[ifit-users] OFF file problem
farhi
farhi at ill.fr
Mon Feb 11 18:53:23 CET 2019
Hello Peter,
Would you be so kind to send me your H3 McStas model, as well as the
15.off file so that I can nail down the error ?
Emmanuel.
Le 2019-02-11 17:29, Петр Коник a écrit :
> Dear all!
>
> We currently try to use a quiet large .off file to finely represent a
> complex geometry guide. While mcstas itself works well (if executed
> from the mcgui), ifit script, which we use to scan parameters,
> irregularly crash. Here is the error - it looks like it is some
> trouble with the array allocated sizes. Any ideas how to fix that?
>
> Sorry for large text - we really don't know which part is important.
>
> Best regards,
> Peter Konik
>
> mpirun -n 8 /tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.out
> --ncount=1000000 --dir=/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/sim
> L=15 guide_m=6 lambda=2
> mpirun -n 8 /tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.out
> --ncount=1000000 --dir=/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/sim
> L=15 guide_m=6 lambda=2: Quit
> Simulation 'H3'
> (/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.instr): running
> on 8 nodes (master is 'konik-N46JV', MPI version 3.1).
> [H3] Initialize
> [H3] Initialize
> [H3] Initialize
> [H3] Initialize
> Loading geometry file (OFF/PLY): data/length/extra_fine/15.off
> Number of vertices: 5694
> [H3] Initialize
> [H3] Initialize
> [H3] Initialize
> [H3] Initialize
> Number of polygons: 11366
> Warning: Neither xwidth, yheight or zdepth are defined.
> The file-defined (non-scaled) geometry the OFF geometry
> data/length/extra_fine/15.off will be applied!
> Bounding box dimensions for geometry data/length/extra_fine/15.off:
> Length=0.150000 (100.000%)
> Width= 15.000000 (100.000%)
> Depth= 0.150000 (100.000%)
> *** stack smashing detected ***: <unknown> terminated
>
> # McStas 2.5 - Dec. 12, 2018: [pid 13264] Signal 6 detected [proc 7]
> SIGABRT (Abort)
> # Simulation: H3
> (/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.instr)
> # Breakpoint: Octo_sm (Trace) 6.47 % ( 8089.0/ 125000.0)
> # Date: Mon Feb 11 19:13:44 2019
> # Started: Mon Feb 11 19:13:43 2019
> # Last I/O Error: Function not implemented
> # McStas 2.5 - Dec. 12, 2018: Simulation stop (abort).
>
> # McStas 2.5 - Dec. 12, 2018: [pid 13258] Signal 15 detected [proc 6]
> SIGTERM (Termination)
> # Simulation: H3
> (/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.instr)
> # Breakpoint: screw (Trace) 20.96 % ( 26205.0/ 125000.0)
> # Date: Mon Feb 11 19:13:45 2019
> # Started: Mon Feb 11 19:13:43 2019
> # McStas 2.5 - Dec. 12, 2018: Finishing simulation (save results and
> exit)
>
> # McStas 2.5 - Dec. 12, 2018: [pid 13255] Signal 15 detected [proc 5]
> SIGTERM (Termination)
> # Simulation: H3
> (/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.instr)
> # Breakpoint: screw (Trace) 19.39 % ( 24240.0/ 125000.0)
> # Date: Mon Feb 11 19:13:45 2019
> # Started: Mon Feb 11 19:13:43 2019
> # McStas 2.5 - Dec. 12, 2018: Finishing simulation (save results and
> exit)
>
> Finally [H3: /tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/sim]. Time: 2
> [s]
>
> # McStas 2.5 - Dec. 12, 2018: [pid 13248] Signal 15 detected [proc 2]
> SIGTERM (Termination)
> # Simulation: H3
> (/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.instr)
> # Breakpoint: screw (Trace) 19.55 % ( 24443.0/ 125000.0)
> # Date: Mon Feb 11 19:13:45 2019
> # Started: Mon Feb 11 19:13:43 2019
> # McStas 2.5 - Dec. 12, 2018: Finishing simulation (save results and
> exit)
>
> Finally [H3: /tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/sim]. Time: 2
> [s]
>
> # McStas 2.5 - Dec. 12, 2018: [pid 13247] Signal 15 detected [proc 1]
> SIGTERM (Termination)
> # Simulation: H3
> (/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.instr)
> # Breakpoint: screw (Trace) 20.48 % ( 25600.0/ 125000.0)
> # Date: Mon Feb 11 19:13:45 2019
> # Started: Mon Feb 11 19:13:43 2019
> # McStas 2.5 - Dec. 12, 2018: Finishing simulation (save results and
> exit)
>
> Finally [H3: /tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/sim]. Time: 2
> [s]
>
> # McStas 2.5 - Dec. 12, 2018: [pid 13250] Signal 15 detected [proc 4]
> SIGTERM (Termination)
> # Simulation: H3
> (/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.instr)
> # Breakpoint: screw (Trace) 20.61 % ( 25768.0/ 125000.0)
> # Date: Mon Feb 11 19:13:45 2019
> # Started: Mon Feb 11 19:13:43 2019
> # McStas 2.5 - Dec. 12, 2018: Finishing simulation (save results and
> exit)
>
> # McStas 2.5 - Dec. 12, 2018: [pid 13249] Signal 15 detected [proc 3]
> SIGTERM (Termination)
> # Simulation: H3
> (/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.instr)
> # Breakpoint: screw (Trace) 26.14 % ( 32672.0/ 125000.0)
> # Date: Mon Feb 11 19:13:45 2019
> # Started: Mon Feb 11 19:13:43 2019
> # McStas 2.5 - Dec. 12, 2018: Finishing simulation (save results and
> exit)
>
> Finally [H3: /tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/sim]. Time: 2
> [s]
>
> # McStas 2.5 - Dec. 12, 2018: [pid 13246] Signal 15 detected [proc 0]
> SIGTERM (Termination)
> # Simulation: H3
> (/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.instr)
> # Breakpoint: screw (Trace) 20.70 % ( 25879.0/ 125000.0)
> # Date: Mon Feb 11 19:13:45 2019
> # Started: Mon Feb 11 19:13:43 2019
> # McStas 2.5 - Dec. 12, 2018: Finishing simulation (save results and
> exit)
>
> Save [H3]
> [warn] Epoll ADD(4) on fd 49 failed. Old events were 0; read change
> was 0 (none); write change was 1 (add): Bad file descriptor
> [warn] Epoll ADD(4) on fd 43 failed. Old events were 0; read change
> was 0 (none); write change was 1 (add): Bad file descriptor
> --------------------------------------------------------------------------
> mpirun noticed that process rank 7 with PID 0 on node konik-N46JV
> exited on signal 3 (Quit).
> --------------------------------------------------------------------------
>
> Error: Could not evaluate Expression in model screw_n.instr McCode
> [mccode] iF495774
> self = iFunc_McCode (methods,doc,plot,code) 1D model: "screw_n.instr
> McCode [mccode]"
> Expression: UD = this.UserData; options=UD.options;if
> ~isempty(options.dir) && ...
> Description: McCode virtual experiment screw_n.instr
> Set UserData.options.monitor to specify a given monitor file pattern,
> or [] to get the last.
> Monitors are stored in UserData.monitors
> Available monitors:
> * Octo_large
> * Octo_med
> * Octo_sm
> iData iD500632=load(iData,... [100 1] Intensity [n/s/bin](x)
> "mccode.sim McCode sim file I=1.02353e+09 I_err=1.02353e+09 N=1
> X0=0.0131313 dX=0;"
> </tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/sim/Octo_sm_1549901622.vd>
> Axis 1 "x" label is "Vert. Divergence [deg]", range [-0.1:0.1]
> Tag: 'iF495774'
> Date: '11-Feb-2019 19:12:49'
> Name: 'screw_n.instr McCode [mccode]'
> Parameters: {3×1 cell}
> Guess: [10 6 5]
> Constraint: [1×1 struct]
> Dimension: 1
> ParameterValues: [3×1 double]
> UserData: [1×1 struct]
> Duration: 0.7051
> class: 'iFunc_McCode'
>
> Parameters (3):
> p( 1)= L=15
> p( 2)= guide_m=6
> p( 3)= lambda=2
> Other Parameters:
> ''
> 'UD = this.UserData; options=UD.options;'
> 'if ~isempty(options.dir) && isempty(dir(options.dir));'
> 'try; mkdir(options.dir); end;'
> 'end;'
> 'if isempty(options.dir) || isempty(dir(options.dir));'
> 'options.dir=tempname;'
> 'mkdir(options.dir);'
> 'options.use_tmpdir = true;'
> 'else options.use_tmpdir = false;'
>
> ...
> 'ax='x,y,z,t';'
> 'nd=exist('t')+exist('z')+exist('y')+exist('x');'
> 'if min(nd,this.Dimension)>0, ax=eval([ '{'
> ax(1:(2*min(nd,this.Dimension))) '}']); else ax={}; end;'
> 'if ~isempty(ax) && exist('x') && ~isempty(x) &&
> ~all(isnan(x(:))), signal = interp(signal, ax{:});'
> 'else x=getaxis(signal,1); y=getaxis(signal,2);
> z=getaxis(signal,3); t=getaxis(signal,4); end;'
> 'end;'
>
> Name Size Bytes Class
> Attributes
>
> ME 1x1 3878 MException
> UD 1x1 1029966 struct
> cmd 1x163 326 char
> duration 1x1 8 double
> f 0x1 0 cell
> iFunc_ax 1x14 28 char
> iFunc_dim 1x1 8 double
> iFunc_t0 1x6 48 double
> iFunc_this 1x1 1070328 iFunc_McCode
> index 0x0 0 double
> options 1x1 2461 struct
> p 1x3 24 double
> result 1x4667 9334 char
> signal 0x0 0 double
> status 1x1 8 double
> struct_p 1x1 552 struct
> this 1x1 1070328 iFunc_McCode
> varargin 1x0 0 cell
> x 51x1 408 double
>
> Error using iFunc/feval>iFunc_feval_expr (line 414)
> Model screw_n.instr McCode [mccode] iF495774 failed to execute mpirun
> -n 8 /tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/screw_n.out
> --ncount=1000000 --dir=/tmp/tp538a3bb9_21a0_4166_b4ea_597a15889e55/sim
> L=15 guide_m=6 lambda=2
> iFunc:feval: Saved state in
> /media/konik/a09e43d5-7f1d-47d7-b0ae-2df53071d43b/JOB/Octagon-guide/Octagon-guide/simulation/iFunc_feval_error
> Error using iFunc/feval>iFunc_feval_expr (line 432)
> Failed model evaluation. Saved state in
> /media/konik/a09e43d5-7f1d-47d7-b0ae-2df53071d43b/JOB/Octagon-guide/Octagon-guide/simulation/iFunc_feval_error
>
> Error in iFunc/feval (line 344)
> [signal,ax,p,model,duration] = iFunc_feval_expr(model, varargin{:});
>
> Error in iFunc_McCode/feval (line 139)
> [signal, self, ax, name] = feval at iFunc(self, varargin{:});
>
> Error in iData>iData_iFunc2iData (line 268)
> [signals, this_in, axs, names] = feval(this_in, varargin{:});
>
> Error in iData (line 189)
> [this_out, this_in] = iData_iFunc2iData(this_in, axes_in,
> varargin{2:end});
>
> Error in screw_length_scan (line 42)
> results = iData(model,parameters);
> _______________________________________________
> ifit-users mailing list
> ifit-users at mccode.org
> https://mailman2.mccode.org/mailman/listinfo/ifit-users
--
FARHI Emmanuel <farhi at ill.fr>
Groupe DS/CS, ILL4/156, Tel (33) 4 76 20 71 35
ILL, Grenoble
More information about the ifit-users
mailing list