Help to compile SMINA

[Marcel Patek]

I compiled OpenBabel 3.0.0 and Boost 1.54 on Ubuntu and edited makefile to set path to both. When running

~/Computation/smina/smina/build/linux/release $ make
I get,
g++ -ansi -O3 -DNDEBUG -g -I /usr/include/boost -I /usr/local/include/openbabel3 -I ../../../src/lib -o main.o -c ../../../src/main/main.cpp

and in the next line a warning:

../../../src/lib/Eigen/src/Core/arch/SSE/PacketMath.h:29:39: warning: ignoring attributes on template argument ‘__m128 {aka __vector(4) float}’ [-Wignored-attributes]
template<> struct is_arithmetic<__m128> { enum { value = true }; };

... later then ..

In file included from ../../../src/main/main.cpp:48:0:
../../../src/lib/box.h: In member function ‘void Box::add_ligand_box(OpenBabel::OBMol&)’:
../../../src/lib/box.h:23:20: error: ‘a’ was not declared in this scope
FOR_ATOMS_OF_MOL(a, mol)
^
../../../src/lib/box.h:23:3: error: ‘FOR_ATOMS_OF_MOL’ was not declared in this scope
FOR_ATOMS_OF_MOL(a, mol)
^~~~~~~~~~~~~~~~

and at the end,

../../makefile_common:19: recipe for target 'main.o' failed
make: *** [main.o] Error 1

I reinstalled Boost and OpenBabel (the latter works), but cannot finish installation of Smina. What I am missing?
Thank you.

[David Koes]

Are you sure you have the latest version of the source code? These macros are defined in openbabel/obiter.h which is included in lib/common.h. This header didn't use to need to be explicitly included since other openbable headers included it, but this changed with openbabel 3.0. A commit in May (e6620331e3dadd3be20d70ac42c85c2a9ede0a8) fixed the problem.

[Marcel Patek]

For Smina, I used 'git clone' (https://github.com/mwojcikowski/smina) and then 'cd'ed to smina/build/linux/release (it shows 5 years old?). I guess I should have used the latest code from SourceForge (2020)? [git clone https://git.code.sf.net/p/smina/code smina-code]
For the OpenBabel, I used the tarball from their site (openbabel-3.0.0-source.tar.bz2). Boost is libboost 1.64 from Ubuntu repos.

[David Koes]

Yes, the sourceforge git is the official respository, you need to use that.

[Marcel Patek]

Thank you. I used the > git clone https://git.code.sf.net/p/smina/code and compiled after modifying make files. The compilation run much longer, but it failed with the output below? There is a lot of Eigen-related warnings but it seems that it failed at boost?

dpkg -s libboost-dev | grep Version
Version: 1.58.0.1ubuntu1

make

~/Computation/smina/code/build/linux/release $ make
g++ -ansi -O3 -DNDEBUG -g **-I /usr/include/boost -I /usr/local/include/openbabel3 -I ../../../src/lib -o main.o -c ../../../src/main/main.cpp

---

g++ -ansi -O3 -DNDEBUG -g -I /usr/include/boost -I /usr/local/include/openbabel3 -o smina main.o builtinscoring.o cache.o coords.o custom_terms.o everything.o flexinfo.o grid.o szv_grid.o model.o monte_carlo.o mutate.o my_pid.o naive_non_cache.o non_cache.o obmolopener.o parallel_mc.o parse_pdbqt.o pdb.o quasi_newton.o quaternion.o random.o ssd.o terms.o weighted_terms.o molgetter.o result_info.o PDBQTUtilities.o SminaConverter.o -l openbabel -l boost_iostreams -l boost_timer -lz -l boost_system -l boost_regex -l boost_thread -l boost_serialization -l boost_filesystem -l boost_program_options -l boost_date_time
main.o: In function boost::cpp_regex_traits<char>::transform_primary[abi:cxx11](char const*, char const*) const': /usr/include/boost/regex/v4/cpp_regex_traits.hpp:965: undefined reference toboost::re_detail::cpp_regex_traits_implementation<char>::transform_primaryabi:cxx11 const'
main.o: In function boost::cpp_regex_traits<char>::transform[abi:cxx11](char const*, char const*) const': /usr/include/boost/regex/v4/cpp_regex_traits.hpp:961: undefined reference toboost::re_detail::cpp_regex_traits_implementation<char>::transformabi:cxx11 const'
collect2: error: ld returned 1 exit status
../../makefile_common:30: recipe for target 'smina' failed
make: *** [smina] Error 1</char></char>

I assume that the compiled binary will ultimately be in /usr/local/bin?
Thank you.

[David Koes]

Have you tried using the cmake build system?
mkdir build-cmake
cd build-cmake
cmake ..

[Marcel Patek]

Created cmake-build as:
/smina/code/build/build-cmake
cd to it and then to point to CMakeLists.txt, run

cmake ../../

---

'CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
CMake 3.10 or higher is required. You are running version 3.5.1'

Changed the minimum version at line 1 to 3.5.1 and it started well. However, it failed again at 100% - at the very end after some checking. File liblibsmina.a was created. I attached CmakeError.log

"undefined reference to boost::re_detail::cpp_regex_traits_implementation<char>::transform_primaryabi:cxx11 const
main.cpp:(.text._ZN5boost9re_detail16re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost9re_detail16re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x41f): undefined reference to `boost::re_detail::cpp_regex_traits_implementation<char>::transformabi:cxx11 const'
collect2: error: ld returned 1 exit status
CMakeFiles/smina.dir/build.make:108: recipe for target 'smina' failed
make[2]: [smina] Error 1
CMakeFiles/Makefile2:104: recipe for target 'CMakeFiles/smina.dir/all' failed
make[1]: [CMakeFiles/smina.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2"</char></char>

---

[David Koes]

What operating system is this?

The two most likely issues are that you have mulitple copies of boost installed and are linking to a library that is a different version than the headers you are building against (if this was they case I was hoping cmake would do a better job selecting library paths) or somehow your boost libraries are built with a different version of the compiler being used to build smina.

[Marcel Patek]

Mint 18.3 Cinnamon 64-bit. I'll try uninstall all boost versions and compile myself. Installed Boost libs are from unbuntu repo. Cmake though shows that it found Boost:

-- Found Boost include files at /usr/include
-- Found Boost libraries at /usr/lib/x86_64-linux-gnu/libboost_iostreams.so;/usr/lib/x86_64-linux-gnu/libboost_timer.so;/usr/lib/x86_64-linux-gnu/libboost_system.so;/usr/lib/x86_64-linux-gnu/libboost_regex.so;/usr/lib/x86_64-linux-gnu/libboost_thread.so;/usr/lib/x86_64-linux-gnu/libboost_serialization.so;/usr/lib/x86_64-linux-gnu/libboost_filesystem.so;/usr/lib/x86_64-linux-gnu/libboost_program_options.so;/usr/lib/x86_64-linux-gnu/libboost_date_time.so;/usr/lib/x86_64-linux-gnu/libboost_chrono.so;/usr/lib/x86_64-linux-gnu/libboost_atomic.so;/usr/lib/x86_64-linux-gnu/libpthread.so

Cmake complains about not seing eigen3 (it is in /usr/include/eigen3). Where do I enter "eigen3_DIR"=/usr/include/eigen3?
Thank you.

[Marcel Patek]

Well. I removed libboost and installed version 1.68 (latest in package manager). Run the make from /code/linux/release, got close to 100% and got different error:
is that //lib/x86 a correct path?

---

/usr/bin/ld: parallel_mc.o: undefined reference to symbol 'pthread_condattr_setclock@@GLIBC_2.3.3'
//lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
../../makefile_common:34: recipe for target 'tosmina' failed
make: *** [tosmina] Error 1

---

I'll have to try diffrent machine.

[David Koes]

I pulled this docker image:
https://hub.docker.com/r/linuxmintd/mint18-amd64
And had no trouble building smina either with the cmake build system or the classical build system.
Packages installed
libboost-all-dev
zlib1g-dev
ssh
cmake
vim
eigen3-dev
zlib-dev

OpenBabel 3 was built from source. I changed the cmake version requirement to get the cmake build to work.

I recommend trying to figure out what is different between your setup and a vanilla setup.

[Marcel Patek]

Good idea. I'll run the docker image and will compare both.
Thank you.

[Marcel Patek]

OK. I was able to compile smina on Mint 19 virtual machine with Boost1.65 (default) and Openbabel3. It required reinstalling libeigen3 from the package manager.
As for the main system, I was not able to trace the cause of failure. Cmake was able to create Makefile without any warning while the final make failed at 100% compiled and linking.
It is clearly my machine that needs fixes. Thank you for the help.

[Marcel Patek]

Finally, I was able to compile (and run) smina on my main machine. The problem was a conflict in multiple gcc versions. Dropping from 7.0 to the default 5.5 solved the issue. So it was compiler mixup.

[Ho Leung Ng]

I was able to compile with gcc7 on linuxmint 19.3. I've had some problems compiling too but using cmake fixed it.

[Rémi Lacroix]

I had the same issue today using CMake.

It took some figuring out but in fact the problem comes from the fact that my boost is installed with boost-cmake (https://cmake.org/cmake/help/latest/module/FindBoost.html#boost-cmake).

It breaks smina CMake unless you add -DBoost_NO_BOOST_CMAKE=ON. It should probably be added to the CMakeList.txt.

[David Koes]

I've pushed the Boost_NO_BOOST_CMAKE=ON configuration as well as removed the legacy build files.

[Rémi Lacroix]

Thanks, it does solve the issue for me.