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Merged
briandrawert merged 1 commit into from
Nov 11, 2020
Merged

uploading more files #61

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120 changes: 95 additions & 25 deletions examples/cdc42/cdc42.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13205,7 +13205,7 @@
},
{
"cell_type": "code",
"execution_count": 59,
"execution_count": 65,
"metadata": {
"scrolled": false
},
Expand All @@ -13214,40 +13214,110 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Volumes: DX=50\n",
"\textracellular\t2.9119999999999404 (1820 paticles)\n",
"\tmembrane\t0.608000000000001 (380 paticles) 3.23% error\n",
"\tcytoplasm\t0.479999999999998 (300 paticles) 4.51% error\n",
"Compiling Solver. Build dir: /tmp/spatialpy_build_c7a_lig9\n",
"Elapsed seconds: 0.01\n",
"Volumes: DX=10\n",
"\textracellular\t3.040000000000002 (76 paticles)\n",
"\tmembrane\t0.4799999999999999 (12 paticles) 23.61% error\n",
"\tcytoplasm\t0.4799999999999999 (12 paticles) 4.51% error\n",
"Compiling Solver. Build dir: /tmp/spatialpy_build_xei68ljy\n",
"Elapsed seconds: 0.00\n",
"*************** initialize_rdme ******************\n",
"Creating thread to process 312 particles\n",
"Creating thread to process 312 particles\n",
"Creating thread to process 312 particles\n",
"[WORKER 1] waiting to begin step 0\n",
"Creating thread to process 12 particles\n",
"Creating thread to process 12 particles\n",
"Creating thread to process 12 particles\n",
"Creating thread to process 12 particles\n",
"[WORKER 0] waiting to begin step 0\n",
"Creating thread to process 312 particles\n",
"[WORKER 2] waiting to begin step 0\n",
"Creating thread to process 312 particles\n",
"Creating thread to process 12 particles\n",
"[WORKER 3] waiting to begin step 0\n",
"Creating thread to process 312 particles\n",
"Creating thread to process 312 particles\n",
"[WORKER 2] waiting to begin step 0\n",
"Creating thread to process 12 particles\n",
"[WORKER 1] waiting to begin step 0\n",
"Creating thread to process 12 particles\n",
"[WORKER 5] waiting to begin step 0\n",
"Creating thread to process 16 particles\n",
"[WORKER 4] waiting to begin step 0\n",
"Creating thread to process 316 particles\n",
"[WORKER 6] waiting to begin step 0\n",
"Creating thread to update x-position index\n",
"Creating thread to create output files\n",
"[0] Starting the Sort Index threads\n",
"[WORKER 7] waiting to begin step 0\n",
"[SORT] begin sort\n",
"[0] Starting the Output threads\n",
"[OUT] start output_vtk__sync_step()\n",
"[SORT] sort complete took 473 us\n",
"[WORKER 6] waiting to begin step 0\n",
"[WORKER 7] waiting to begin step 0\n",
"[OUT] done output_vtk__sync_step()\n",
"[OUT] start output_vtk__async_step()\n",
"Writing file 'output0_boundingBox.vtk'\n",
"[0] Output threads finished\n",
"[SORT] begin sort\n",
"[SORT] sort complete 5 us\n",
"[0] Sort Index threads finished\n",
"[0] Starting the Worker threads\n",
"Writing file 'output0.vtk'\n",
"[WORKER 0] completed step 0, substep 0/3, processed 12 particles\n",
"[WORKER 3] completed step 0, substep 0/3, processed 12 particles\n",
"[WORKER 1] completed step 0, substep 0/3, processed 12 particles\n",
"[WORKER 2] completed step 0, substep 0/3, processed 12 particles\n",
"[WORKER 4] completed step 0, substep 0/3, processed 12 particles\n",
"[WORKER 5] completed step 0, substep 0/3, processed 12 particles\n",
"[WORKER 6] completed step 0, substep 0/3, processed 12 particles\n",
"[WORKER 7] completed step 0, substep 0/3, processed 16 particles\n",
"[0] Worker threads finished substep 0/3\n",
"[WORKER 2] completed step 0, substep 1/3, processed 12 particles\n",
"[WORKER 7] completed step 0, substep 1/3, processed 16 particles\n",
"[WORKER 6] completed step 0, substep 1/3, processed 12 particles\n",
"[WORKER 0] completed step 0, substep 1/3, processed 12 particles\n",
"[WORKER 1] completed step 0, substep 1/3, processed 12 particles\n",
"[WORKER 3] completed step 0, substep 1/3, processed 12 particles\n",
"[WORKER 4] completed step 0, substep 1/3, processed 12 particles\n",
"[WORKER 5] completed step 0, substep 1/3, processed 12 particles\n",
"[0] Worker threads finished substep 1/3\n",
"[WORKER 6] completed step 0, substep 2/3, processed 12 particles\n",
"[WORKER 0] completed step 0, substep 2/3, processed 12 particles\n",
"[WORKER 1] completed step 0, substep 2/3, processed 12 particles\n",
"[WORKER 3] completed step 0, substep 2/3, processed 12 particles\n",
"[WORKER 4] completed step 0, substep 2/3, processed 12 particles\n",
"[WORKER 5] completed step 0, substep 2/3, processed 12 particles\n",
"[WORKER 2] completed step 0, substep 2/3, processed 12 particles\n",
"[WORKER 7] completed step 0, substep 2/3, processed 16 particles\n",
"[0] Worker threads finished substep 2/3\n",
"[0] starting RDME simulation\n",
"\tnsm_core__initialize_rxn_propensities\n",
"[WORKER 6] waiting to begin step 1\n",
"[WORKER 0] waiting to begin step 1\n",
"[WORKER 3] waiting to begin step 1\n",
"[WORKER 5] waiting to begin step 1\n",
"[WORKER 7] waiting to begin step 1\n",
"\tnsm_core__initialize_diff_propensities\n",
"[WORKER 2] waiting to begin step 1\n",
"\tnsm_core__initialize_heap\n",
"[WORKER 1] waiting to begin step 1\n",
"[WORKER 4] waiting to begin step 1\n",
"before sort\n",
"========================================================\n",
"tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=8.651057e-07, tt=4.089383e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=6.329065e-07, tt=8.093082e-03, tt=9.483580e-03, tt=4.698511e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=2.220386e-06, tt=1.733538e-03, tt=2.419926e-02, tt=2.134093e-01, tt=1.120176e-03, tt=8.792504e-07, tt=inf, tt=inf, tt=inf, tt=inf, tt=3.261944e-06, tt=2.750354e-02, tt=1.076719e-01, tt=3.032052e-02, tt=4.225202e-02, tt=1.488286e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=2.917986e-06, tt=6.648724e-03, tt=1.578200e-04, tt=3.897571e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=5.361157e-07, tt=2.315782e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, ========================================================\n",
"after sort\n",
"========================================================\n",
"tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=8.651057e-07, tt=4.089383e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=6.329065e-07, tt=8.093082e-03, tt=9.483580e-03, tt=4.698511e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=2.220386e-06, tt=1.733538e-03, tt=2.419926e-02, tt=2.134093e-01, tt=1.120176e-03, tt=8.792504e-07, tt=inf, tt=inf, tt=inf, tt=inf, tt=3.261944e-06, tt=2.750354e-02, tt=1.076719e-01, tt=3.032052e-02, tt=4.225202e-02, tt=1.488286e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=2.917986e-06, tt=6.648724e-03, tt=1.578200e-04, tt=3.897571e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=5.361157e-07, tt=2.315782e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, ========================================================\n",
"Simulating RDME for 1.000000e+00 seconds\n",
"Error: overflow in trying to determine which destination voxel subvol=0\n",
"subvol->id=0 rand2=0.000000e+00 cum2=0.000000e+00 Current state in voxel 0:\n",
"xx[0] = 0\n",
"xx[1] = 0\n",
"xx[2] = 0\n",
"xx[3] = 0\n",
"xx[4] = 0\n",
"xx[5] = 0\n",
"xx[6] = 0\n",
"xx[7] = 0\n",
"xx[8] = 0\n",
"Neighbors:\n",
"1: nn->D_i_j=2.037652e+01 \n",
"2: nn->D_i_j=5.863151e-01 \n",
"10: nn->D_i_j=2.037652e+01 \n",
"11: nn->D_i_j=8.943732e+00 \n",
"20: nn->D_i_j=5.863151e-01 \n",
"\n",
"None\n",
"b'*************** initialize_rdme ******************\\nCreating thread to process 312 particles\\nCreating thread to process 312 particles\\nCreating thread to process 312 particles\\n[WORKER 1] waiting to begin step 0\\n[WORKER 0] waiting to begin step 0\\nCreating thread to process 312 particles\\n[WORKER 2] waiting to begin step 0\\nCreating thread to process 312 particles\\n[WORKER 3] waiting to begin step 0\\nCreating thread to process 312 particles\\nCreating thread to process 312 particles\\n[WORKER 5] waiting to begin step 0\\n[WORKER 4] waiting to begin step 0\\nCreating thread to process 316 particles\\n[WORKER 6] waiting to begin step 0\\nCreating thread to update x-position index\\nCreating thread to create output files\\n[0] Starting the Sort Index threads\\n[WORKER 7] waiting to begin step 0\\n[SORT] begin sort\\n[0] Starting the Output threads\\n[OUT] start output_vtk__sync_step()\\n[SORT] sort complete took 473 us\\n'\n",
"solver_cmd = cd /tmp/spatialpy_result_jkrq7w6w;/tmp/spatialpy_build_c7a_lig9/ssa_sdpd\n"
"b\"*************** initialize_rdme ******************\\nCreating thread to process 12 particles\\nCreating thread to process 12 particles\\nCreating thread to process 12 particles\\nCreating thread to process 12 particles\\n[WORKER 0] waiting to begin step 0\\nCreating thread to process 12 particles\\n[WORKER 3] waiting to begin step 0\\n[WORKER 2] waiting to begin step 0\\nCreating thread to process 12 particles\\n[WORKER 1] waiting to begin step 0\\nCreating thread to process 12 particles\\n[WORKER 5] waiting to begin step 0\\nCreating thread to process 16 particles\\n[WORKER 4] waiting to begin step 0\\nCreating thread to update x-position index\\nCreating thread to create output files\\n[0] Starting the Sort Index threads\\n[0] Starting the Output threads\\n[OUT] start output_vtk__sync_step()\\n[WORKER 6] waiting to begin step 0\\n[WORKER 7] waiting to begin step 0\\n[OUT] done output_vtk__sync_step()\\n[OUT] start output_vtk__async_step()\\nWriting file 'output0_boundingBox.vtk'\\n[0] Output threads finished\\n[SORT] begin sort\\n[SORT] sort complete 5 us\\n[0] Sort Index threads finished\\n[0] Starting the Worker threads\\nWriting file 'output0.vtk'\\n[WORKER 0] completed step 0, substep 0/3, processed 12 particles\\n[WORKER 3] completed step 0, substep 0/3, processed 12 particles\\n[WORKER 1] completed step 0, substep 0/3, processed 12 particles\\n[WORKER 2] completed step 0, substep 0/3, processed 12 particles\\n[WORKER 4] completed step 0, substep 0/3, processed 12 particles\\n[WORKER 5] completed step 0, substep 0/3, processed 12 particles\\n[WORKER 6] completed step 0, substep 0/3, processed 12 particles\\n[WORKER 7] completed step 0, substep 0/3, processed 16 particles\\n[0] Worker threads finished substep 0/3\\n[WORKER 2] completed step 0, substep 1/3, processed 12 particles\\n[WORKER 7] completed step 0, substep 1/3, processed 16 particles\\n[WORKER 6] completed step 0, substep 1/3, processed 12 particles\\n[WORKER 0] completed step 0, substep 1/3, processed 12 particles\\n[WORKER 1] completed step 0, substep 1/3, processed 12 particles\\n[WORKER 3] completed step 0, substep 1/3, processed 12 particles\\n[WORKER 4] completed step 0, substep 1/3, processed 12 particles\\n[WORKER 5] completed step 0, substep 1/3, processed 12 particles\\n[0] Worker threads finished substep 1/3\\n[WORKER 6] completed step 0, substep 2/3, processed 12 particles\\n[WORKER 0] completed step 0, substep 2/3, processed 12 particles\\n[WORKER 1] completed step 0, substep 2/3, processed 12 particles\\n[WORKER 3] completed step 0, substep 2/3, processed 12 particles\\n[WORKER 4] completed step 0, substep 2/3, processed 12 particles\\n[WORKER 5] completed step 0, substep 2/3, processed 12 particles\\n[WORKER 2] completed step 0, substep 2/3, processed 12 particles\\n[WORKER 7] completed step 0, substep 2/3, processed 16 particles\\n[0] Worker threads finished substep 2/3\\n[0] starting RDME simulation\\n\\tnsm_core__initialize_rxn_propensities\\n[WORKER 6] waiting to begin step 1\\n[WORKER 0] waiting to begin step 1\\n[WORKER 3] waiting to begin step 1\\n[WORKER 5] waiting to begin step 1\\n[WORKER 7] waiting to begin step 1\\n\\tnsm_core__initialize_diff_propensities\\n[WORKER 2] waiting to begin step 1\\n\\tnsm_core__initialize_heap\\n[WORKER 1] waiting to begin step 1\\n[WORKER 4] waiting to begin step 1\\nbefore sort\\n========================================================\\ntt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=8.651057e-07, tt=4.089383e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=6.329065e-07, tt=8.093082e-03, tt=9.483580e-03, tt=4.698511e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=2.220386e-06, tt=1.733538e-03, tt=2.419926e-02, tt=2.134093e-01, tt=1.120176e-03, tt=8.792504e-07, tt=inf, tt=inf, tt=inf, tt=inf, tt=3.261944e-06, tt=2.750354e-02, tt=1.076719e-01, tt=3.032052e-02, tt=4.225202e-02, tt=1.488286e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=2.917986e-06, tt=6.648724e-03, tt=1.578200e-04, tt=3.897571e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=5.361157e-07, tt=2.315782e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, ========================================================\\nafter sort\\n========================================================\\ntt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=8.651057e-07, tt=4.089383e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=6.329065e-07, tt=8.093082e-03, tt=9.483580e-03, tt=4.698511e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=2.220386e-06, tt=1.733538e-03, tt=2.419926e-02, tt=2.134093e-01, tt=1.120176e-03, tt=8.792504e-07, tt=inf, tt=inf, tt=inf, tt=inf, tt=3.261944e-06, tt=2.750354e-02, tt=1.076719e-01, tt=3.032052e-02, tt=4.225202e-02, tt=1.488286e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=2.917986e-06, tt=6.648724e-03, tt=1.578200e-04, tt=3.897571e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=5.361157e-07, tt=2.315782e-06, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, tt=inf, ========================================================\\nSimulating RDME for 1.000000e+00 seconds\\nError: overflow in trying to determine which destination voxel subvol=0\\nsubvol->id=0 rand2=0.000000e+00 cum2=0.000000e+00 Current state in voxel 0:\\nxx[0] = 0\\nxx[1] = 0\\nxx[2] = 0\\nxx[3] = 0\\nxx[4] = 0\\nxx[5] = 0\\nxx[6] = 0\\nxx[7] = 0\\nxx[8] = 0\\nNeighbors:\\n1: nn->D_i_j=2.037652e+01 \\n2: nn->D_i_j=5.863151e-01 \\n10: nn->D_i_j=2.037652e+01 \\n11: nn->D_i_j=8.943732e+00 \\n20: nn->D_i_j=5.863151e-01 \\n\"\n",
"solver_cmd = cd /tmp/spatialpy_result_imh96o5z;/tmp/spatialpy_build_xei68ljy/ssa_sdpd\n"
]
},
{
Expand All @@ -13257,7 +13327,7 @@
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mSimulationError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-59-55db495e6ef0>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;31m## sol.run()\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0mm_tmp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCdc42_cycle_2D_SpatialPy_SDPD\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mDX\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m50\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mm_tmp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdebug_level\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m<ipython-input-65-4252afbdf33d>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;31m## sol.run()\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0mm_tmp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCdc42_cycle_2D_SpatialPy_SDPD\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mDX\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mm_tmp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdebug_level\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/Desktop/research/SpatialPy/spatialpy/Model.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, number_of_trajectories, seed, number_of_threads, debug_level)\u001b[0m\n\u001b[1;32m 69\u001b[0m \u001b[0msol\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSolver\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdebug_level\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdebug_level\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 70\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 71\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0msol\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mnumber_of_trajectories\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mnumber_of_trajectories\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mseed\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mseed\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnumber_of_threads\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mnumber_of_threads\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 72\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 73\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/Desktop/research/SpatialPy/spatialpy/Solver.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, number_of_trajectories, seed, timeout, number_of_threads)\u001b[0m\n\u001b[1;32m 201\u001b[0m \u001b[0;32mpass\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 202\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"solver_cmd = {0}\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msolver_cmd\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 203\u001b[0;31m raise SimulationError(\n\u001b[0m\u001b[1;32m 204\u001b[0m \"Solver execution failed, return code = {0}\".format(return_code))\n\u001b[1;32m 205\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mSimulationError\u001b[0m: Solver execution failed, return code = 1"
Expand All @@ -13266,7 +13336,7 @@
],
"source": [
"## sol.run()\n",
"m_tmp = Cdc42_cycle_2D_SpatialPy_SDPD(DX=50)\n",
"m_tmp = Cdc42_cycle_2D_SpatialPy_SDPD(DX=10)\n",
"m_tmp.run(debug_level=1)"
]
},
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