[CP2K:6204] Error in compiling CP2K trunk version with PLUMED-2.1.1

[Iain Bethune]

OK that error is nothing to with zlib, but rather that some of the C++ std library stuff that is required by PLUMED is not available.  In your earlier arch file you added -lstdc++ already, so have a look at the output from your compiler, before all the undefined symbol stuff.  Either it will say it can’t find libstdc++, or perhaps you compiled PLUMED with a different compiler version to CP2K?

In any case please when posting error messages post the whole thing (if it is short), or if too long, attach the log in a file.

Thanks

- Iain

--

Iain Bethune
Project Manager, EPCC

Email: ibet... at epcc.ed.ac.uk
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> On 7 Mar 2015, at 15:47, Hang Xiao <xiaoh... at gmail.com> wrote:
> 
> Hi Iain,
> 
> Thank you for your help. After I add  -L/usr/lib/x86_64-linux-gnu to the LDFLAGS, I still got the same error message as the one shown above. 
> 
> I will show you more lines of the error message:
> 
> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_erase(std::_Rb_tree_node<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >*)]+0x62): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_M_destroy(std::allocator<char> const&)'
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE8_M_eraseEPSt13_Rb_tree_nodeISB_E[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_erase(std::_Rb_tree_node<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >*)]+0x6a): undefined reference to `operator delete(void*)'
> /usr/local/lib/plumed///src/vesselbase/VesselRegister.o: In function `std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_erase_aux(std::_Rb_tree_const_iterator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >)':
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE12_M_erase_auxESt23_Rb_tree_const_iteratorISB_E[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_erase_aux(std::_Rb_tree_const_iterator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >)]+0x19): undefined reference to `std::_Rb_tree_rebalance_for_erase(std::_Rb_tree_node_base*, std::_Rb_tree_node_base&)'
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE12_M_erase_auxESt23_Rb_tree_const_iteratorISB_E[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_erase_aux(std::_Rb_tree_const_iterator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >)]+0x2b): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage'
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE12_M_erase_auxESt23_Rb_tree_const_iteratorISB_E[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_erase_aux(std::_Rb_tree_const_iterator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >)]+0x5a): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_M_destroy(std::allocator<char> const&)'
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE12_M_erase_auxESt23_Rb_tree_const_iteratorISB_E[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_erase_aux(std::_Rb_tree_const_iterator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >)]+0x62): undefined reference to `operator delete(void*)'
> /usr/local/lib/plumed///src/vesselbase/VesselRegister.o: In function `std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)':
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE10_M_insert_EPKSt18_Rb_tree_node_baseSK_RKSB_[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)]+0x92): undefined reference to `operator new(unsigned long)'
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE10_M_insert_EPKSt18_Rb_tree_node_baseSK_RKSB_[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)]+0xa7): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE10_M_insert_EPKSt18_Rb_tree_node_baseSK_RKSB_[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)]+0xc3): undefined reference to `std::_Rb_tree_insert_and_rebalance(bool, std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, std::_Rb_tree_node_base&)'
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE10_M_insert_EPKSt18_Rb_tree_node_baseSK_RKSB_[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)]+0xf6): undefined reference to `__cxa_end_catch'
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE10_M_insert_EPKSt18_Rb_tree_node_baseSK_RKSB_[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)]+0x106): undefined reference to `__cxa_begin_catch'
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE10_M_insert_EPKSt18_Rb_tree_node_baseSK_RKSB_[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)]+0x10e): undefined reference to `operator delete(void*)'
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE10_M_insert_EPKSt18_Rb_tree_node_baseSK_RKSB_[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)]+0x113): undefined reference to `__cxa_rethrow'
> /usr/local/lib/plumed///src/vesselbase/VesselRegister.o: In function `std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_unique(std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)':
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE16_M_insert_uniqueERKSB_[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_unique(std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)]+0xc1): undefined reference to `std::_Rb_tree_decrement(std::_Rb_tree_node_base*)'
> /usr/local/lib/plumed///src/vesselbase/VesselRegister.o: In function `std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)':
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE17_M_insert_unique_ESt23_Rb_tree_const_iteratorISB_ERKSB_[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)]+0x123): undefined reference to `std::_Rb_tree_decrement(std::_Rb_tree_node_base const*)'
> VesselRegister.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSsPFPN4PLMD10vesselbase6VesselERKNS3_13VesselOptionsEEESt10_Select1stISB_ESt4lessISsESaISB_EE17_M_insert_unique_ESt23_Rb_tree_const_iteratorISB_ERKSB_[std::_Rb_tree<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)>, std::_Select1st<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> >, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, PLMD::vesselbase::Vessel* (*)(PLMD::vesselbase::VesselOptions const&)> const&)]+0x20f): undefined reference to `std::_Rb_tree_increment(std::_Rb_tree_node_base const*)'
> /usr/local/lib/plumed///src/config/ConfigInstall.o: In function `PLMD::config::getSoExt()':
> ConfigInstall.cpp:(.text+0x15): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
> /usr/local/lib/plumed///src/config/ConfigInstall.o: In function `PLMD::config::getPlumedRoot()':
> ConfigInstall.cpp:(.text+0x3d): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
> /usr/local/lib/plumed///src/config/ConfigInstall.o: In function `PLMD::config::getVersion()':
> ConfigInstall.cpp:(.text+0x5f): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
> /usr/local/lib/plumed///src/config/ConfigInstall.o: In function `PLMD::config::getVersionLong()':
> ConfigInstall.cpp:(.text+0x81): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
> /usr/local/lib/plumed///src/config/ConfigInstall.o: In function `PLMD::config::getVersionGit()':
> ConfigInstall.cpp:(.text+0xa3): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
> /usr/local/lib/plumed///src/config/ConfigInstall.o: In function `char* std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag)':
> ConfigInstall.cpp:(.text._ZNSs12_S_constructIPKcEEPcT_S3_RKSaIcESt20forward_iterator_tag[char* std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag)]+0x36): undefined reference to `std::__throw_logic_error(char const*)'
> ConfigInstall.cpp:(.text._ZNSs12_S_constructIPKcEEPcT_S3_RKSaIcESt20forward_iterator_tag[char* std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag)]+0x55): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage'
> ConfigInstall.cpp:(.text._ZNSs12_S_constructIPKcEEPcT_S3_RKSaIcESt20forward_iterator_tag[char* std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag)]+0x73): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage'
> ConfigInstall.cpp:(.text._ZNSs12_S_constructIPKcEEPcT_S3_RKSaIcESt20forward_iterator_tag[char* std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag)]+0xa6): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_create(unsigned long, unsigned long, std::allocator<char> const&)'
> ConfigInstall.cpp:(.text._ZNSs12_S_constructIPKcEEPcT_S3_RKSaIcESt20forward_iterator_tag[char* std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag)]+0xc8): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_create(unsigned long, unsigned long, std::allocator<char> const&)'
> collect2: ld returned 1 exit status
> make[3]: *** [/home/xxx007/cp2k/cp2k/exe/Linux-x86-64-gfortran2/dbcsr_example_1.popt] Error 1
> make[2]: *** [all] Error 2
> make[1]: *** [popt] Error 2
> make: *** [all] Error 2
> 
> I am using 64 bit ubuntu 12.04, and I have installed 64 bit version libz. So I am really confusing what is wrong with this compiling process. 
> 
> Hang Xiao 
> 
> PhD student
> Room 829, Mudd Building
> Department of Earth and Environmental Engineering
> Columbia University
> New York, NY, 10027
> 
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