Dear all,
I tried to compile AMBER20 in a cluster with CentOS 7 installed.
The configuration went smoothly.
When I tried to compile AMBER20 in serial mode, I got errors from metatwist.cpp as following:
make[2]: Entering directory `/root/softwares/amber20_src/AmberTools/src/moft'
[MoFT] CXX /root/softwares/amber20_src/bin/metatwist
metatwist.o: In function `boost::iostreams::gzip_error::gzip_error(int)':
metatwist.cpp:(.text._ZN5boost9iostreams10gzip_errorC2Ei[_ZN5boost9iostreams10gzip_errorC5Ei]+0x7d): undefined reference to `boost::iostreams::zlib::okay'
metatwist.o: In function `boost::iostreams::detail::gzip_header::gzip_header()':
metatwist.cpp:(.text._ZN5boost9iostreams6detail11gzip_headerC2Ev[_ZN5boost9iostreams6detail11gzip_headerC5Ev]+0x31): undefined reference to `boost::iostreams::detail::gzip_header::reset()'
metatwist.o: In function `boost::iostreams::detail::gzip_footer::gzip_footer()':
metatwist.cpp:(.text._ZN5boost9iostreams6detail11gzip_footerC2Ev[_ZN5boost9iostreams6detail11gzip_footerC5Ev]+0x14): undefined reference to `boost::iostreams::detail::gzip_footer::reset()'
metatwist.o: In function `boost::iostreams::basic_gzip_decompressor<std::allocator<char> >::make_params(int)':
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi]+0x59): undefined reference to `boost::iostreams::zlib::default_strategy'
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi]+0x62): undefined reference to `boost::iostreams::zlib::deflated'
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi]+0x6b): undefined reference to `boost::iostreams::zlib::default_compression'
metatwist.o: In function `boost::iostreams::detail::bzip2_decompressor_impl<std::allocator<char> >::~bzip2_decompressor_impl()':
metatwist.cpp:(.text._ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEED2Ev[_ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEED5Ev]+0x20): undefined reference to `boost::iostreams::detail::bzip2_base::~bzip2_base()'
metatwist.o: In function `boost::iostreams::detail::bzip2_decompressor_impl<std::allocator<char> >::bzip2_decompressor_impl(bool)':
metatwist.cpp:(.text._ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEEC2Eb[_ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEEC5Eb]+0x32): undefined reference to `boost::iostreams::detail::bzip2_base::bzip2_base(boost::iostreams::bzip2_params const&)'
metatwist.o: In function `boost::iostreams::detail::zlib_decompressor_impl<std::allocator<char> >::zlib_decompressor_impl(boost::iostreams::zlib_params const&)':
metatwist.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEEC2ERKNS0_11zlib_paramsE[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEEC5ERKNS0_11zlib_paramsE]+0x19): undefined reference to `boost::iostreams::detail::zlib_base::zlib_base()'
metatwist.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEEC2ERKNS0_11zlib_paramsE[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEEC5ERKNS0_11zlib_paramsE]+0x66): undefined reference to `boost::iostreams::detail::zlib_base::~zlib_base()'
metatwist.o: In function `boost::iostreams::detail::zlib_decompressor_impl<std::allocator<char> >::~zlib_decompressor_impl()':
metatwist.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEED2Ev[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEED5Ev]+0x1e): undefined reference to `boost::iostreams::detail::zlib_base::reset(bool, bool)'
metatwist.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEED2Ev[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEED5Ev]+0x36): undefined reference to `boost::iostreams::detail::zlib_base::~zlib_base()'
metatwist.o: In function `void boost::iostreams::detail::zlib_base::init<std::allocator<char> >(boost::iostreams::zlib_params const&, bool, boost::iostreams::detail::zlib_allocator<std::allocator<char>, boost::iostreams::detail::zlib_allocator_traits<std::allocator<char> >::type>&)':
metatwist.cpp:(.text._ZN5boost9iostreams6detail9zlib_base4initISaIcEEEvRKNS0_11zlib_paramsEbRNS1_14zlib_allocatorIT_NS1_21zlib_allocator_traitsIS9_E4typeEEE[_ZN5boost9iostreams6detail9zlib_base4initISaIcEEEvRKNS0_11zlib_paramsEbRNS1_14zlib_allocatorIT_NS1_21zlib_allocator_traitsIS9_E4typeEEE]+0x66): undefined reference to `boost::iostreams::detail::zlib_base::do_init(boost::iostreams::zlib_params const&, bool, void* (*)(void*, unsigned int, unsigned int), void (*)(void*, void*), void*)'
metatwist.o: In function `long boost::iostreams::basic_gzip_decompressor<std::allocator<char> >::write<boost::iostreams::detail::linked_streambuf<char, std::char_traits<char> > >(boost::iostreams::detail::linked_streambuf<char, std::char_traits<char> >&, char const*, long)':
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl]+0x52): undefined reference to `boost::iostreams::detail::gzip_header::reset()'
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl]+0x62): undefined reference to `boost::iostreams::detail::gzip_footer::reset()'
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl]+0xa8): undefined reference to `boost::iostreams::detail::gzip_header::process(char)'
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl]+0x1f2): undefined reference to `boost::iostreams::detail::gzip_footer::process(char)'
metatwist.o: In function `boost::iostreams::detail::bzip2_decompressor_impl<std::allocator<char> >::filter(char const*&, char const*, char*&, char*, bool)':
metatwist.cpp:(.text._ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x8e): undefined reference to `boost::iostreams::detail::bzip2_base::before(char const*&, char const*, char*&, char*)'
metatwist.cpp:(.text._ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x9a): undefined reference to `boost::iostreams::detail::bzip2_base::decompress()'
metatwist.cpp:(.text._ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0xa4): undefined reference to `boost::iostreams::bzip2::ok'
metatwist.cpp:(.text._ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0xce): undefined reference to `boost::iostreams::detail::bzip2_base::check_end(char const*, char const*)'
metatwist.cpp:(.text._ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0xe8): undefined reference to `boost::iostreams::detail::bzip2_base::after(char const*&, char*&)'
metatwist.cpp:(.text._ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0xf2): undefined reference to `boost::iostreams::bzip2_error::check(int)'
metatwist.cpp:(.text._ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0xf9): undefined reference to `boost::iostreams::bzip2::stream_end'
metatwist.o: In function `boost::iostreams::detail::bzip2_decompressor_impl<std::allocator<char> >::close()':
metatwist.cpp:(.text._ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE5closeEv[_ZN5boost9iostreams6detail23bzip2_decompressor_implISaIcEE5closeEv]+0x1a): undefined reference to `boost::iostreams::detail::bzip2_base::end(bool)'
metatwist.o: In function `boost::iostreams::detail::zlib_decompressor_impl<std::allocator<char> >::filter(char const*&, char const*, char*&, char*, bool)':
metatwist.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x3d): undefined reference to `boost::iostreams::detail::zlib_base::before(char const*&, char const*, char*&, char*)'
metatwist.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x44): undefined reference to `boost::iostreams::zlib::sync_flush'
metatwist.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x54): undefined reference to `boost::iostreams::detail::zlib_base::xinflate(int)'
metatwist.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x70): undefined reference to `boost::iostreams::detail::zlib_base::after(char const*&, char*&, bool)'
metatwist.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x7a): undefined reference to `boost::iostreams::zlib_error::check(int)'
metatwist.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x81): undefined reference to `boost::iostreams::zlib::stream_end'
metatwist.o: In function `void boost::iostreams::detail::bzip2_base::init<std::allocator<char> >(bool, boost::iostreams::detail::bzip2_allocator<std::allocator<char>, boost::iostreams::detail::bzip2_allocator_traits<std::allocator<char> >::type>&)':
metatwist.cpp:(.text._ZN5boost9iostreams6detail10bzip2_base4initISaIcEEEvbRNS1_15bzip2_allocatorIT_NS1_22bzip2_allocator_traitsIS6_E4typeEEE[_ZN5boost9iostreams6detail10bzip2_base4initISaIcEEEvbRNS1_15bzip2_allocatorIT_NS1_22bzip2_allocator_traitsIS6_E4typeEEE]+0x67): undefined reference to `boost::iostreams::detail::bzip2_base::do_init(bool, void* (*)(void*, int, int), void (*)(void*, void*), void*)'
metatwist.o: In function `boost::iostreams::detail::zlib_decompressor_impl<std::allocator<char> >::close()':
metatwist.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE5closeEv[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE5closeEv]+0x26): undefined reference to `boost::iostreams::detail::zlib_base::reset(bool, bool)'
metatwist.o: In function `long boost::iostreams::basic_gzip_decompressor<std::allocator<char> >::read<boost::iostreams::detail::linked_streambuf<char, std::char_traits<char> > >(boost::iostreams::detail::linked_streambuf<char, std::char_traits<char> >&, char*, long)':
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0x87): undefined reference to `boost::iostreams::detail::gzip_header::reset()'
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0x9a): undefined reference to `boost::iostreams::detail::gzip_footer::reset()'
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0x11e): undefined reference to `boost::iostreams::detail::gzip_header::process(char)'
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0x283): undefined reference to `boost::iostreams::detail::gzip_footer::process(char)'
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0x36e): undefined reference to `boost::iostreams::detail::gzip_header::reset()'
metatwist.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0x381): undefined reference to `boost::iostreams::detail::gzip_footer::reset()'
collect2: error: ld returned 1 exit status
make[2]: *** [/root/softwares/amber20_src/bin/metatwist] Error 1
make[2]: Leaving directory `/root/softwares/amber20_src/AmberTools/src/moft'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/root/softwares/amber20_src/AmberTools/src'
make: *** [install] Error 2
All patches have been installed. Package boost169, boost169-iostreams, zlib-devel are also installed. Any clue of that?
Thank you in advance.
Best regards,
Fuming Ying, Engineer
Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry
Xiamen University
Tel: 86-592-2187396
Mob: (86)15260202135
应富鸣，工程师
福建省理论与计算化学重点实验室
厦门大学化学系
电话：86-592-2187396
移动：(86)15260202135
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Received on Sun Mar 07 2021 - 23:00:02 PST
