[gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

[Glenn (Gedaliah) Wolosh]

Hi,

Thanks for the response. What is interesting is that the same build on a Scientific Linux 7.x environment works fine. It is also hard to explain why the other gmx commands work and, so far, only grompp fails. At any rate, I have a work around using singularity. I can have gromacs run in a Scientific Linux 7 container on the Scientific Linux 6.x cluster. I have to finish the testing but I got past the grompp segfault.

GW

> On Dec 8, 2019, at 8:35 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> Hi,
> 
> That's clearly a mismatch between the std library headers used at compile
> time and the one used at (dynamic) linking time. I don't know how to fix
> it, but on such systems, I've always resorted to scl environments to get
> the appropriate gcc compiler+libraries, and if so then that would be the
> right time to source the Intel scripts.
> 
> Mark
> 
> On Sun, 8 Dec 2019 at 00:56, Glenn (Gedaliah) Wolosh <gwolosh at njit.edu>
> wrote:
> 
>> Here ya go
>> 
>> Program received signal SIGSEGV, Segmentation fault.
>> 0x00002aaab21e63aa in
>> std::local_Rb_tree_decrement(std::_Rb_tree_node_base*) ()
>>    at ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc:98 <
>> http://tree.cc:98/>
>> 98      ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc <
>> http://tree.cc/>: No such file or directory.
>>        in ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc <
>> http://tree.cc/>
>> Missing separate debuginfos, use: debuginfo-install
>> glibc-2.12-1.212.el6.x86_64
>> (gdb) bt
>> #0  0x00002aaab21e63aa in
>> std::local_Rb_tree_decrement(std::_Rb_tree_node_base*) ()
>>    at ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc:98 <
>> http://tree.cc:98/>
>> #1  0x00002aaab1103c03 in std::_Rb_tree<unsigned char, std::pair<unsigned
>> char const, void (*)(gmx::KeyValueTreeValueBuilder*, gmx
>> ::ISerializer*)>, std::_Select1st<std::pair<unsigned char const, void
>> (*)(gmx::KeyValueTreeValueBuilder*, gmx::ISerializer*)> >, s
>> td::less<unsigned char>, std::allocator<std::pair<unsigned char const,
>> void (*)(gmx::KeyValueTreeValueBuilder*, gmx::ISerializer*)
>>>> 
>>> ::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator<std::pair<unsigned
>> char const, void (*)(gmx::KeyValueTreeValueBu
>> ilder*, gmx::ISerializer*)> >, unsigned char const&) ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #2  0x00002aaab11011f0 in gmx::(anonymous
>> namespace)::ValueSerializer::initSerializers() ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #3  0x00002aaab10ffee2 in
>> gmx::serializeKeyValueTree(gmx::KeyValueTreeObject const&,
>> gmx::ISerializer*) ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #4  0x00002aaab115ca27 in _INTERNAL2c7c030d::do_inputrec(t_fileio*,
>> t_inputrec*, bool, int) ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #5  0x00002aaab1154df1 in _INTERNAL2c7c030d::do_tpx(t_fileio*, bool,
>> t_inputrec*, t_state*, float (*) [3], float (*) [3], gmx_mtop_t*) () from
>> /afs/cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4
>> <http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #6  0x00002aaab11548ed in write_tpx_state(char const*, t_inputrec const*,
>> t_state const*, gmx_mtop_t const*) ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #7  0x00002aaab132cae4 in gmx_grompp(int, char**) ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #8  0x00002aaab1039549 in gmx::CommandLineModuleManager::run(int, char**)
>> ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #9  0x0000000000407928 in main ()
>> 
>> GW