From 104pet104 at gmail.com  Mon Feb 11 17:29:43 2019
From: 104pet104 at gmail.com (=?UTF-8?B?0J/QtdGC0YAg0JrQvtC90LjQug==?=)
Date: Mon, 11 Feb 2019 19:29:43 +0300
Subject: [ifit-users] OFF file problem
Message-ID: <CAFZRTKSWb+zFQFTK1cFmLq2XdS_xGWAVNoN3jcO-CeaLjdo0vQ@mail.gmail.com>

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);

From farhi at ill.fr  Mon Feb 11 18:53:23 2019
From: farhi at ill.fr (farhi)
Date: Mon, 11 Feb 2019 18:53:23 +0100
Subject: [ifit-users] OFF file problem
In-Reply-To: <CAFZRTKSWb+zFQFTK1cFmLq2XdS_xGWAVNoN3jcO-CeaLjdo0vQ@mail.gmail.com>
References: <CAFZRTKSWb+zFQFTK1cFmLq2XdS_xGWAVNoN3jcO-CeaLjdo0vQ@mail.gmail.com>
Message-ID: <da26b2ba7f463f4c8b50a43f761e40d1@ill.fr>

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, ???? ????? a ?crit?:
> 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

From farhi at ill.fr  Tue Feb 12 12:10:18 2019
From: farhi at ill.fr (Emmanuel FARHI)
Date: Tue, 12 Feb 2019 12:10:18 +0100
Subject: [ifit-users] McStas/MPI OFF file problem. iFit execution/scans.
In-Reply-To: <da26b2ba7f463f4c8b50a43f761e40d1@ill.fr>
References: <CAFZRTKSWb+zFQFTK1cFmLq2XdS_xGWAVNoN3jcO-CeaLjdo0vQ@mail.gmail.com>
 <da26b2ba7f463f4c8b50a43f761e40d1@ill.fr>
Message-ID: <3c14730c-430b-e63e-0c10-45e05e6c2d2c@ill.fr>

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From 104pet104 at gmail.com  Tue Feb 12 12:12:57 2019
From: 104pet104 at gmail.com (=?UTF-8?B?0J/QtdGC0YAg0JrQvtC90LjQug==?=)
Date: Tue, 12 Feb 2019 14:12:57 +0300
Subject: [ifit-users] McStas/MPI OFF file problem. iFit execution/scans.
In-Reply-To: <3c14730c-430b-e63e-0c10-45e05e6c2d2c@ill.fr>
References: <CAFZRTKSWb+zFQFTK1cFmLq2XdS_xGWAVNoN3jcO-CeaLjdo0vQ@mail.gmail.com>
 <da26b2ba7f463f4c8b50a43f761e40d1@ill.fr>
 <3c14730c-430b-e63e-0c10-45e05e6c2d2c@ill.fr>
Message-ID: <CAFZRTKQdQWa6zNbj24nO7OzsaEDjQVw+-jhP1uYtZswu=vMGZQ@mail.gmail.com>

Thank you very much for such a rapid help! I will test it in a couple
of days and provide feedback.
For the last question - yes of course you may freely use it (one note
- PIK is usually written with I)

Best regards,
Peter Konik

??, 12 ????. 2019 ?. ? 14:05, Emmanuel FARHI <farhi at ill.fr>:
>
> Hi Peter,
>
> I had a look at the 'stack smashing detected' error you reported (below) when using:
>
> instrument screw_n
> Guide_anyshape component with large OFF (nice twisted guide made of triangles)
> mpi with 24 cores
>
> I can reproduce the bug. I find that wether it is controlled from iFit or from the command line with mcrun does not make any difference. The bug occurs in both usages, even with very few neutron counts (1e4), in the middle of the TRACE (not at final data merge).
>
> The reported error is:
>
> *** stack smashing detected ***: <unknown> terminated
>
> and it mostly takes place at the 'screw' component which is the Guide_anyshape(OFF). It triggers a SIGTERM or SIGABRT which usually saves results but stops further neutron events (partial computation). But it also involves the Octo_sm monitor (Monitor_nD).
>
> McStas 2.5 test (Ubuntu 18.04)
>
> When executed from iFit, the error also shows as:
>
> # Fatal : unrecoverable loop ! Suicide (naughty boy).
> [warn] Epoll ADD(4) on fd 37 failed.  Old events were 0; read change was 0 (none); write change was 1 (add): Bad file descriptor
> [farhimacpro:05429] pmix_usock_msg_send_bytes: write failed: Broken pipe (32) [sd = 112]
>
> This is clearly related to openMPI, and more specifically to libevent.
>
> I have executed the same with a serial computation, and it all goes OK, even when compiled with MPI, and executed with --mpi=1.
>
> I have no idea why this happens, as Guide_anyshape has no I/O routine except at the start (read the OFF), but the issue comes in the middle of the TRACE, in connection with Octo_sm...
>
> Conclusion
>
> I have no idea what the error is, as of today.
>
> Fallback solutions
>
> In all cases, make sure the 'L' value is larger than the Guide_anyshape length (OFF 'width').
>
> Solution 1: Removing the Octo_sm component seems to solve the issue. So this is a possibility.
>
> Solution 2: (recommended) You can as well replace it with e.g.:
>
> COMPONENT Octo_sm = Divergence_monitor(xwidth = h, yheight = w,
>   nh=100, nv=100, maxdiv_h=10, maxdiv_v=0.1, filename="Octo_sm.dat")
> AT (0, 0, L+0.04) RELATIVE arm_geks
>
> Solution 3: An other solution is serial execution which works, as far as I have seen. You can force iFit/mccode to work in serial with:
>
> m=mccode('screw_n.instr','mpi=1');    % at creation
>
> or
>
> m=mccode('screw_n.instr');
> m.UserData.options.mpi=1;    % after creation
>
> Then you can run parameter scans and optimisations. It is just longer.
>
> Final question
>
> Would you accept if I add one of your OFF twisted guides into McStas/Data, as well as the PYK reactor source parameters in Source_gen doc ?
>
> Emmanuel.
>
> On 2/11/19 6:53 PM, farhi wrote:
>
> 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, ???? ????? a ?crit :
>
> 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
>
>
> --
> Emmanuel FARHI,                                           \|/ ____ \|/
> Spectroscopy Group Institut Laue-Langevin (ILL) Grenoble  ~@-/ oO \-@~
> 71 av des Martyrs,CS 20156,38042 Grenoble Cedex 9,France  /_( \__/ )_\
> Work :Tel (33/0) 4 76 20 71 35. Fax (33/0) 4 76 48 39 06     \__U_/

From farhi at ill.fr  Sat Mar 23 17:34:15 2019
From: farhi at ill.fr (farhi)
Date: Sat, 23 Mar 2019 17:34:15 +0100
Subject: [ifit-users] ifit - a fits.m function correction
In-Reply-To: <c1634769-027f-e347-77cb-8dc8e274e04e@physics.muni.cz>
References: <c1634769-027f-e347-77cb-8dc8e274e04e@physics.muni.cz>
Message-ID: <89462e2b23522b1fcf1b5892301e563d@ill.fr>

Hello Jiri,

many thanks for reporting and finding fix to iFunc/fits with additional 
parameters. This has been pushed to the repo.

The current repo is not stabilized these days, as I'm changing the way 
importers are made available to iLoad. Also, I'm working hard to 
dramatically improve the data set handling speed. The current iData 
objects are slow to load, check and manipulate.

Cheers, Emmanuel.

Le 2019-03-22 13:43, Jiri Novak a ?crit?:
> _________________________________________________________________
> 
>  WARNING: Viruses are often found in attached files of type
>  document (.xls .doc etc.) and compressed (.zip .rar etc.).
>  Please be EXTREMELY careful when opening this kind of file.
>  In case of doubt, please contact the sender for confirmation.
> 
> Dear Emmanuel,
> I'm writing regarding a possible deficiency in the fits.m script of
> the iFit package and a possible correction for the (supposed)
> malfunction.
> 
> Symptoms:
> The reported behaviour concerns iFit versions 1.9 and 2.0.1. Having
> Matlab 2017a.
> It seems that one cannot fit data with a model taking additional
> arguments beyond parameters  (e.g. say additional parameters, which
> are never fitted). To check that, please find attached a simple pair
> of scripts (a model Gauss2ConstArg.m and the initialization script of
> the fit init_Gauss2ConstArg.m).
> 
> The possibility of the usage of additional parameters of the model
> function and the fits function is documented at
> http://ifit.mccode.org/Fit.html#mozTocId345729
> 
> A solution:
> A small change in the "Objects/@iFunc/fits.m" script corrects for the 
> problem:
> Line 486 of Objects/@iFunc/fits.m (iFit version 1.9
> Replace
>  % [output.modelValue, model] = feval(model, pars2, a.Axes{:});    %
> this also changed pars_out into iFunc
> 
> with
> [output.modelValue, model] = feval(model, pars2,
> a.Axes{:},varargin{:}); % this also changed pars_out into iFunc
> 
> the command is few lines (10 or so) further in iFit 2.0.1 (I do not
> have the version installed, just have corrected the problem at master
> student computer a hour ago)
> 
> Now calling of iFit and of models with additional parameters seems to 
> work fine.
> 
> Otherwise, let me thank you for the iFit package - I like it very
> much. Great work !
> 
> Best wishes,
> Jiri

-- 
FARHI Emmanuel <farhi at ill.fr>
Groupe DS/CS, ILL4/156, Tel (33) 4 76 20 71 35
ILL, Grenoble