Hello all and happy new year! I am using Ubuntu 18.04, and Yade 2019-08-08.git-775ae74 I want to code a 3D-triaxial test problem which applies a rate of strain for the deviatoric part. I run my code which takes a lot of time, I left it to be run for 3 days, and get this error: Obviously it cannot be converged in the deviatoric section! ********** ERROR ************ axial deformation (%) -2575.3325503377832 ~~~~~~~~~~~~~ Phase_02: Converging to Deviatoric Compression, Strain Rate ~~~~~~~~~~~~~ step= 882430 unbalanced force: 2.6340108400409105e-06 sigma2: -3927217.501133026 q= -3877217.501133026 axial deformation (%) -2575.3325503377832 ~~~~~~~~~~~~~ Phase_02: Converging to Deviatoric Compression, Strain Rate ~~~~~~~~~~~~~ step= 882500 unbalanced force: 2.4289637626032886e-06 sigma2: -3927217.5011330247 q= -3877217.5011330247 axial deformation (%) -2575.3325503377832 ~~~~~~~~~~~~~ Phase_02: Converging to Deviatoric Compression, Strain Rate ~~~~~~~~~~~~~ Traceback (most recent call last): File "/home/ehsan/yade/install/bin/yade-2019-08-08.git-775ae74", line 336, in runScript execfile(script,globals()) File "/usr/lib/python3/dist-packages/past/builtins/misc.py", line 82, in execfile exec_(code, myglobals, mylocals) File "Q.py", line 154, in O.run(1000, True) RuntimeError: boost::thread_resource_error: Resource temporarily unavailable [[ ^L clears screen, ^U kills line. F12 controller, F11 3D view (press "h" in 3D view for help), F10 both, F9 generator, F8 plot. ]] ^[[55;1R--------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) ~/yade/install/bin/yade-2019-08-08.git-775ae74 in 402 import yade.qt 403 qapp=QApplication(sys.argv) --> 404 userSession(gui=gui,qapp=qapp) 405 406 if __name__ == "__main__": ~/yade/install/bin/yade-2019-08-08.git-775ae74 in userSession(gui, qapp) 351 if yade.runtime.opts.exitAfter: sys.exit(0) 352 ## start interpreter --> 353 if not opts.mpi_mode: ipshell() 354 355 ~/.local/lib/python3.6/site-packages/IPython/terminal/embed.py in __call__(self, header, local_ns, module, dummy, stack_depth, global_ns, compile_flags, **kw) 227 # our call and get the original caller's namespaces. 228 self.mainloop(local_ns, module, stack_depth=stack_depth, --> 229 global_ns=global_ns, compile_flags=compile_flags) 230 231 self.banner2 = self.old_banner2 ~/.local/lib/python3.6/site-packages/IPython/terminal/embed.py in mainloop(self, local_ns, module, stack_depth, display_banner, global_ns, compile_flags) 322 323 with self.builtin_trap, self.display_trap: --> 324 self.interact() 325 326 # now, purge out the local namespace of IPython's hidden variables. ~/.local/lib/python3.6/site-packages/IPython/terminal/interactiveshell.py in interact(self, display_banner) 479 480 try: --> 481 code = self.prompt_for_code() 482 except EOFError: 483 if (not self.confirm_exit) \ ~/.local/lib/python3.6/site-packages/IPython/terminal/interactiveshell.py in prompt_for_code(self) 408 default=default, 409 # pre_run=self.pre_prompt,# reset_current_buffer=True, --> 410 **self._extra_prompt_options()) 411 return text 412 ~/.local/lib/python3.6/site-packages/prompt_toolkit/shortcuts/prompt.py in prompt(self, message, editing_mode, refresh_interval, vi_mode, lexer, completer, complete_in_thread, is_password, key_bindings, bottom_toolbar, style, color_depth, include_default_pygments_style, style_transformation, swap_light_and_dark_colors, rprompt, multiline, prompt_continuation, wrap_lines, enable_history_search, search_ignore_case, complete_while_typing, validate_while_typing, complete_style, auto_suggest, validator, clipboard, mouse_support, input_processors, reserve_space_for_menu, enable_system_prompt, enable_suspend, enable_open_in_editor, tempfile_suffix, inputhook, async_, default, accept_default, pre_run) 736 return ensure_future(run_async()) 737 else: --> 738 return run_sync() 739 740 @property ~/.local/lib/python3.6/site-packages/prompt_toolkit/shortcuts/prompt.py in run_sync() 725 with self._auto_refresh_context(): 726 self.default_buffer.reset(Document(default)) --> 727 return self.app.run(inputhook=self.inputhook, pre_run=pre_run2) 728 729 def run_async(): ~/.local/lib/python3.6/site-packages/prompt_toolkit/application/application.py in run(self, pre_run, set_exception_handler, inputhook) 707 loop.set_exception_handler(handle_exception) 708 try: --> 709 return run() 710 finally: 711 loop.set_exception_handler(previous_exc_handler) ~/.local/lib/python3.6/site-packages/prompt_toolkit/application/application.py in run() 680 def run(): 681 f = self.run_async(pre_run=pre_run) --> 682 run_until_complete(f, inputhook=inputhook) 683 return f.result() 684 ~/.local/lib/python3.6/site-packages/prompt_toolkit/eventloop/defaults.py in run_until_complete(future, inputhook) 121 Return the Future's result, or raise its exception. 122 """ --> 123 return get_event_loop().run_until_complete(future, inputhook=inputhook) ~/.local/lib/python3.6/site-packages/prompt_toolkit/eventloop/posix.py in run_until_complete(self, future, inputhook) 64 65 while not future.done(): ---> 66 self._run_once(inputhook) 67 68 # Run one last time, to flush the pending `_calls_from_executor`s. ~/.local/lib/python3.6/site-packages/prompt_toolkit/eventloop/posix.py in _run_once(self, inputhook) 83 " True when there is input ready. The inputhook should return control. " 84 return self._ready_for_reading(None if wait else 0) != [] ---> 85 self._inputhook_context.call_inputhook(ready, inputhook) 86 87 # Wait until input is ready. ~/.local/lib/python3.6/site-packages/prompt_toolkit/eventloop/inputhook.py in call_inputhook(self, input_is_ready_func, inputhook) 76 os.write(self._w, b'x') 77 ---> 78 threading.Thread(target=thread).start() 79 80 # Call inputhook. /usr/lib/python3.6/threading.py in start(self) 844 _limbo[self] = self 845 try: --> 846 _start_new_thread(self._bootstrap, ()) 847 except Exception: 848 with _active_limbo_lock: RuntimeError: can't start new thread Fatal Python error: This thread state must be current when releasing Thread 0x00007f6c09bd3740 (most recent call first): Thread 0x00007f6c09bd3740 (most recent call first): Current thread 0x00007f6ba0d31700 (most recent call first): File "/usr/lib/python3.6/bz2.py", line 245 in write File "/home/ehsan/yade/install/lib/x86_64-linux-gnu/yade-2019-08-08.git-775ae74/py/yade/plot.py", line 663 in saveDataTxt File "Q.py", line 84 in checkUnbalanced File "", line 1 in Thread 0x00007f6bdffff700 (most recent call first): File "/usr/lib/python3.6/selectors.py", line 376 in select File "/usr/lib/python3.6/socketserver.py", line 236 in serve_forever File "/home/ehsan/yade/install/lib/x86_64-linux-gnu/yade-2019-08-08.git-775ae74/py/yade/remote.py", line 142 in run Thread 0x00007f6be4f9e700 (most recent call first): File "/usr/lib/python3.6/selectors.py", line 376 in select File "/usr/lib/python3.6/socketserver.py", line 236 in serve_forever File "/home/ehsan/yade/install/lib/x86_64-linux-gnu/yade-2019-08-08.git-775ae74/py/yade/remote.py", line 142 in run Thread 0x00007f6c09bd3740 (most recent call first): Aborted (core dumped) ehsan@ehsan:~/Desktop$ ****************************************************************************** ****************************************************************************** and my code is as follows: ******************************* MY CODE ************************************* ############################################################################################################################ ######### TRIAXIAL PROBLEM, Y IS THE VERTICAL AXIS, X IS THE RIGHT AXIS, Z IS THE FRONT AXIS ######### ############################################################################################################################ print ('************** START **************') import numpy as np import math from yade import pack, plot, qt, export, utils from datetime import datetime ###################################################### ######### DEFINING VARIABLES ######### print ('============ DEFINING VARIABLES ============') nRead=readParamsFromTable( num_spheres=20000, compFricDegree = 30, key='_triax_base_', unknownOk=True ) from yade.params import table num_spheres=table.num_spheres key=table.key targetPorosity = 0.43 compFricDegree = table.compFricDegree finalFricDegree = 30 rate=-0.02 damp=0.2 stabilityThreshold=0.01 young=15e6 poisson=0.4 mn,mx=Vector3(0,0,0),Vector3(20,20,20) sigmaIso=-50e3 ###################################################### ######### DEFINING MATERIALS ######### print ('============ DEFINING MATERIALS ============') O.materials.append(FrictMat(young=young,poisson=poisson,frictionAngle=radians(compFricDegree),density=2600,label='spheres')) O.materials.append(FrictMat(young=young,poisson=poisson,frictionAngle=0,density=0,label='frictionlesswalls')) #################################################### ######### DEFINING PACKING ######### print ('============ DEFINING PACKING ============') walls=aabbWalls([mn,mx],thickness=0,material='frictionlesswalls') wallIds=O.bodies.append(walls) sp=pack.SpherePack() volume = (mx[0]-mn[0])*(mx[1]-mn[1])*(mx[2]-mn[2]) mean_rad = pow(0.09*volume/num_spheres,0.3333) clumps=False if clumps: volume = (mx[0]-mn[0])*(mx[1]-mn[1])*(mx[2]-mn[2]) mean_rad = pow(0.09*volume/num_spheres,0.3333) c1=pack.SpherePack([((-0.2*mean_rad,0,0),0.5*mean_rad),((0.2*mean_rad,0,0),0.5*mean_rad)]) sp.makeClumpCloud(mn,mx,[c1],periodic=False) sp.toSimulation(material='spheres') O.bodies.updateClumpProperties() else: sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp]) ########################################################## ######### DEFINING TRIAXIAL TEST ######### print ('============ DEFINING TRIAXIAL TEST ============') triax=TriaxialStressController( maxMultiplier=1.+2e4/young, finalMaxMultiplier=1.+2e3/young, thickness = 0, stressMask = 7, internalCompaction=False ) ###################################################### ######### DEFINING FUNCTIONS ######### print ('============ DEFINING FUNCTIONS ============') def checkUnbalanced(): if unbalancedForce()<.05: O.pause() plot.saveDataTxt('bbb.txt.bz2') def history(): plot.addData(e11=-triax.strain[0], e22=-triax.strain[1], e33=-triax.strain[2], ev=-triax.strain[0]-triax.strain[1]-triax.strain[2], s11=-triax.stress(triax.wall_right_id)[0], s22=-triax.stress(triax.wall_top_id)[1], s33=-triax.stress(triax.wall_front_id)[2], i=O.iter,unbalanced=unbalancedForce() ) #################################################### ######### DEFINING ENGINES ######### print ('============ DEFINING ENGINES ============') newton=NewtonIntegrator(damping=damp) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8), triax, TriaxialStateRecorder(iterPeriod=100,file='WallStresses'+table.key), newton, PyRunner(iterPeriod=20,command='history()',label='recorder'), PyRunner(command='checkUnbalanced()',realPeriod=2) ] Gl1_Sphere.stripes=True if nRead==0: yade.qt.Controller(), yade.qt.View() print ('Number of elements: ', len(O.bodies)) print ('Box Volume: ', triax.boxVolume) print ('Box Volume calculated: ', volume) ############################################################### ######### APPLYING CONFINING PRESSURE ######### print ('============ APPLYING CONFINING PRESSURE ============') triax.internalCompaction=False setContactFriction=radians(compFricDegree) triax.stressmask=7 triax.goal1=sigmaIso triax.goal2=sigmaIso triax.goal3=sigmaIso while 1: O.run(1000, True) unb=unbalancedForce() meanS=(triax.stress(triax.wall_right_id)[0]+triax.stress(triax.wall_top_id)[1]+triax.stress(triax.wall_front_id)[2])/3 print ('unbalanced force:',unb,' mean stress engine: ',triax.meanStress,' mean stress (Calculated): ',meanS) print ('porosity=',triax.porosity) print ('void ratio=',triax.porosity/(1-triax.porosity)) print ('~~~~~~~~~~~~~ Phase_01: Converging to Isotropic Compression, 50kPa ~~~~~~~~~~~~~') if unb=0.3 : break O.save('final.xml') print ('################## Deviatoric phase is finished and saved successfully ##################') ######################################################## ######### RECORD AND PLOT DATA ######### print ('============ RECORD AND PLOT DATA ============') O.run(5000,True) plot.plots={'e22':('s11','s22','s33'),'e22':('ev')} plot.labels={'s11':'$\sigma_{11}$' , 's22':'$\sigma_{22}$' , 's33':'$\sigma_{33}$' , 'e11':'$\epsilon_{11}$' , 'e22':'$\epsilon_{22}$' , 'e33':'$\epsilon_{33}$' , 'ev':'$\epsilon_{V}$'} plot.plot() plot.saveDataTxt('results'+key) plot.saveGnuplot('plotScript'+key) print ('************** END **************') ****************************************************************************** So I have following questions: 1 - Why it takes so long to be run? 2- Is there any way to run this code in a shorter time? 3- Why it cannot be converged? 4- What is the meaning of this error and what do I do to debug it? Thank you very much for you kind helps. Bests,

When	Who	Action	New State
2020-01-03	Robert Caulk	Request for more information	Needs information
2020-01-03	ehsan benabbas	Give more information	Open
2020-01-03	Robert Caulk	Answer	Answered
2020-01-03	Robert Caulk	Answer	Answered
2020-01-03	ehsan benabbas	Confirm	Solved

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