Hello,
Sorry for the late answer, as you can see in the svn, the data was ok.
Because there are no modifications of the original data. :)
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$
*Anyway, the problem was solved :), was my mistake. *
The location of the plugins was set to
: BABEL_LIBDIR=/home/jperaltac/local/lib/openbabel/ and must be
: BABEL_LIBDIR=/home/jperaltac/local/lib/openbabel/2.3.2/
Thanks to everyone for the help.
All the best
Joaquin
I chage
On Sat, Sep 15, 2012 at 3:36 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> 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
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Got visibility?
> >> Most devs has no idea what their production app looks like.
> >> Find out how fast your code is with AppDynamics Lite.
> >> http://ad.doubleclick.net/clk;262219671;13503038;y?
> >> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> >> _______________________________________________
> >> OpenBabel-discuss mailing list
> >> 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.
> > http://ad.doubleclick.net/clk;262219671;13503038;y?
> > http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> > _______________________________________________
> > OpenBabel-discuss mailing list
> > 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?.*
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