search

Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
127 stars 62 forks source link

Problem of installing apbs-1.4.1 #475

Closed ghost closed 7 years ago

ghost commented 7 years ago

I tried apbs-1.4. And I used cmake -DCMAKE_INSTALL_PREFIX=/opt/apbs -DENABLE_BEM=off -DENABLE_iAPBS=on -DENABLE_GEOFLOW=ON .. option to install apbs-1.4.1, and could not compile it with libapbs_geoflow successfully. It seems the installation skipped the geoflow installation which is needed by g_mmpbsa. Part of the output after 'make' is as follows:

Scanning dependencies of target geoflow
[  1%] Creating directories for 'geoflow'
[  2%] No download step for 'geoflow'
[  3%] No patch step for 'geoflow'
[  4%] No update step for 'geoflow'
[  5%] Performing configure step for 'geoflow'
-- The CXX compiler identification is GNU 4.8.4
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Boost version: 1.54.0
-- The C compiler identification is GNU 4.8.4
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to: /home/apple/desktop/ttt/apbs-pdb2pqr-master/apbs/build/geoflow-prefix/src/geoflow-build
[  6%] Performing build step for 'geoflow'
Scanning dependencies of target GeometricFlowLib
[ 33%] Building CXX object src/CMakeFiles/GeometricFlowLib.dir/GeometricFlowWrap.cpp.o
[ 66%] Building CXX object src/CMakeFiles/GeometricFlowLib.dir/GeometricFlow.cpp.o
[100%] Building CXX object src/CMakeFiles/GeometricFlowLib.dir/Atom.cpp.o
Linking CXX static library ../lib/libGeometricFlowLib.a
[100%] Built target GeometricFlowLib
[  7%] No install step for 'geoflow'
[  9%] Completed 'geoflow'
[  9%] Built target geoflow

So, what should I do to compile apbs with geoflow? Thank you in advance.

kozlac commented 7 years ago

@howiedlut is there a specific reason you are using APBS 1.4.1? The reason I'm asking is that from your post it seems you want to use Geoflow. However, Geoflow was a preliminary implementation in this version. If the APBS version is not an issue I would recommend downloading APBS 1.5.

Otherwise, could you please attached the full cmake and make outputs on a clean build folder?

ghost commented 7 years ago

@kozlac The reason I want to use Geoflow is that g_mmpbsa needs libapbs_geoflow.

Required Libraries from APBS: libmaloc, libapbs_geoflow, libapbs_mg, libapbs_pmgc and libapbs_generic.

However, I could find this file in the lib folder of the pre-compiled binary release of APBS-1.4.1 but not in the folder I compiled myself.

Thank you again for your help.

ghost commented 7 years ago

Now I tried compiling the source codes of APBS-1.5.

First of all, I copied fetk and geoflow_c to the externals folder of apbs. And I add set(EIGEN3_INCLUDE_DIR /home/wangah/tmp/source/apbs-pdb2pqr-apbs-1.5/apbs/include ) to the apbs-pdb2pqr-apbs-1.5/apbs/externals/geoflow_c/CMakeLists.txt file (line 39) to tell it the location of Eigen3.

Then I started cmake with 

mkdir build && cd build 
cmake ../ -DENABLE_BEM=off -DENABLE_iAPBS=on -DENABLE_GEOFLOW=ON \
    -DCMAKE_CXX_COMPILER=/raid3/opt/cpu/gcc-4.8.1/bin/g++    \
    -DCMAKE_C_COMPILER=/raid3/opt/cpu/gcc-4.8.1/bin/gcc      \
    -DCMAKE_INSTALL_PREFIX=/raid3/home/wanganhui/bin2/mmpbsa_gmx/apbs-1.5

Here is the complete output:

-- The C compiler identification is GNU 4.8.1
-- The CXX compiler identification is GNU 4.8.1
-- Check for working C compiler: /raid3/opt/cpu/gcc-4.8.1/bin/gcc
-- Check for working C compiler: /raid3/opt/cpu/gcc-4.8.1/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /raid3/opt/cpu/gcc-4.8.1/bin/g++
-- Check for working CXX compiler: /raid3/opt/cpu/gcc-4.8.1/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Setting project paths
-- Setting lookup paths for headers and libraries
-- Computing machine epsilon values
-- Floating point epsilon is 2.220446e-16
-- Double precision epsilon is 2.220446e-16
-- Looking for time
-- Looking for time - found
-- Looking for rand
-- Looking for rand - found
-- Looking for srand
-- Looking for srand - found
-- Setting project paths
-- Setting lookup paths for headers and libraries
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of mode_t
-- Check size of mode_t - done
-- Check size of pid_t
-- Check size of pid_t - done
-- Check size of size_t
-- Check size of size_t - done
-- Looking for 4 include files stdlib.h, ..., float.h
-- Looking for 4 include files stdlib.h, ..., float.h - found
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file sys/stat.h
-- Looking for include file sys/stat.h - found
-- Looking for include file sys/socket.h
-- Looking for include file sys/socket.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file sys/un.h
-- Looking for include file sys/un.h - found
-- Looking for include file sys/wait.h
-- Looking for include file sys/wait.h - found
-- Looking for include file fcntl.h
-- Looking for include file fcntl.h - found
-- Looking for include file netinet/in.h
-- Looking for include file netinet/in.h - found
-- Looking for include file arpa/inet.h
-- Looking for include file arpa/inet.h - found
-- Looking for include file netdb.h
-- Looking for include file netdb.h - found
-- Looking for include file rpc/rpc.h
-- Looking for include file rpc/rpc.h - found
-- Looking for getcwd
-- Looking for getcwd - found
-- Looking for O_NONBLOCK
-- Looking for O_NONBLOCK - found
-- With sources: base/maloc_base.c;psh/psh.c;psh/vcom.c;psh/vmp.c;psh/vmpi.c;vsh/vlex.c;vsh/vpars.c;vsh/vpup.c;vsh/vsh.c;vsh/vyacc.c;vsys/vio.c;vsys/viofb.c;vsys/vmem.c;vsy
s/vnm.c;vsys/vnmfb.c;vsys/vpred.c;vsys/vset.c;vsys/ziofb.c-- With external headers: base/maloc/maloc.h;base/maloc/maloc_base.h;psh/maloc/psh.h;psh/maloc/vcom.h;psh/maloc/vmp.h;psh/maloc/vmpi.h;vsh/maloc/vsh.h;vsys/maloc/vio.h;vsys
/maloc/vmem.h;vsys/maloc/vnm.h;vsys/maloc/vset.h;vsys/maloc/vsys.h;vsys/maloc/vpred.h-- With internal headers: base/maloc_base_p.h;psh/psh_p.h;psh/vcom_p.h;psh/vmpi_p.h;psh/vmp_p.h;vsh/vpup.h;vsh/vsh_p.h;vsh/vyacc.h;vsys/vio_p.h;vsys/vmem_p.h;vsys/vnm_p.h;v
sys/vpred_p.h;vsys/vset_p.h-- Building GEOFLOW
-- Inline functions enabled
-- Verbose debugging mode enabled
-- Adding apbs_generic
-- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;
vparam.c;vgreen.c-- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;v
string.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h-- With internal header files 
-- With library dependencies m;stdc++;maloc;GeometricFlowLib
-- Added apbs_generic
-- Adding apbs_pmgc
-- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoo
thd.c;mgfasd.c-- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powe
rd.h;smoothd.h;mgfasd.h-- With internal header files 
-- With library dependencies m;stdc++;maloc;GeometricFlowLib
-- Added apbs_pmgc
-- Adding apbs_mg
-- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c
-- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h
-- With internal header files 
-- With library dependencies m;stdc++;maloc;GeometricFlowLib;apbs_generic;apbs_pmgc
-- Added apbs_mg
-- Adding apbs_routines
-- With source files routines.c
-- With external header files 
-- With internal header files 
-- With library dependencies m;stdc++;maloc;GeometricFlowLib
-- Added apbs_routines
-- 
***************************
--  
-- APBS Libraries: m;stdc++;maloc;GeometricFlowLib
-- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_routines
--  
***************************
-- 
-- Supplemental tools enabled
-- Building mesh
-- libraries: apbs_generic;apbs_mg;apbs_pmgc
-- Building manip
-- libraries: apbs_generic;apbs_mg;apbs_pmgc
-- Building of iAPBS interface enabled
-- Configuring done
-- Generating done
-- Build files have been written to: /home/wanganhui/tmp/source/test/apbs-pdb2pqr-apbs-1.5/apbs/build

And the output after make -j 8 is

Scanning dependencies of target geoflow
Scanning dependencies of target iapbs
Scanning dependencies of target maloc
[  1%] [  2%] Creating directories for 'geoflow'
[  3%] [  4%] [  6%] Building C object contrib/iapbs/src/CMakeFiles/iapbs.dir/apbs_driver.c.o
[  7%] [  7%] [  9%] [ 10%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vmp.c.o
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/base/maloc_base.c.o
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vlex.c.o
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vcom.c.o
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vmpi.c.o
No download step for 'geoflow'
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/psh.c.o
[ 11%] No patch step for 'geoflow'
[ 12%] [ 13%] [ 14%] [ 15%] No update step for 'geoflow'
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vpars.c.o
[ 17%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vsh.c.o
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vpup.c.o
[ 18%] [ 19%] Performing configure step for 'geoflow'
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vio.c.o
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vyacc.c.o
[ 20%] [ 21%] [ 22%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vmem.c.o
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vnm.c.o
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/viofb.c.o
Linking C static library ../../../lib/libiapbs.a
[ 23%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vnmfb.c.o
[ 25%] [ 26%] [ 27%] [ 27%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/ziofb.c.o
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vpred.c.o
Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vset.c.o
Built target iapbs
-- The CXX compiler identification is GNU 4.8.1
-- Check for working CXX compiler: /opt/cpu/gcc-4.8.1/bin/c++
Linking C static library ../../../../../externals/fetk/maloc/lib/libmaloc.a
-- Check for working CXX compiler: /opt/cpu/gcc-4.8.1/bin/c++ -- works
[ 27%] -- Detecting CXX compiler ABI info
Built target maloc
Scanning dependencies of target apbs_routines
Scanning dependencies of target apbs_pmgc
Scanning dependencies of target apbs_generic
[ 28%] [ 30%] [ 30%] [ 31%] [ 32%] [ 34%] [ 35%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o
Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o
Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o
Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o
Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o
Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o
Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o
[ 36%] [ 37%] [ 38%] [ 39%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o
[ 40%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o
Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o
Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o
Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o
-- Detecting CXX compiler ABI info - done
[ 42%] [ 43%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o
Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o
[ 44%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o
Linking C static library ../lib/libapbs_routines.a
[ 45%] [ 46%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o
[ 47%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o
[ 47%] [ 48%] Built target apbs_routines
[ 50%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o
Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o
Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o
[ 51%] [ 52%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o
[ 53%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o
[ 54%] [ 55%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o
Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o
[ 56%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o
[ 57%] [ 59%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o
Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o
Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o
[ 60%] [ 61%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o
[ 62%] -- Boost version: 1.33.1
[ 63%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o
Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o
[ 64%] [ 65%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o
Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o
Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o
[ 67%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o
[ 68%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o
[ 69%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o
-- The C compiler identification is GNU 4.8.1
-- Check for working C compiler: /opt/cpu/gcc-4.8.1/bin/gcc
Linking C static library ../../lib/libapbs_generic.a
Linking C static library ../../lib/libapbs_pmgc.a
[ 69%] Built target apbs_generic
[ 69%] Built target apbs_pmgc
Scanning dependencies of target apbs_mg
[ 70%] [ 71%] [ 72%] [ 73%] [ 75%] -- Check for working C compiler: /opt/cpu/gcc-4.8.1/bin/gcc -- works
Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o
Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o
Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o
Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o
-- Detecting C compiler ABI info
Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o
-- Detecting C compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to: /home/wanganhui/tmp/source/test/apbs-pdb2pqr-apbs-1.5/apbs/build/geoflow-prefix/src/geoflow-build
[ 76%] Performing build step for 'geoflow'
gmake[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
Scanning dependencies of target GeometricFlowLib
[ 33%] Building CXX object src/CMakeFiles/GeometricFlowLib.dir/GeometricFlowWrap.cpp.o
Linking C static library ../../lib/libapbs_mg.a
[ 76%] Built target apbs_mg
Scanning dependencies of target apbs
Scanning dependencies of target del2dx
Scanning dependencies of target benchmark
Scanning dependencies of target dx2mol
Scanning dependencies of target dx2uhbd
Scanning dependencies of target dxmath
Scanning dependencies of target analysis
[ 79%] [ 79%] [ 79%] [ 80%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o
Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o
Building C object tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o
Building C object src/CMakeFiles/apbs.dir/main.c.o
[ 81%] [ 82%] Building C object tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o
Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o
[ 84%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o
Linking C executable ../bin/dx2uhbd
Linking C executable ../bin/del2dx
Linking C executable ../bin/dx2mol
/usr/bin/ld: cannot find -lGeometricFlowLib
collect2: error: ld returned 1 exit status
make[2]: *** [tools/bin/dx2uhbd] Error 1
make[1]: *** [tools/mesh/CMakeFiles/dx2uhbd.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 85%] /usr/bin/ld: cannot find -lGeometricFlowLib
collect2: error: ld returned 1 exit status
Building C object src/CMakeFiles/apbs.dir/routines.c.o
make[2]: *** [tools/bin/del2dx] Error 1
make[1]: *** [tools/mesh/CMakeFiles/del2dx.dir/all] Error 2
Linking C executable ../bin/analysis
/usr/bin/ld: cannot find -lGeometricFlowLib
collect2: error: ld returned 1 exit status
make[2]: *** [tools/bin/dx2mol] Error 1
make[1]: *** [tools/mesh/CMakeFiles/dx2mol.dir/all] Error 2
Linking C executable ../bin/dxmath
/usr/bin/ld: cannot find -lGeometricFlowLib
collect2: error: ld returned 1 exit status
make[2]: *** [tools/bin/analysis] Error 1
make[1]: *** [tools/mesh/CMakeFiles/analysis.dir/all] Error 2
/usr/bin/ld: cannot find -lGeometricFlowLib
collect2: error: ld returned 1 exit status
make[2]: *** [tools/bin/dxmath] Error 1
make[1]: *** [tools/mesh/CMakeFiles/dxmath.dir/all] Error 2
Linking C executable ../bin/benchmark
/usr/bin/ld: cannot find -lGeometricFlowLib
collect2: error: ld returned 1 exit status
make[2]: *** [tools/bin/benchmark] Error 1
make[1]: *** [tools/mesh/CMakeFiles/benchmark.dir/all] Error 2
Linking C executable ../bin/apbs
/usr/bin/ld: cannot find -lGeometricFlowLib
collect2: error: ld returned 1 exit status
make[2]: *** [bin/apbs] Error 1
make[1]: *** [src/CMakeFiles/apbs.dir/all] Error 2
[ 66%] Building CXX object src/CMakeFiles/GeometricFlowLib.dir/GeometricFlow.cpp.o
[100%] Building CXX object src/CMakeFiles/GeometricFlowLib.dir/Atom.cpp.o
In file included from /usr/include/boost/algorithm/string/split.hpp:15:0,
                 from /home/wanganhui/tmp/source/test/apbs-pdb2pqr-apbs-1.5/apbs/externals/geoflow_c/src/Atom.cpp:56:
/usr/include/boost/algorithm/string/iter_find.hpp: In instantiation of ‘SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&, FinderT) [with Sequenc
eSequenceT = std::vector<std::basic_string<char> >; RangeT = std::basic_string<char>; FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char> >]’:/usr/include/boost/algorithm/string/split.hpp:148:49:   required from ‘SequenceSequenceT& boost::algorithm::split(SequenceSequenceT&, RangeT&, PredicateT, boost::algorithm
::token_compress_mode_type) [with SequenceSequenceT = std::vector<std::basic_string<char> >; RangeT = std::basic_string<char>; PredicateT = boost::algorithm::detail::is_any_ofF<char>]’/home/wanganhui/tmp/source/test/apbs-pdb2pqr-apbs-1.5/apbs/externals/geoflow_c/src/Atom.cpp:160:88:   required from here
/usr/include/boost/algorithm/string/iter_find.hpp:154:51: error: call of overloaded ‘end(std::basic_string<char>&)’ is ambiguous
             input_iterator_type InputEnd=end(Input);
                                                   ^
/usr/include/boost/algorithm/string/iter_find.hpp:154:51: note: candidates are:
In file included from /usr/include/boost/range/functions.hpp:19:0,
                 from /usr/include/boost/range/iterator_range.hpp:25,
                 from /usr/include/boost/algorithm/string/iter_find.hpp:18,
                 from /usr/include/boost/algorithm/string/split.hpp:15,
                 from /home/wanganhui/tmp/source/test/apbs-pdb2pqr-apbs-1.5/apbs/externals/geoflow_c/src/Atom.cpp:56:
/usr/include/boost/range/end.hpp:145:56: note: typename boost::range_iterator<typename boost::remove_const<T>::type>::type boost::end(T&) [with T = std::basic_string<char>;
 typename boost::range_iterator<typename boost::remove_const<T>::type>::type = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >]                 typename remove_const<T>::type >::type end( T& r )
                                                        ^
/usr/include/boost/range/end.hpp:156:61: note: typename boost::range_const_iterator<C>::type boost::end(const T&) [with T = std::basic_string<char>; typename boost::range_c
onst_iterator<C>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >] inline BOOST_DEDUCED_TYPENAME range_const_iterator<T>::type end( const T& r )
                                                             ^
In file included from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/string:51:0,
                 from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/bits/locale_classes.h:40,
                 from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/bits/ios_base.h:41,
                 from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/ios:42,
                 from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/ostream:38,
                 from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/iostream:39,
                 from /home/wanganhui/tmp/source/test/apbs-pdb2pqr-apbs-1.5/apbs/externals/geoflow_c/src/Atom.h:57,
                 from /home/wanganhui/tmp/source/test/apbs-pdb2pqr-apbs-1.5/apbs/externals/geoflow_c/src/Atom.cpp:54:
/raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/bits/range_access.h:78:5: note: decltype (__cont.end()) std::end(const _Container&) [with _Container = std::basic_string<char>; d
ecltype (__cont.end()) = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]     end(const _Container& __cont) -> decltype(__cont.end())
     ^
/raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/bits/range_access.h:68:5: note: decltype (__cont.end()) std::end(_Container&) [with _Container = std::basic_string<char>; decltyp
e (__cont.end()) = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >]     end(_Container& __cont) -> decltype(__cont.end())
     ^
In file included from /usr/include/boost/algorithm/string/split.hpp:15:0,
                 from /home/wanganhui/tmp/source/test/apbs-pdb2pqr-apbs-1.5/apbs/externals/geoflow_c/src/Atom.cpp:56:
/usr/include/boost/algorithm/string/iter_find.hpp:161:52: error: call of overloaded ‘begin(std::basic_string<char>&)’ is ambiguous
                     find_iterator_type( begin(Input), InputEnd, Finder ),
                                                    ^
/usr/include/boost/algorithm/string/iter_find.hpp:161:52: note: candidates are:
In file included from /usr/include/boost/range/functions.hpp:18:0,
                 from /usr/include/boost/range/iterator_range.hpp:25,
                 from /usr/include/boost/algorithm/string/iter_find.hpp:18,
                 from /usr/include/boost/algorithm/string/split.hpp:15,
                 from /home/wanganhui/tmp/source/test/apbs-pdb2pqr-apbs-1.5/apbs/externals/geoflow_c/src/Atom.cpp:56:
/usr/include/boost/range/begin.hpp:146:64: note: typename boost::range_iterator<typename boost::remove_const<T>::type>::type boost::begin(T&) [with T = std::basic_string<ch
ar>; typename boost::range_iterator<typename boost::remove_const<T>::type>::type = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >]                         typename remove_const<T>::type >::type begin( T& r )
                                                                ^
/usr/include/boost/range/begin.hpp:157:61: note: typename boost::range_const_iterator<C>::type boost::begin(const T&) [with T = std::basic_string<char>; typename boost::ran
ge_const_iterator<C>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >] inline BOOST_DEDUCED_TYPENAME range_const_iterator<T>::type begin( const T& r )
                                                             ^
In file included from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/string:51:0,
                 from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/bits/locale_classes.h:40,
                 from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/bits/ios_base.h:41,
                 from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/ios:42,
                 from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/ostream:38,
                 from /raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/iostream:39,
                 from /home/wanganhui/tmp/source/test/apbs-pdb2pqr-apbs-1.5/apbs/externals/geoflow_c/src/Atom.h:57,
                 from /home/wanganhui/tmp/source/test/apbs-pdb2pqr-apbs-1.5/apbs/externals/geoflow_c/src/Atom.cpp:54:
/raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/bits/range_access.h:58:5: note: decltype (__cont.begin()) std::begin(const _Container&) [with _Container = std::basic_string<char
>; decltype (__cont.begin()) = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]     begin(const _Container& __cont) -> decltype(__cont.begin())
     ^
/raid3/opt/cpu/gcc-4.8.1/include/c++/4.8.1/bits/range_access.h:48:5: note: decltype (__cont.begin()) std::begin(_Container&) [with _Container = std::basic_string<char>; dec
ltype (__cont.begin()) = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >]     begin(_Container& __cont) -> decltype(__cont.begin())
     ^
gmake[6]: *** [src/CMakeFiles/GeometricFlowLib.dir/Atom.cpp.o] Error 1
gmake[5]: *** [src/CMakeFiles/GeometricFlowLib.dir/all] Error 2
gmake[4]: *** [src/CMakeFiles/GeometricFlowLib.dir/rule] Error 2
gmake[3]: *** [GeometricFlowLib] Error 2
make[2]: *** [geoflow-prefix/src/geoflow-stamp/geoflow-build] Error 2
make[1]: *** [CMakeFiles/geoflow.dir/all] Error 2
make: *** [all] Error 2

which gave the error message as above.

Looking forward to your reply. : )

kozlac commented 7 years ago

@howiedlut did you download the source code in a tar or are you cloning from the repo? It already looks like you did but I just want to make sure that if you are cloning from the repo you are also downloading the submodules for geoflow and fetk repos with:

~$git submodule init
~$git submodule update

After that your cmake build command looks good. Can you try to build with make without the -j flag:

~$make

It seems that some dependencies are not being built before they are being scanned. Hopefully, that fixes the other errors. Please let me know if this fixes it. Thanks!!

ghost commented 7 years ago

Thank you for your reply. I could successfully install APBS-1.5 now.

However, APBS-1.4.1 and libapbs_geoflow is needed for me because g_mmpbsa depends on APBS-1.4.1 and the API might have changed in later version of APBS.

So, could you please give me the source code of APBS-1.4.1 with geoflow supported ? In other words, could you compile APBS-1.4.1 from source code in 1.4.1-binary-release branch and generate libapbs_geoflow.a(so) successfully?

Another notable thing is that I compiled these codes on Centos 5.* machine, on which the low version of GLIBC could not be used for the binary executable files you provided.

keith923 commented 7 years ago

APBS-1.4.1-binary may be found here: https://github.com/Electrostatics/apbs-pdb2pqr/tree/1.4.1-binary-release/apbs With the build instructions here: https://github.com/Electrostatics/apbs-pdb2pqr/blob/1.4.1-binary-release/apbs/BUILD.md

It's very different building this old version compared to master. It's also got an old implementation of Geometric Flow that is known to have bugs.

From: howiedlut notifications@github.com Reply-To: Electrostatics/apbs-pdb2pqr reply@reply.github.com Date: Monday, May 15, 2017 at 11:19 PM To: Electrostatics/apbs-pdb2pqr apbs-pdb2pqr@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [Electrostatics/apbs-pdb2pqr] Problem of installing apbs-1.4.1 (#475)

Thank you for your reply. I could successfully install APBS-1.5 now.

However, APBS-1.4.1 and libapbs_geoflow is needed for me because g_mmpbsahttps://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html#install-with-apbs14 depends on APBS-1.4.1 and the API might have changed in later version of APBS.

So, could you please give me the source code of APBS-1.4.1 with geoflow supported ? In other words, could you compile APBS-1.4.1 from source code in 1.4.1-binary-release branch and generate libapbs_geoflow.a(so) successfully?

Another notable thing is that I compiled these codes on Centos 5.* machine, on which the low version of GLIBC could not be used for the binary executable files you provided.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Electrostatics/apbs-pdb2pqr/issues/475#issuecomment-301686493, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGGzFBMlbVM8KHYphOafslZJTohn3hlyks5r6UALgaJpZM4NZBCE.

ghost commented 7 years ago

@kozlac @keith923 Thank you for your reply.