簡単な操作でprotobufのバージョンの問題を解決するために、コピーして貼り付けることができます。

for req in $(cat requirements.txt); do pip install $req; done

libtool: install: (cd /usr/local/lib && { ln -s -f libprotoc.so.9.0.1 libprotoc.so.9 || { rm -f libprotoc.so.9 && ln -s libprotoc. so.9.0.1 libprotoc.so.9; }; })
libtool: install: (cd /usr/local/lib && { ln -s -f libprotoc.so.9.0.1 libprotoc.so || { rm -f libprotoc.so && ln -s libprotoc.so.9. 0.1 libprotoc.so; }; })
libtool: install: /usr/bin/install -c .libs/libprotoc.lai /usr/local/lib/libprotoc.la
libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.a /usr/local/lib/libprotobuf-lite.a
libtool: install: chmod 644 /usr/local/lib/libprotobuf-lite.a
libtool: install: ranlib /usr/local/lib/libprotobuf-lite.a
libtool: install: /usr/bin/install -c .libs/libprotobuf.a /usr/local/lib/libprotobuf.a
libtool: install: chmod 644 /usr/local/lib/libprotobuf.a
libtool: install: ranlib /usr/local/lib/libprotobuf.a
libtool: install: /usr/bin/install -c .libs/libprotoc.a /usr/local/lib/libprotoc.a
libtool: install: chmod 644 /usr/local/lib/libprotoc.a
libtool: install: ranlib /usr/local/lib/libprotoc.a
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/sbin" ldconfig -n /usr/local/ lib
----------------------------------------------------------------------
Libraries have been installed in:
/usr/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
/bin/mkdir -p '/usr/local/bin'
/bin/bash ... /libtool --mode=install /usr/bin/install -c protoc '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/protoc /usr/local/bin/protoc
/bin/mkdir -p '/usr/local/include'
/bin/mkdir -p '/usr/local/include/google/protobuf'
/usr/bin/install -c -m 644 google/protobuf/descriptor.proto '/usr/local/include/google/protobuf'
/bin/mkdir -p '/usr/local/include/google/protobuf/compiler'
/usr/bin/install -c -m 644 google/protobuf/compiler/plugin.proto '/usr/local/include/google/protobuf/compiler'
/bin/mkdir -p '/usr/local/include'
/bin/mkdir -p '/usr/local/include/google/protobuf/compiler/cpp'

root@test:~# whereis protoc
protoc: /usr/bin/protoc /usr/bin/X11/protoc /usr/local/bin/protoc /usr/share/man/man1/protoc.1.gz
root@test:~# pip show protobuf
Name: protobuf
Version: 3.4.1
Summary: Protocol Buffers
Home-page: https://developers.google.com/protocol-buffers/
Author: [email protected]
Author-email: [email protected]
License: 3-Clause BSD License
Location: /root/anaconda2/lib/python2.7/site-packages
Requires: six, setuptools
You are using pip version 9.0.1, however version 9.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
root@test:~# which protoc
/root/anaconda2/bin/protoc
root@test:~# protoc --version
libprotoc 3.4.0
root@test:~# 

-- Release CXX flags : -O3 -DNDEBUG -fPIC -Wall -Wno-sign-compare -Wno-uninitialized
-- Debug CXX flags : -g -fPIC -Wall -Wno-sign-compare -Wno-uninitialized
-- Build type : Release
-- 
-- BUILD_SHARED_LIBS : ON
-- BUILD_python : ON
-- BUILD_matlab : OFF
-- BUILD_docs : ON
-- CPU_ONLY : OFF
-- 
-- Dependencies:
-- BLAS : Yes (Atlas)
-- Boost : Yes (ver. 1.54)
-- glog : Yes
-- gflags : Yes
-- protobuf : Yes (ver. 2.6.1)
-- lmdb : Yes (ver. 0.9.16)
-- Snappy : Yes (ver. 1.1.0)
-- LevelDB : Yes (ver. 1.15)
-- OpenCV : Yes (ver. 2.4.8)
-- CUDA : Yes (ver. 8.0)

CXX tools/upgrade_net_proto_text.cpp
CXX/LD -o .build_release/tools/upgrade_net_proto_text.bin
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std:: string const&, google::protobuf::io::CodedOutputStream*)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std:: string const&, unsigned char*)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::AssignDescriptors(std::string const&, google:: protobuf::internal::MigrationSchema const*, google::protobuf::Message const* const*, unsigned int const*, google::protobuf::MessageFactory *, google::protobuf::Metadata*, google::protobuf::EnumDescriptor const**, google::protobuf::ServiceDescriptor const**)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() const'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) const'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::string const&))'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::DebugString() const'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::OnShutdownDestroyString(std::string const*)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std:: string const&, google::protobuf::io::CodedOutputStream*)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::fixed_address_empty_string'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteString(int, std::string const& amp;, google::protobuf::io::CodedOutputStream*)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io:: CodedInputStream*, std::string*)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::InitializationErrorString() const'
collect2: error: ld returned 1 exit status
make: *** [.build_release/tools/upgrade_net_proto_text.bin] Error 1
root@test:/dev/LT/SegNet/caffe-segnet# 

. /configure --prefix=/root/LT

protoc --version