6/7/8/9) because it every time says it can't find stdlib.h even though the file is definitely there:

XX src/caffe/syncedmem.cpp
In file included from /usr/include/boost/config/platform/linux.hpp:15,
                 from /usr/include/boost/config.hpp:57,
                 from /usr/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /usr/include/boost/shared_ptr.hpp:17,
                 from ./include/caffe/common.hpp:4,
                 from src/caffe/syncedmem.cpp:1:
/usr/include/c++/9/cstdlib:75:15: fatal error: stdlib.h: No such file or directory
   75 | #include_next <stdlib.h>
      |               ^~~~~~~~~~
compilation terminated.
make: *** [Makefile:576: .build_release/src/caffe/syncedmem.o] Error 1
make: *** Waiting for unfinished jobs....

I tried solution by @gaoshoufenmu but didn't work. How did you solve this?

[Totemi1324]

Ok , I managed to solve it. The solution by @gaoshoufenmu doesn't work and makes it even worse. You simply have to delete usr/include from your INCLUDE_DIRS in Makefile.config.
The simple reason for this is that C++ will search for global headers (the ones enclosed in < >) outside of the INCLUDE_DIRS, and only there. This means that you have to remove all paths that may contain global headers.