most of the example failed

[WeiLiPenguin]

Hi,
I try to run the examples with the script, but:

terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_S_construct null not valid

Please help me,
what kind of information do you need?

Best Regards!
Thanks for the tool.

[orex]

Hi, Wei Li.

This error looks like system related stuff. Please, provide me an information about

1. Your system.
2. Please, recompile the program with cmake -DCMAKE_BUILD_TYPE=Debug ../ . It will produce more verbose output.
3. Please also run command
   supercell -d -i Ca2Al2SiO7.cif and print all output you have.

Best,
Kirill.

[WeiLiPenguin]

Hi, Kirill
OS: ubuntu 14.04 64
g++ (Ubuntu 4.8.4-2ubuntu1~14.04.1) 4.8.4

ldd supercell

        linux-vdso.so.1 =>  (0x00007ffd6d35c000)
        libopenbabel.so.4 => /usr/local/lib/libopenbabel.so.4 (0x00007fbf28896000)
        libboost_regex.so.1.54.0 => /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.54.0 (0x00007fbf2857a000)
        libboost_program_options.so.1.54.0 => /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.54.0 (0x00007fbf2830b000)
        libboost_system.so.1.54.0 => /usr/lib/x86_64-linux-gnu/libboost_system.so.1.54.0 (0x00007fbf28107000)
        libarchive.so.13 => /usr/lib/x86_64-linux-gnu/libarchive.so.13 (0x00007fbf27e66000)
        libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fbf27b61000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fbf2785b000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fbf27645000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fbf2727f000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fbf2707b000)
        libicuuc.so.52 => /usr/lib/x86_64-linux-gnu/libicuuc.so.52 (0x00007fbf26d02000)
        libicui18n.so.52 => /usr/lib/x86_64-linux-gnu/libicui18n.so.52 (0x00007fbf268fa000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fbf266dc000)
        libnettle.so.4 => /usr/lib/x86_64-linux-gnu/libnettle.so.4 (0x00007fbf264ad000)
        libattr.so.1 => /lib/x86_64-linux-gnu/libattr.so.1 (0x00007fbf262a7000)
        liblzo2.so.2 => /lib/x86_64-linux-gnu/liblzo2.so.2 (0x00007fbf26086000)
        liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007fbf25e64000)
        libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007fbf25c53000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fbf25a3a000)
        libxml2.so.2 => /usr/lib/x86_64-linux-gnu/libxml2.so.2 (0x00007fbf256d3000)
        /lib64/ld-linux-x86-64.so.2 (0x0000556eb93c9000)
        libicudata.so.52 => /usr/lib/x86_64-linux-gnu/libicudata.so.52 (0x00007fbf23e65000)

the output is the same like before,

debug compiler flags seems still have -O3

I will try -O0 and with gdb to find where cause the error.

could you please add a test in the .travis.yaml to see if have the same error?

I find code crash at around d2o_main_class.cpp:1632, is that could be related to the openbabel read cif file ?

Best Regards!

[orex]

Hi, Wei Li.

I can confirm, that openbabel is a weak place of my program. I will add the test shortly, but what version of openbabel you are using?

-O0 will not help you. You should use -g.

For me it is very strange, that you don't have anything else in the output. You should have at least header of my program run.

Kirill.

[WeiLiPenguin]

Yes, Kinrill
It has only your header and that error.
I mean your cmake hardcoded with the Debug flag with -g -O3, I try to change to -g -O0.
I install openbabel like your .travis.yaml file, so clone from its repo, should be newest one? but it also have apt-get install openbabel. I am confused now.

Wei

[orex]

You should remove openbabel from ubuntu repository. Most probably they cannot live together. Just before remove openbabel from repository, can you run openbabel itself? From both /usr/bin and /usr/local/bin folder. Most probaly the problem here.

I've add the test. It is failed, but with another error. I'm going to research the problem.

[orex]

I've just add the test. The funny thing, that it has passed with clang, but failed with gcc. I'm very surprised. Your help in solving of the issue is crucial.

[orex]

It looks like this is even GCC compiler bug. The workaround is not to use "-O0" option in OpenBabel compiling. Use default cmake options for openbabel (cmake ../ -DCMAKE_BUILD_TYPE=Release) to make the supercell program working.

[WeiLiPenguin]

Great! It works!
BTW:
is that possible run in parallel?

[orex]

You can run my program in parallel only for some cases, now. Although, the enumerating algorithm can be parallelized very efficiently I don't see now any strong reason to implement this. If it is not a secret, can you briefly describe your project. We can discuss and I can implement this. You can do this public (creating a new issue) or privately (my e-mail in git log).