id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1076	Signs of memory leak during toolshed install	Tristan Croll	Conrad Huang	"OK, this is doing my head in somewhat. In my ISOLDE source, if I add

{{{
from simtk import openmm
}}}

to my top-level __init__.py (not what I was doing originally, but what it boils down to), then on running `make app-install` in Linux, at the end of an otherwise successful installation I get a traceback (the details of which I've copied below), indicating that something is trying to free up memory that's already been freed (and probably doesn't belong to it). 
{{{
Executing: toolshed install './dist/ChimeraX_ISOLDE-0.9.24-cp36-cp36m-linux_x86_64.whl' reinstall true
unloading module chimerax.isolde
Successfully installed ChimeraX-ISOLDE-0.9.24
Installed ChimeraX-ISOLDE (0.9.24)

Executing: exit
Exiting ...
*** Error in `/home/tic20/apps/chimerax/bin/ChimeraX': double free or corruption (!prev): 0x0000000002b8fab0 ***
======= Backtrace: =========
}}}

Last entry in the log when running under Valgrind:

{{{
==2079== Invalid free() / delete / delete[] / realloc()
==2079==    at 0x4C2B18D: operator delete(void*) (vg_replace_malloc.c:576)
==2079==    by 0x5BCFA68: __run_exit_handlers (exit.c:77)
==2079==    by 0x5BCFAB4: exit (exit.c:99)
==2079==    by 0x4FCC4A8: Py_Exit (pylifecycle.c:1550)
==2079==    by 0x4FCF5E3: handle_system_exit.part.3 (pythonrun.c:626)
==2079==    by 0x4FCF974: handle_system_exit (pythonrun.c:658)
==2079==    by 0x4FCF974: PyErr_PrintEx (pythonrun.c:636)
==2079==    by 0x4FEC4AC: RunModule (main.c:215)
==2079==    by 0x4FED080: Py_Main (main.c:750)
==2079==    by 0x4008C2: main (in /home/tic20/apps/chimerax/bin/ChimeraX)
==2079==  Address 0xd233d30 is 0 bytes inside a block of size 1,194 free'd
==2079==    at 0x4C2B18D: operator delete(void*) (vg_replace_malloc.c:576)
==2079==    by 0x5BCFA68: __run_exit_handlers (exit.c:77)
==2079==    by 0x5BCFAB4: exit (exit.c:99)
==2079==    by 0x4FCC4A8: Py_Exit (pylifecycle.c:1550)
==2079==    by 0x4FCF5E3: handle_system_exit.part.3 (pythonrun.c:626)
==2079==    by 0x4FCF974: handle_system_exit (pythonrun.c:658)
==2079==    by 0x4FCF974: PyErr_PrintEx (pythonrun.c:636)
==2079==    by 0x4FEC4AC: RunModule (main.c:215)
==2079==    by 0x4FED080: Py_Main (main.c:750)
==2079==    by 0x4008C2: main (in /home/tic20/apps/chimerax/bin/ChimeraX)
==2079==  Block was alloc'd at
==2079==    at 0x4C2A203: operator new(unsigned long) (vg_replace_malloc.c:334)
==2079==    by 0x5432158: allocate (new_allocator.h:104)
==2079==    by 0x5432158: std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator<char> const&) (basic_string.tcc:607)
==2079==    by 0x5433AD4: char* std::string::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag) (basic_string.tcc:138)
==2079==    by 0x5433F05: _S_construct_aux<char const*> (basic_string.h:1743)
==2079==    by 0x5433F05: _S_construct<char const*> (basic_string.h:1764)
==2079==    by 0x5433F05: std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) (basic_string.tcc:215)
==2079==    by 0x76611F93: __cxx_global_var_init.3 (OpenCLDrudeKernelSources.cpp:290)
==2079==    by 0x76611F93: _GLOBAL__sub_I_OpenCLDrudeKernelSources.cpp (OpenCLDrudeKernelSources.cpp:0)
==2079==    by 0x400F4C2: call_init (dl-init.c:82)
==2079==    by 0x400F4C2: _dl_init (dl-init.c:131)
==2079==    by 0x4013BD5: dl_open_worker (dl-open.c:560)
==2079==    by 0x400F2D3: _dl_catch_error (dl-error.c:177)
==2079==    by 0x40132CA: _dl_open (dl-open.c:650)
==2079==    by 0x6176FBA: dlopen_doit (dlopen.c:66)
==2079==    by 0x400F2D3: _dl_catch_error (dl-error.c:177)
==2079==    by 0x61775BC: _dlerror_run (dlerror.c:163)
}}}

Looking through the full valgrind log, I can't find anything relating to any of my own classes (none of which should have been instantiated in any case) in amongst all the general Python spam. The installation itself works: I can start ChimeraX and ISOLDE, run a simulation, apply all my different restraints, and shut down without error. Furthermore, the error doesn't appear on the Mac. Really not sure where to take it from here.


On another note, I find that if I remove the offending line, I have to run `make app-install` twice before the traceback goes away - not sure if this is by design or not, but it seems the existing bundle installation is loaded during the installation of the new one."	defect	closed	moderate		Tool Shed		can't reproduce		Tom Goddard				Linux64 (X11)	ChimeraX