RDME simulation fails in infinite loop

[briandrawert]

set enable_rdme=True
and run in the terminal for the following errors:

Simulating RDME for 1.000000e-05 seconds
nsm: tt=1.170501e-05 subvol=1429
nsm: tt=1.170501e-05 subvol=1429 type=3 Diff 1429->1377    xx[1429]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1321    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1270    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1268    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1321    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1321    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1217    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1217    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1268    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1217    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1270    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1268    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1321    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1218    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1268    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1321    xx[1269]=[0 ]

This happens on the 2nd time the NRM solver is called (step #2)

[briandrawert]

Full output:

brian@thor:/tmp/spatialpy_build_78o2vrbt$ ./ssa_sdpd | more
initialize_rdme()
Creating 8 simulation threads
Creating thread to process 338 particles
Creating thread to process 338 particles
[WORKER 0] waiting to begin step 0
Creating thread to process 338 particles
[WORKER 1] waiting to begin step 0
Creating thread to process 338 particles
Creating thread to process 338 particles
[WORKER 3] waiting to begin step 0
Creating thread to process 338 particles
[WORKER 4] waiting to begin step 0
Creating thread to process 338 particles
[WORKER 5] waiting to begin step 0
Creating thread to process 338 particles
[WORKER 6] waiting to begin step 0
[WORKER 2] waiting to begin step 0
Creating thread to update sort index
[WORKER 7] waiting to begin step 0
Creating thread to create output files
[0] Starting the Sort Index threads
[0] Starting the Output threads
[OUT] start output_vtk__sync_step()
[SORT] begin sort
[OUT] done output_vtk__sync_step()
[OUT] start output_vtk__async_step()
Writing file 'output0_boundingBox.vtk'
[0] Output threads finished
Writing file 'output0.vtk'
[SORT] sort complete
[0] Sort Index threads finished
[0] Starting the Worker threads
[WORKER 4] completed step 0, substep 0/3, processed 338 particles
[OUT] done output_vtk__async_step()
[WORKER 6] completed step 0, substep 0/3, processed 338 particles
[WORKER 2] completed step 0, substep 0/3, processed 338 particles
[WORKER 3] completed step 0, substep 0/3, processed 338 particles
[WORKER 5] completed step 0, substep 0/3, processed 338 particles
[WORKER 1] completed step 0, substep 0/3, processed 338 particles
[WORKER 0] completed step 0, substep 0/3, processed 338 particles
[WORKER 7] completed step 0, substep 0/3, processed 338 particles
[0] Worker threads finished substep 0/3
[WORKER 1] completed step 0, substep 1/3, processed 338 particles
[WORKER 0] completed step 0, substep 1/3, processed 338 particles
[WORKER 7] completed step 0, substep 1/3, processed 338 particles
[WORKER 3] completed step 0, substep 1/3, processed 338 particles
[WORKER 4] completed step 0, substep 1/3, processed 338 particles
[WORKER 6] completed step 0, substep 1/3, processed 338 particles
[WORKER 2] completed step 0, substep 1/3, processed 338 particles
[WORKER 5] completed step 0, substep 1/3, processed 338 particles
[0] Worker threads finished substep 1/3
[WORKER 1] completed step 0, substep 2/3, processed 338 particles
[WORKER 0] completed step 0, substep 2/3, processed 338 particles
[WORKER 7] completed step 0, substep 2/3, processed 338 particles
[WORKER 4] completed step 0, substep 2/3, processed 338 particles
[WORKER 3] completed step 0, substep 2/3, processed 338 particles
[WORKER 2] completed step 0, substep 2/3, processed 338 particles
[WORKER 5] completed step 0, substep 2/3, processed 338 particles
[WORKER 6] completed step 0, substep 2/3, processed 338 particles
[0] Worker threads finished substep 2/3
[WORKER 0] waiting to begin step 1
[0] starting RDME simulation
	nsm_core__initialize_rxn_propensities
[WORKER 7] waiting to begin step 1
[WORKER 6] waiting to begin step 1
[WORKER 5] waiting to begin step 1
	nsm_core__initialize_diff_propensities
[WORKER 3] waiting to begin step 1
[WORKER 1] waiting to begin step 1
[WORKER 4] waiting to begin step 1
[WORKER 2] waiting to begin step 1
	nsm_core__initialize_heap
Simulating RDME for 1.000000e-05 seconds
nsm: tt=1.305424e-05 subvol=1171
nsm: tt=1.305424e-05 subvol=1171 type=3 Diff 1171->1223    xx[1171]=[0 ]
[0] Finish RDME simulation
[1] Starting the Sort Index threads
[1] Starting the Output threads
[SORT] begin sort
[OUT] start output_vtk__sync_step()
[OUT] done output_vtk__sync_step()
[OUT] start output_vtk__async_step()
Writing file 'output1.vtk'
[1] Output threads finished
[SORT] sort complete
[1] Sort Index threads finished
[1] Starting the Worker threads
[OUT] done output_vtk__async_step()
[WORKER 3] completed step 1, substep 0/3, processed 338 particles
[WORKER 0] completed step 1, substep 0/3, processed 338 particles
[WORKER 6] completed step 1, substep 0/3, processed 338 particles
[WORKER 4] completed step 1, substep 0/3, processed 338 particles
[WORKER 2] completed step 1, substep 0/3, processed 338 particles
[WORKER 5] completed step 1, substep 0/3, processed 338 particles
[WORKER 1] completed step 1, substep 0/3, processed 338 particles
[WORKER 7] completed step 1, substep 0/3, processed 338 particles
[1] Worker threads finished substep 0/3
[WORKER 4] completed step 1, substep 1/3, processed 338 particles
[WORKER 2] completed step 1, substep 1/3, processed 338 particles
[WORKER 3] completed step 1, substep 1/3, processed 338 particles
[WORKER 6] completed step 1, substep 1/3, processed 338 particles
[WORKER 5] completed step 1, substep 1/3, processed 338 particles
[WORKER 0] completed step 1, substep 1/3, processed 338 particles
[WORKER 7] completed step 1, substep 1/3, processed 338 particles
[WORKER 1] completed step 1, substep 1/3, processed 338 particles
[1] Worker threads finished substep 1/3
[WORKER 2] completed step 1, substep 2/3, processed 338 particles
[WORKER 0] completed step 1, substep 2/3, processed 338 particles
[WORKER 4] completed step 1, substep 2/3, processed 338 particles
[WORKER 5] completed step 1, substep 2/3, processed 338 particles
[WORKER 1] completed step 1, substep 2/3, processed 338 particles
[WORKER 3] completed step 1, substep 2/3, processed 338 particles
[WORKER 6] completed step 1, substep 2/3, processed 338 particles
[WORKER 7] completed step 1, substep 2/3, processed 338 particles
[1] Worker threads finished substep 2/3
[WORKER 2] waiting to begin step 2
[WORKER 0] waiting to begin step 2
[WORKER 4] waiting to begin step 2
[WORKER 5] waiting to begin step 2
[WORKER 3] waiting to begin step 2
[WORKER 7] waiting to begin step 2
[1] starting RDME simulation
	nsm_core__initialize_rxn_propensities
[WORKER 1] waiting to begin step 2
[WORKER 6] waiting to begin step 2
	nsm_core__initialize_diff_propensities
	nsm_core__initialize_heap
Simulating RDME for 1.000000e-05 seconds
nsm: tt=1.170501e-05 subvol=1429
nsm: tt=1.170501e-05 subvol=1429 type=3 Diff 1429->1377    xx[1429]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1321    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1270    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1268    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1321    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1321    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1217    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1217    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1268    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1217    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1270    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1268    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1321    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1218    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1268    xx[1269]=[0 ]
nsm: tt=1.555651e-05 subvol=1269
nsm: tt=1.555651e-05 subvol=1269 type=3 Diff 1269->1321    xx[1269]=[0 ]