Rerun (-l_from) simulation inside openworm container

[lungd]

There is an issue with the rerun of the Sibernetic simulatoin: openworm/OpenWorm#291
(Sibernetic crashes while rerunning simulation)

It seems like that issue starts with 688a717 (compile error) and 1b63814

I did some debugging and figuered out the following:
Sibernetic crashes at line

sibernetic/src/owWorldSimulation.cpp

Line 404 in a52006e

((p_cpp[i * 4] + p_cpp[j * 4] + 4 * p_cpp[k * 4]) / 6 -

'i' (

sibernetic/src/owWorldSimulation.cpp

Line 398 in a52006e

i = md_cpp[i_m * 3 + 0];

) is a random int.
I think the random value comes from an array initialization with 0 elements

sibernetic/src/owHelper.cpp

Line 658 in 4c29d5f

membranes = new int[4 * m_count];

After removing the comment from

sibernetic/src/owHelper.cpp

Line 656 in 4c29d5f

// membranesFile >> m_count;

, the recording of the Sibernetic simulation (startet with -l_from) works but there is an issue with the membranes.
The recorded output looks like the following

If I remove the loop for drawing the membranes

sibernetic/src/owWorldSimulation.cpp

Line 397 in a52006e

for (unsigned int i_m = 0; i_m < localConfig->numOfMembranes; ++i_m) {

, the recorded output looks more like it is supposed to look like

I am not sure whether the membrane issue is related to the code of Sibernetic (loadTo / loadFrom) or to a misconfigured system.

Any ideas?

[lungd]

And I think there is an issue with the code starting with

sibernetic/src/owHelper.cpp

Line 655 in 4c29d5f

int m_count = 0;

:

I think it should be:

      int m_count = 0;
      membranesFile >> m_count;
      int i = 0;
      membranes = new int[3 * m_count];
      while (membranesFile.good() && i < m_count) {
        membranesFile >> membranes[3 * i + 0] >> membranes[3 * i + 1] >> membranes[3 * i + 2];
        i++;
      }

and not:

      int m_count = 0;
      membranesFile >> m_count;
      int i = 0;
      membranes = new int[4 * m_count];
      while (membranesFile.good() && i < m_count) {
        membranesFile >> membranes[4 * i + 0] >> membranes[4 * i + 1] >> membranes[4 * i + 2] >> membranes[4 * i + 3];
        i++;
      }

But this patch doesn't change the membrane issue described above

[lungd]

Update:
The membrane issue is most likely related to the implementation of OpenGL.

I think with a prev version of Sibernetic, the membranes didn't get displayed while rerunning a simulation.
With the current version, including the changes described above, the membranes get displayed but the result looks pretty bad because of the CPU only docker container.

@a-palyanov @skhayrulin, what do you think about adding a parameter defining whether the membranes should get displayed?

[skhayrulin]

Hi @lungd sorry for late answer, I'll review this at the near time

[lungd]

Fixed