Turns out if I checkout an earlier version of simbody (before this assert existed) I nonetheless get a crash, except without this nicer and more informative assert. This even happens when I roll back to an earlier version of MMB. Actually even old binaries that once worked now do not work. I guess t...

Hi Guys, I am trying to compile OpenMM in Debug mode. However in my target lib directory I only see: ../openmm/lib/libOpenMM.so I was expecting to see a _d suffix like this:: ../openmm/lib/libOpenMM_d.so I don't see that CMakeLists calls for this suffix to be added. Should I treat ../openmm/lib/libO...

Hi Guys, Have you changed something about how CompoundSystem::realizeTopology() works? I realize that is actually implemented in System. I am getting the following error: MMB: /home/samuelf/SimTK/include/simbody/SimTKcommon/internal/Stage.h:157: SimTK::String SimTK::Stage::getName() const: Assertion...

I am not building CUDA or OpenCL libs (cmake variable settings below). All I really use from OpenMM is the neighborlisting, which is fast even without the GPU. Sam OPENMM_BUILD_AMOEBA_CUDA_LIB OFF OPENMM_BUILD_AMOEBA_PLUGIN ON OPENMM_BUILD_CPU_LIB ON OPENMM_BUILD_CUDA_COMPILER_PLU OFF OPENMM_BUILD_C...

by the way, the program is exiting cleanly in OSX, if that is a clue.

Seems unlikely. All libraries -- OpenMM, simbody, and molmodel, are compiled on Uppmax. The Uppmax people didn't want to upgrade their glibc, so all are built using the same rather old glibc. Their argument (not entirely unreasonable) was that that glibc would not cause memory leaks, but could expos...

Very well. But it is not just valgrind that gives me an error message. Executing on Linux actually runs to completion, but then dumps a scary error message about a corrupted double-linked list (appended below). Note that OpenMM is mentioned in the last lines of the memory map, though I don't know if...

Guys, We have been cleaning up memory leaks in MMB. I think I got all that came from MMB and molmodel, but there is a problem remaining, apparently involving OpenMM. This one is quite insidious, in that I was unable to get a location in the source. At least it is completing the calculation and not h...

Well I deleted two tests, TestOpenCLVirtualSites.cpp, and TestOpenCLRpmd.cpp. Then I was able to compile just fine. c++11 is a little more strict about namespaces somehow, so I had to fix an issue along those lines in MMB. I found I didn't really need to copy ResidueInfo objects, except out of vanit...

Well, Simbody is now hard wired to compile to c++11. Of course, one can edit the CMakeLists.txt and turn that off. However I'm having problems with molmodel when I do that. All in all, it seems a good idea to keep up with standards, especially one that is now four years old.I think c++11 is a bit mo...