You are not using a clean svn version (see the output of your "svn st"
command). Just start over. Remove the install directory. Check out a
clean version from SVN and try to get that to build. There's no point
trying to write a plugin until you can successfully run Open Babel
from SVN.
- Noel
On 15 September 2012 00:08, joaquin peralta <jperal...@gmail.com> wrote:
> Hello,
>
> Before I put all the text, just allow me to explain :
>
> I'm not compiling with my plugin, it is just a clean svn version. I tried
> with make clean and make and the problem still, I just set all environment
> variables and the problem still.
>
> The problem is running : babel -H (that single command send me a segfault)
> so I did this with gdb :
>
> ===================================================================================
> jperaltac@baco:~/buildob$ gdb "/home/jperaltac/local/bin/babel"
> ..........
> Reading symbols from /home/jperaltac/local/bin/babel...done.
> (gdb) run -H
> Starting program: /home/jperaltac/local/bin/babel -H
> Open Babel converts chemical structures from one file format to another
>
> Usage: babel <input spec> <output spec> [Options]
>
> Each spec can be a file whose extension decides the format.
> Optionally the format can be specified by preceding the file by
> -i<format-type> e.g. -icml, for input and -o<format-type> for output
>
> See below for available format-types, which are the same as the
> file extensions and are case independent.
> If no input or output file is given stdin or stdout are used instead.
>
> More than one input file can be specified and their names can contain
> wildcard chars (* and ?).The molecules are aggregated in the output file.
>
> Conversion options
> -f <#> Start import at molecule # specified
> -l <#> End import at molecule # specified
> -e Continue with next object after error, if possible
> -z Compress the output with gzip
> -k Attempt to translate keywords
> -H Outputs this help text
> -V Outputs version number
> -L <category> Lists plugin classes of this category, e.g. <formats>
> Use just -L for a list of plugin categories.
> Use -L <ID> e.g. -L sdf for details of a format or other plugin.
> -m Produces multiple output files, to allow:
> Splitting: e.g. babel infile.mol new.smi -m
> puts each molecule into new1.smi new2.smi etc
> Batch conversion: e.g. babel *.mol -osmi -m
> converts each input file to a .smi file
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x000000000040769f in std::vector<std::string, std::allocator<std::string>
>>::max_size (this=0x7fffff7ff130) at
> /usr/include/c++/4.6/bits/stl_vector.h:576
> 576 { return _M_get_Tp_allocator().max_size(); }
> (gdb)
>
> ===================================================================================
>
> then looking with 'where' in gdb I have :
>
> ===================================================================================
>
> #0 0x000000000040769f in std::vector<std::string,
> std::allocator<std::string> >::max_size (this=0x7fffff7ff130) at
> /usr/include/c++/4.6/bits/stl_vector.h:576
> #1 0x00000000004072c9 in std::vector<std::string,
> std::allocator<std::string> >::_M_check_len (this=0x7fffff7ff130, __n=1,
> __s=0x4083da "vector::_M_insert_aux")
> at /usr/include/c++/4.6/bits/stl_vector.h:1241
> #2 0x0000000000406d43 in std::vector<std::string,
> std::allocator<std::string> >::_M_insert_aux (this=0x7fffff7ff130,
> __position=..., __x=...) at /usr/include/c++/4.6/bits/vector.tcc:325
> #3 0x000000000040694a in std::vector<std::string,
> std::allocator<std::string> >::push_back (this=0x7fffff7ff130, __x=...) at
> /usr/include/c++/4.6/bits/stl_vector.h:834
> #4 0x00007ffff7704c33 in DLHandler::findFiles (file_list=..., pattern=...,
> path=...) at /home/jperaltac/Projects/openbabel/src/dlhandler_unix.cpp:82
> #5 0x00007ffff76c1fc4 in OpenBabel::OBPlugin::LoadAllPlugins () at
> /home/jperaltac/Projects/openbabel/src/plugin.cpp:61
> #6 0x00007ffff76c1ed6 in OpenBabel::OBPlugin::GetTypeMap
> (PluginID=0x7ffff7762d07 "loaders") at
> /home/jperaltac/Projects/openbabel/src/plugin.cpp:34
> #7 0x00007ffff76c23b9 in OpenBabel::OBPlugin::GetPlugin
> (Type=0x7ffff7762d07 "loaders", ID=0x7ffff7762d00 "define") at
> /home/jperaltac/Projects/openbabel/src/plugin.cpp:110
> #8 0x00007ffff76c207b in OpenBabel::OBPlugin::LoadAllPlugins () at
> /home/jperaltac/Projects/openbabel/src/plugin.cpp:80
>
> ... The lines #6,#7, and #8 are repeated a lot after that ...
> ===================================================================================
>
> Now the document that I attahced before about the process :
>
> ===================================================================================
> My installation process from svn.
>
> jperaltac@baco:~/Projects/openbabel$ sudo find / -iname "abinitformat.so"
> jperaltac@baco:~/Projects/openbabel$ svn st
> ? test/files/prueba.xyz
> ? test/files/Au.lpmd
> A src/formats/lpmdformat.cpp
> jperaltac@baco:~/Projects/openbabel$ svn up
> At revision 5011.
> jperaltac@baco:~/Projects/openbabel$
>
> Compiling
>
> jperaltac@baco:~/Projects/openbabel$ export
> BABEL_LIBDIR=/home/jperaltac/local/lib/openbabel/
> jperaltac@baco:~/Projects/openbabel$
>
> Then
> jperaltac@baco:~/Projects/openbabel$ cd ~/buildob/
> jperaltac@baco:~/buildob$ ls
> jperaltac@baco:~/buildob$ cmake -DCMAKE_BUILD_TYPE=Debug
> -DCMAKE_INSTALL_PREFIX=/home/jperaltac/local/ ~/Projects/openbabel/
> -- The C compiler identification is GNU
> -- The CXX compiler identification is GNU
> -- Check for working C compiler: /usr/bin/gcc
> -- Check for working C compiler: /usr/bin/gcc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- 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
> -- Using included inchi library.
> -- Could NOT find LibXml2 (missing: LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)
> CMake Warning at CMakeLists.txt:152 (message):
> libxml2 not found - disabling CML support!
>
>
> -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.3.4")
> -- Could NOT find wxWidgets (missing: wxWidgets_FOUND)
> -- Looking for conio.h
> -- Looking for conio.h - not found
> -- Looking for sys/time.h
> -- Looking for sys/time.h - found
> -- Looking for time.h
> -- Looking for time.h - found
> -- Looking for strings.h
> -- Looking for strings.h - found
> -- Looking for rpc/xdr.h
> -- Looking for rpc/xdr.h - found
> -- Looking for regex.h
> -- Looking for regex.h - found
> -- Looking for C++ include sstream
> -- Looking for C++ include sstream - found
> -- Looking for rint
> -- Looking for rint - not found.
> -- Looking for snprintf
> -- Looking for snprintf - found
> -- Looking for sranddev
> -- Looking for sranddev - not found.
> -- Looking for strcasecmp
> -- Looking for strcasecmp - found
> -- Looking for strncasecmp
> -- Looking for strncasecmp - found
> -- Looking for dlopen in dl
> -- Looking for dlopen in dl - found
> -- 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 clock_t
> -- Check size of clock_t - done
> -- Performing Test SCANDIR_NEEDS_CONST
> -- Performing Test SCANDIR_NEEDS_CONST - Failed
> -- Performing Test HAVE_GCC_VISIBILITY
> -- Performing Test HAVE_GCC_VISIBILITY - Success
> -- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
> (Required is at least version "2.91.0")
> -- Could NOT find Eigen2 (missing: EIGEN2_INCLUDE_DIR EIGEN2_VERSION_OK)
> (Required is at least version "2.0.0")
> -- checking for module 'cairo'
> -- package 'cairo' not found
> -- Could NOT find Cairo. PNG output will NOT be supported.
> -- Looking for getopt
> -- Looking for getopt - found
> -- Attempting to build the GUI
> -- wxWidgets not found => GUI will not be built
> -- Found PythonInterp: /usr/bin/python (found version "2.7.3")
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/jperaltac/buildob
>
> Compiling
>
> make ; make instal
>
> Work finw without error message nor suspissious warnings. Then :
>
> jperaltac@baco:~/buildob$ babel
> No output file or format spec!
> Open Babel 2.3.2 -- Sep 14 2012 -- 17:07:39
> Usage: babel [-i<input-type>] <name> [-o<output-type>] <name>
> Try -H option for more information.
> jperaltac@baco:~/buildob$ babel -H
> Open Babel converts chemical structures from one file format to another
>
> Usage: babel <input spec> <output spec> [Options]
>
> Each spec can be a file whose extension decides the format.
> Optionally the format can be specified by preceding the file by
> -i<format-type> e.g. -icml, for input and -o<format-type> for output
>
> See below for available format-types, which are the same as the
> file extensions and are case independent.
> If no input or output file is given stdin or stdout are used instead.
>
> More than one input file can be specified and their names can contain
> wildcard chars (* and ?).The molecules are aggregated in the output file.
>
> Conversion options
> -f <#> Start import at molecule # specified
> -l <#> End import at molecule # specified
> -e Continue with next object after error, if possible
> -z Compress the output with gzip
> -k Attempt to translate keywords
> -H Outputs this help text
> -V Outputs version number
> -L <category> Lists plugin classes of this category, e.g. <formats>
> Use just -L for a list of plugin categories.
> Use -L <ID> e.g. -L sdf for details of a format or other plugin.
> -m Produces multiple output files, to allow:
> Splitting: e.g. babel infile.mol new.smi -m
> puts each molecule into new1.smi new2.smi etc
> Batch conversion: e.g. babel *.mol -osmi -m
> converts each input file to a .smi file
> Segmentation fault (core dumped)
> jperaltac@baco:~/buildob$
>
> Looks like somethings is wrong here, I don't know why the segmentation
> fault!. Any hint now with this ?
>
> And my environments variables :
>
> jperaltac@baco:~/buildob$ env | grep bab
> BABEL_LIBDIR=/home/jperaltac/local/lib/openbabel/
> OLDPWD=/home/jperaltac/Projects/openbabel
> jperaltac@baco:~/buildob$
>
> Finallym the valgrind output :
>
> ==1485== Stack overflow in thread 1: can't grow stack to 0x7fe801ff8
> ==1485==
> ==1485== Process terminating with default action of signal 11 (SIGSEGV)
> ==1485== Access not within mapped region at address 0x7FE801FF8
> ==1485== at 0x40790A: std::string*
> std::__uninitialized_copy<false>::__uninit_copy<std::string*,
> std::string*>(std::string*, std::string*, std::string*)
> (stl_uninitialized.h:70)
> ==1485== If you believe this happened as a result of a stack
> ==1485== overflow in your program's main thread (unlikely but
> ==1485== possible), you can try to increase the size of the
> ==1485== main thread stack using the --main-stacksize= flag.
> ==1485== The main thread stack size used in this run was 8388608.
> ==1485== Stack overflow in thread 1: can't grow stack to 0x7fe801fe8
> ==1485==
> ==1485== Process terminating with default action of signal 11 (SIGSEGV)
> ==1485== Access not within mapped region at address 0x7FE801FE8
> ==1485== at 0x4A255A0: _vgnU_freeres (in
> /usr/lib/valgrind/vgpreload_core-amd64-linux.so)
> ==1485== If you believe this happened as a result of a stack
> ==1485== overflow in your program's main thread (unlikely but
> ==1485== possible), you can try to increase the size of the
> ==1485== main thread stack using the --main-stacksize= flag.
> ==1485== The main thread stack size used in this run was 8388608.
> ==1485==
> ==1485== HEAP SUMMARY:
> ==1485== in use at exit: 1,813,622 bytes in 28,223 blocks
> ==1485== total heap usage: 288,894 allocs, 260,671 frees, 866,039,001
> bytes allocated
> ==1485==
> ==1485== LEAK SUMMARY:
> ==1485== definitely lost: 0 bytes in 0 blocks
> ==1485== indirectly lost: 0 bytes in 0 blocks
> ==1485== possibly lost: 1,758,118 bytes in 26,375 blocks
> ==1485== still reachable: 55,504 bytes in 1,848 blocks
> ==1485== suppressed: 0 bytes in 0 blocks
> ==1485== Rerun with --leak-check=full to see details of leaked memory
> ==1485==
> ==1485== For counts of detected and suppressed errors, rerun with: -v
> ==1485== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 2 from 2)
> Segmentation fault (core dumped)
>
> ===================================================================================
>
> that's it!
>
> Thanks for all the help, and sorry about the long e-mail.
>
> Regards
> Joaquin
>
> On Fri, Sep 14, 2012 at 5:45 PM, My Th <rei4...@gmail.com> wrote:
>>
>> Pk, 2012-09-14 17:17 -0500, joaquin peralta rakstīja:
>> > Hello,
>>
>> >
>> > Thanks very much for the answer but the problem looks worse now :( ...
>> > I assign the environment variable, but still there.
>> >
>> >
>> > I don't have any other version of openbabel in the system, and I'm
>> > using the last subversion. My Os is ubuntu 12.04 and g++ versin is
>> > 4.6.3. I'm installing in my home folder, and the PATH are well
>> > defined.
>> >
>> >
>> > I attached a file with all the detail, because is to much to put it in
>> > the e-mail (and probably unnecessary).
>>
>> It is ok to put that much into the email.
>>
>> > Any hint about this segfault ?
>>
>> Try cleaning the build dir and recompile without installing:
>> make clean ; make
>>
>> and then try to run it from your build dir setting environment
>> appropriately.
>>
>> Did you try also setting LD_LIBRARY_PATH to point to were
>> libopenbabel.so is located? In general you need to set all three
>> variables mentioned in the docs and make sure you are running babel
>> binary you just compiled.
>>
>> If still getting segfault try compiling with debug symbols and getting
>> backtrace using gdb:
>> gdb bin/babel core-file
>> (gdb) bt full
>>
>> Posting your code would make much easier to help.
>>
>>
>> Reinis
>>
>>
>>
>> ------------------------------------------------------------------------------
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>> Find out how fast your code is with AppDynamics Lite.
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>> _______________________________________________
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>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
>
>
> --
> Joaquín Peralta C.
> Postdoctoral Research Associate
> Materials Science and Engineering
> Iowa State University
> 3326 Hoover Hall
> Ames, IA 50011
> Phone Lab: 515-294-9547
> http://www.lpmd.cl/jperalta
> http://www.gnm.cl
> -----------------------------------------------
> In a world without frontiers,
> who needs Gates and Windows?.
>
>
> ------------------------------------------------------------------------------
> Got visibility?
> Most devs has no idea what their production app looks like.
> Find out how fast your code is with AppDynamics Lite.
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> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> _______________________________________________
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> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
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