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[OctDev] Panic in sparse matrix code

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Orion Poplawski
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[OctDev] Panic in sparse matrix code

Orion Poplawski
Running octave 2.1.71 with octave-forge-2005-06.13 on Fedora Core 4.
With the attached files:

octave test.m

runs ok.

octave test2.m

aborts with the following.  test is basically test2 with the function
call folded into the main code.  The code is matlab code I'm trying to
run in octave that I haven't explored very much.

GNU Octave, version 2.1.71 (i686-pc-linux-gnu).
Copyright (C) 2005 John W. Eaton.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTIBILITY or
FITNESS FOR A PARTICULAR PURPOSE.  For details, type `warranty'.

Additional information about Octave is available at http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/help-wanted.html

Report bugs to <[hidden email]> (but first, please read
http://www.octave.org/bugs.html to learn how to write a helpful report).

*** glibc detected *** octave: double free or corruption (!prev):
0x09ce7748 ***
======= Backtrace: =========
/lib/libc.so.6[0x289124]
/lib/libc.so.6(__libc_free+0x77)[0x28965f]
/usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/sparse.oct(oct_sparse_free+0x21)[0xd894fb]
/usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/sparse.oct(Destroy_CompCol_Matrix+0x32)[0xdbd9ff]
/usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/sparse.oct(_Z30oct_sparse_Destroy_SuperMatrix11SuperMatrix+0x52)[0xd89616]
/usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/sparse.oct(_ZN13octave_sparseD0Ev+0x40)[0xd7df18]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZN12octave_valueD1Ev+0x44)[0x417712a]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZSt8_DestroyIN9__gnu_cxx17__normal_iteratorIP12octave_valueSt6vectorIS2_SaIS2_EEEES5_EvT_S8_T0_+0x1a)[0x3f8439e]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZNSt6vectorI12octave_valueSaIS0_EEaSERKS2_+0x1cf)[0x3f8581f]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZN19tree_statement_list4evalEbi+0x14c)[0x4299d54]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZN20octave_user_function17do_multi_index_opEiRK17octave_value_list+0x553)[0x41a6d39]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZN20octave_user_function7subsrefERKSsRKSt4listI17octave_value_listSaIS3_EEi+0x23c)[0x41a7fb4]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZN12octave_value7subsrefERKSsRKSt4listI17octave_value_listSaIS3_EEi+0x9c)[0x4178d9a]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZN21tree_index_expression6rvalueEi+0x415)[0x4272a33]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZN21tree_index_expression6rvalueEv+0x3f)[0x4271549]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZN22tree_simple_assignment6rvalueEv+0x4f)[0x4256755]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZN22tree_simple_assignment6rvalueEi+0x603)[0x4259269]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZN14tree_statement4evalEbib+0x116)[0x42992ba]
/usr/lib/octave-2.1.71/liboctinterp.so(_ZN19tree_statement_list4evalEbi+0x12e)[0x4299d36]
/usr/lib/octave-2.1.71/liboctinterp.so(_Z9main_loopRKSs+0xec)[0x40e1c5e]
/usr/lib/octave-2.1.71/liboctinterp.so(octave_main+0x11e7)[0x443de9d]
octave(main+0x19)[0x804864d]
/lib/libc.so.6(__libc_start_main+0xdf)[0x23ad5f]
octave[0x80485b1]
======= Memory map: ========
00111000-001a1000 r-xp 00000000 03:02 109433     /usr/lib/libfftw3.so.3.0.1
001a1000-001a5000 rwxp 00090000 03:02 109433     /usr/lib/libfftw3.so.3.0.1
001a5000-001ae000 r-xp 00000000 03:02 864932     /lib/libnss_files-2.3.5.so
001ae000-001af000 r-xp 00008000 03:02 864932     /lib/libnss_files-2.3.5.so
001af000-001b0000 rwxp 00009000 03:02 864932     /lib/libnss_files-2.3.5.so
00208000-00222000 r-xp 00000000 03:02 867425     /lib/ld-2.3.5.so
00222000-00223000 r-xp 00019000 03:02 867425     /lib/ld-2.3.5.so
00223000-00224000 rwxp 0001a000 03:02 867425     /lib/ld-2.3.5.so
00226000-00349000 r-xp 00000000 03:02 867426     /lib/libc-2.3.5.so
00349000-0034b000 r-xp 00123000 03:02 867426     /lib/libc-2.3.5.so
0034b000-0034d000 rwxp 00125000 03:02 867426     /lib/libc-2.3.5.so
0034d000-0034f000 rwxp 0034d000 00:00 0
00351000-00374000 r-xp 00000000 03:02 867427     /lib/libm-2.3.5.so
00374000-00375000 r-xp 00022000 03:02 867427     /lib/libm-2.3.5.so
00375000-00376000 rwxp 00023000 03:02 867427     /lib/libm-2.3.5.so
00378000-0037a000 r-xp 00000000 03:02 867428     /lib/libdl-2.3.5.so
0037a000-0037b000 r-xp 00001000 03:02 867428     /lib/libdl-2.3.5.so
0037b000-0037c000 rwxp 00002000 03:02 867428     /lib/libdl-2.3.5.so
0037e000-00390000 r-xp 00000000 03:02 111368     /usr/lib/libz.so.1.2.2.2
00390000-00391000 rwxp 00011000 03:02 111368     /usr/lib/libz.so.1.2.2.2
00398000-00399000 r-xp 00398000 00:00 0
00469000-00477000 r-xp 00000000 03:02 867435     /lib/libpthread-2.3.5.so
00477000-00478000 r-xp 0000d000 03:02 867435     /lib/libpthread-2.3.5.so
00478000-00479000 rwxp 0000e000 03:02 867435     /lib/libpthread-2.3.5.so
00479000-0047b000 rwxp 00479000 00:00 0
0048e000-004b5000 r-xp 00000000 03:02 110766     /usr/lib/libreadline.so.5.0
004b5000-004b9000 rwxp 00027000 03:02 110766     /usr/lib/libreadline.so.5.0
004b9000-004ba000 rwxp 004b9000 00:00 0
004bc000-004fe000 r-xp 00000000 03:02 128642
/usr/lib/octave-2.1.71/libcruft.so.2.1.71
004fe000-00502000 rwxp 00041000 03:02 128642
/usr/lib/octave-2.1.71/libcruft.so.2.1.71
00502000-00503000 rwxp 00502000 00:00 0
00505000-0055c000 r-xp 00000000 03:02 103091
/usr/lib/libgfortran.so.0.0.0
0055c000-0055e000 rwxp 00056000 03:02 103091
/usr/lib/libgfortran.so.0.0.0
0055e000-00562000 rwxp 0055e000 00:00 0
0057b000-0058a000 r-xp 00000000 03:02 867429     /lib/libresolv-2.3.5.so
0058a000-0058b000 r-xp 0000e000 03:02 867429     /lib/libresolv-2.3.5.so
0058b000-0058c000 rwxp 0000f000 03:02 867429     /lib/libresolv-2.3.5.so
0058c000-0058e000 rwxp 0058c000 00:00 0
00590000-00599000 r-xp 00000000 03:02 867440
/lib/libgcc_s-4.0.1-20050727.so.1
00599000-0059a000 rwxp 00009000 03:02 867440
/lib/libgcc_s-4.0.1-20050727.so.1
0059c000-0067c000 r-xp 00000000 03:02 111392     /usr/lib/libstdc++.so.6.0.5
0067c000-00681000 rwxp 000df000 03:02 111392     /usr/lib/libstdc++.so.6.0.5
00681000-00687000 rwxp 00681000 00:00 0
00689000-006df000 r-xp 00000000 03:02 99344      /usr/lib/libblas.so.3.0.3
006df000-006e0000 rwxp 00055000 03:02 99344      /usr/lib/libblas.so.3.0.3
0070a000-0070c000 r-xp 00000000 03:02 864925     /lib/libcom_err.so.2.1
0070c000-0070d000 rwxp 00001000 03:02 864925     /lib/libcom_err.so.2.1
00787000-0079d000 r-xp 00000000 03:02 201709
/usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/dispatch.oct
0079d000-0079e000 rwxp 00016000 03:02 201709
/usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/dispatch.oct
0097c000-009eb000 r-xp 00000000 03:02 105049     /usr/lib/libkrb5.so.3.2
009eb000-009ee000 rwxp 0006e000 03:02 105049     /usr/lib/libkrb5.so.3.2
009f0000-00a25000 r-xp 00000000 03:02 864979     /lib/libssl.so.0.9.7f
00a25000-00a28000 rwxp 00035000 03:02 864979     /lib/libssl.so.0.9.7f
00a2a000-00a41000 r-xp 00000000 03:02 105050
/usr/lib/libgssapi_krb5.so.2.2
00a41000-00a42000 rwxp 00017000 03:02 105050
/usr/lib/libgssapi_krb5.so.2.2
00cee000-00d11000 r-xp 00000000 03:02 111383     /usr/lib/libk5crypto.so.3.0
00d11000-00d12000 rwxp 00023000 03:02 111383     /usr/lib/libk5crypto.so.3.0
00d14000-00d16000 r-xp 00000000 03:02 106698
/usr/lib/libkrb5support.so.0.0
00d16000-00d17000 rwxp 00001000 03:02 106698
/usr/lib/libkrb5support.so.0.0
00d64000-00ddb000 r-xp 00000000 03:02 201832
/usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/make_sparse.oct
00ddb000-00ddd000 rwxp 00077000 03:02 201832
/usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/make_sparse.oct
02bdb000-02f92000 r-xp 00000000 03:02 99339      /usr/lib/liblapack.so.3.0.3
02f92000-02f95000 rwxp 003b7000 03:02 99339      /usr/lib/liblapack.so.3.0.3
02f95000-03099000 rwxp 02f95000 00:00 0
0309b000-03675000 r-xp 00000000 03:02 128643
/usr/lib/octave-2.1.71/liboctave.so.2.1.71
03675000-03681000 rwxp 005da000 03:02 128643
/usr/lib/octave-2.1.71/liboctave.so.2.1.71
03681000-03682000 rwxp 03681000 00:00 0
03dc0000-03dfe000 r-xp 00000000 03:02 109746     /usr/lib/libncurses.so.5.4
03dfe000-03e07000 rwxp 0003d000 03:02 109746     /usr/lib/libncurses.so.5.4
03e09000-0457d000 r-xp 00000000 03:02 128644
/usr/lib/octave-2.1.71/liboctinterp.so.2.1.71
0457d000-04599000 rwxp 00773000 03:02 128644
/usr/lib/octave-2.1.71/liboctinterp.so.2.1.71
04599000-0459b000 rwxp 04599000 00:00 0
0460f000-04707000 r-xp 00000000 03:02 867431     /lib/libcrypto.so.0.9.7f
04707000-04719000 rwxp 000f8000 03:02 867431     /lib/libcrypto.so.0.9.7f
04719000-0471c000 rwxp 04719000 00:00 0
064f8000-0662c000 r-xp 00000000 03:02 107290     /usr/lib/libhdf5.so.0.0.0
0662c000-0662f000 rwxp 00134000 03:02 107290     /usr/lib/libhdf5.so.0.0.0
08048000-08049000 r-xp 00000000 03:02 99342      /usr/bin/octave-2.1.71
08049000-0804d000 rw-p 00000000 03:02 99342      /usr/bin/octave-2.1.71
09152000-09d2a000 rw-p 09152000 00:00 0          [heap]
b6c00000-b6c21000 rw-p b6c00000 00:00 0
b6c21000-b6d00000 ---p b6c21000 00:00 0
b6de6000-b7c4c000 rw-p b6de6000 00:00 0
b7c4c000-b7c4d000 r--p 00edd000 03:02 107632
/usr/lib/locale/locale-archive
b7c4d000-b7c7e000 r--p 00e5c000 03:02 107632
/usr/lib/locale/locale-archive
b7c7e000-b7e7e000 r--p 00000000 03:02 107632
/usr/lib/locale/locale-archive
b7e7e000-b7fe1000 rw-p b7e7e000 00:00 0
b7ffb000-b7ffc000 rw-p b7ffb000 00:00 0
bfee7000-bfefc000 rw-p bfee7000 00:00 0          [stack]
panic: Aborted -- stopping myself...
attempting to save variables to `octave-core'...
save to `octave-core' complete
Abort

--
Orion Poplawski
System Administrator                   303-415-9701 x222
Colorado Research Associates/NWRA      FAX: 303-415-9702
3380 Mitchell Lane, Boulder CO 80301   http://www.co-ra.com

function [grid,xg,yg]=make_grid(minx,maxx,miny,maxy,dx,dy)

xg=minx:dx:maxx;
yg=maxy:-dy:miny;

k=0;
for x=xg
   for y=yg
      k=k+1;
      grid(k,1)=x;
      grid(k,2)=y;
   end
end
 

%%% function MedBhm_preproc.m

%**************************************************
%**** Make grids for atm
%**************************************************

[grdxyA,xgA,ygA]=make_grid(14.000,37.000,30.000,46.0000,.25,.25);
nxA=length(xgA)-2;
nyA=length(ygA)-2;

MtilB=make_MtilB_sparse(nxA,nyA);

%%% function MedBhm_preproc.m

%**************************************************
%**** Make grids for atm
%**************************************************

[grdxyA,xgA,ygA]=make_grid(14.000,37.000,30.000,46.0000,.25,.25);
nx=length(xgA)-2;
ny=length(ygA)-2;

Nx=nx+2;
Ny=ny+2;
N=Nx*Ny;
n=nx*ny;
NB=2*Nx+2*Ny-4;

MtilB=sparse(NB,N);

for k=1:Ny
   MtilB(k,k)=1;
   MtilB(Ny+Nx-2+k,N+1-k)=1;
end

for i=1:nx
   MtilB(Ny+i,Ny*(i+1))=1;
   MtilB(NB+1-i,(Ny*i)+1)=1;
end


function MtilB=make_MtilB_sparse(nx,ny)

Nx=nx+2;
Ny=ny+2;
N=Nx*Ny;
n=nx*ny;
NB=2*Nx+2*Ny-4;

MtilB=sparse(NB,N);

for k=1:Ny
   MtilB(k,k)=1;
   MtilB(Ny+Nx-2+k,N+1-k)=1;
end

for i=1:nx
   MtilB(Ny+i,Ny*(i+1))=1;
   MtilB(NB+1-i,(Ny*i)+1)=1;
end

Paul Kienzle-3
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Re: [OctDev] Panic in sparse matrix code

Paul Kienzle-3
Is 2.9.x octave available for Fedora?  It has replacement code for the  
octave-forge sparse functions and the octave-forge functions are no  
longer supported [though you are welcome to provide patches if you  
want].

- Paul

On Sep 21, 2005, at 5:19 PM, Orion Poplawski wrote:

> Running octave 2.1.71 with octave-forge-2005-06.13 on Fedora Core 4.  
> With the attached files:
>
> octave test.m
>
> runs ok.
>
> octave test2.m
>
> aborts with the following.  test is basically test2 with the function  
> call folded into the main code.  The code is matlab code I'm trying to  
> run in octave that I haven't explored very much.
>
> GNU Octave, version 2.1.71 (i686-pc-linux-gnu).
> Copyright (C) 2005 John W. Eaton.
> This is free software; see the source code for copying conditions.
> There is ABSOLUTELY NO WARRANTY; not even for MERCHANTIBILITY or
> FITNESS FOR A PARTICULAR PURPOSE.  For details, type `warranty'.
>
> Additional information about Octave is available at  
> http://www.octave.org.
>
> Please contribute if you find this software useful.
> For more information, visit http://www.octave.org/help-wanted.html
>
> Report bugs to <[hidden email]> (but first, please read
> http://www.octave.org/bugs.html to learn how to write a helpful  
> report).
>
> *** glibc detected *** octave: double free or corruption (!prev):  
> 0x09ce7748 ***
> ======= Backtrace: =========
> /lib/libc.so.6[0x289124]
> /lib/libc.so.6(__libc_free+0x77)[0x28965f]
> /usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/
> sparse.oct(oct_sparse_free+0x21)[0xd894fb]
> /usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/
> sparse.oct(Destroy_CompCol_Matrix+0x32)[0xdbd9ff]
> /usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/
> sparse.oct(_Z30oct_sparse_Destroy_SuperMatrix11SuperMatrix+0x52)[0xd896
> 16]
> /usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/
> sparse.oct(_ZN13octave_sparseD0Ev+0x40)[0xd7df18]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZN12octave_valueD1Ev+0x44)[0x417712a]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZSt8_DestroyIN9__gnu_cxx17__normal_iteratorIP12octave_
> valueSt6vectorIS2_SaIS2_EEEES5_EvT_S8_T0_+0x1a)[0x3f8439e]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZNSt6vectorI12octave_valueSaIS0_EEaSERKS2_+0x1cf)[0x3f
> 8581f]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZN19tree_statement_list4evalEbi+0x14c)[0x4299d54]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZN20octave_user_function17do_multi_index_opEiRK17octav
> e_value_list+0x553)[0x41a6d39]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZN20octave_user_function7subsrefERKSsRKSt4listI17octav
> e_value_listSaIS3_EEi+0x23c)[0x41a7fb4]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZN12octave_value7subsrefERKSsRKSt4listI17octave_value_
> listSaIS3_EEi+0x9c)[0x4178d9a]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZN21tree_index_expression6rvalueEi+0x415)[0x4272a33]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZN21tree_index_expression6rvalueEv+0x3f)[0x4271549]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZN22tree_simple_assignment6rvalueEv+0x4f)[0x4256755]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZN22tree_simple_assignment6rvalueEi+0x603)[0x4259269]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZN14tree_statement4evalEbib+0x116)[0x42992ba]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_ZN19tree_statement_list4evalEbi+0x12e)[0x4299d36]
> /usr/lib/octave-2.1.71/
> liboctinterp.so(_Z9main_loopRKSs+0xec)[0x40e1c5e]
> /usr/lib/octave-2.1.71/liboctinterp.so(octave_main+0x11e7)[0x443de9d]
> octave(main+0x19)[0x804864d]
> /lib/libc.so.6(__libc_start_main+0xdf)[0x23ad5f]
> octave[0x80485b1]
> ======= Memory map: ========
> 00111000-001a1000 r-xp 00000000 03:02 109433      
> /usr/lib/libfftw3.so.3.0.1
> 001a1000-001a5000 rwxp 00090000 03:02 109433      
> /usr/lib/libfftw3.so.3.0.1
> 001a5000-001ae000 r-xp 00000000 03:02 864932      
> /lib/libnss_files-2.3.5.so
> 001ae000-001af000 r-xp 00008000 03:02 864932      
> /lib/libnss_files-2.3.5.so
> 001af000-001b0000 rwxp 00009000 03:02 864932      
> /lib/libnss_files-2.3.5.so
> 00208000-00222000 r-xp 00000000 03:02 867425     /lib/ld-2.3.5.so
> 00222000-00223000 r-xp 00019000 03:02 867425     /lib/ld-2.3.5.so
> 00223000-00224000 rwxp 0001a000 03:02 867425     /lib/ld-2.3.5.so
> 00226000-00349000 r-xp 00000000 03:02 867426     /lib/libc-2.3.5.so
> 00349000-0034b000 r-xp 00123000 03:02 867426     /lib/libc-2.3.5.so
> 0034b000-0034d000 rwxp 00125000 03:02 867426     /lib/libc-2.3.5.so
> 0034d000-0034f000 rwxp 0034d000 00:00 0
> 00351000-00374000 r-xp 00000000 03:02 867427     /lib/libm-2.3.5.so
> 00374000-00375000 r-xp 00022000 03:02 867427     /lib/libm-2.3.5.so
> 00375000-00376000 rwxp 00023000 03:02 867427     /lib/libm-2.3.5.so
> 00378000-0037a000 r-xp 00000000 03:02 867428     /lib/libdl-2.3.5.so
> 0037a000-0037b000 r-xp 00001000 03:02 867428     /lib/libdl-2.3.5.so
> 0037b000-0037c000 rwxp 00002000 03:02 867428     /lib/libdl-2.3.5.so
> 0037e000-00390000 r-xp 00000000 03:02 111368      
> /usr/lib/libz.so.1.2.2.2
> 00390000-00391000 rwxp 00011000 03:02 111368      
> /usr/lib/libz.so.1.2.2.2
> 00398000-00399000 r-xp 00398000 00:00 0
> 00469000-00477000 r-xp 00000000 03:02 867435      
> /lib/libpthread-2.3.5.so
> 00477000-00478000 r-xp 0000d000 03:02 867435      
> /lib/libpthread-2.3.5.so
> 00478000-00479000 rwxp 0000e000 03:02 867435      
> /lib/libpthread-2.3.5.so
> 00479000-0047b000 rwxp 00479000 00:00 0
> 0048e000-004b5000 r-xp 00000000 03:02 110766      
> /usr/lib/libreadline.so.5.0
> 004b5000-004b9000 rwxp 00027000 03:02 110766      
> /usr/lib/libreadline.so.5.0
> 004b9000-004ba000 rwxp 004b9000 00:00 0
> 004bc000-004fe000 r-xp 00000000 03:02 128642  
> /usr/lib/octave-2.1.71/libcruft.so.2.1.71
> 004fe000-00502000 rwxp 00041000 03:02 128642  
> /usr/lib/octave-2.1.71/libcruft.so.2.1.71
> 00502000-00503000 rwxp 00502000 00:00 0
> 00505000-0055c000 r-xp 00000000 03:02 103091  
> /usr/lib/libgfortran.so.0.0.0
> 0055c000-0055e000 rwxp 00056000 03:02 103091  
> /usr/lib/libgfortran.so.0.0.0
> 0055e000-00562000 rwxp 0055e000 00:00 0
> 0057b000-0058a000 r-xp 00000000 03:02 867429      
> /lib/libresolv-2.3.5.so
> 0058a000-0058b000 r-xp 0000e000 03:02 867429      
> /lib/libresolv-2.3.5.so
> 0058b000-0058c000 rwxp 0000f000 03:02 867429      
> /lib/libresolv-2.3.5.so
> 0058c000-0058e000 rwxp 0058c000 00:00 0
> 00590000-00599000 r-xp 00000000 03:02 867440  
> /lib/libgcc_s-4.0.1-20050727.so.1
> 00599000-0059a000 rwxp 00009000 03:02 867440  
> /lib/libgcc_s-4.0.1-20050727.so.1
> 0059c000-0067c000 r-xp 00000000 03:02 111392      
> /usr/lib/libstdc++.so.6.0.5
> 0067c000-00681000 rwxp 000df000 03:02 111392      
> /usr/lib/libstdc++.so.6.0.5
> 00681000-00687000 rwxp 00681000 00:00 0
> 00689000-006df000 r-xp 00000000 03:02 99344      
> /usr/lib/libblas.so.3.0.3
> 006df000-006e0000 rwxp 00055000 03:02 99344      
> /usr/lib/libblas.so.3.0.3
> 0070a000-0070c000 r-xp 00000000 03:02 864925     /lib/libcom_err.so.2.1
> 0070c000-0070d000 rwxp 00001000 03:02 864925     /lib/libcom_err.so.2.1
> 00787000-0079d000 r-xp 00000000 03:02 201709  
> /usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/
> dispatch.oct
> 0079d000-0079e000 rwxp 00016000 03:02 201709  
> /usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/
> dispatch.oct
> 0097c000-009eb000 r-xp 00000000 03:02 105049      
> /usr/lib/libkrb5.so.3.2
> 009eb000-009ee000 rwxp 0006e000 03:02 105049      
> /usr/lib/libkrb5.so.3.2
> 009f0000-00a25000 r-xp 00000000 03:02 864979     /lib/libssl.so.0.9.7f
> 00a25000-00a28000 rwxp 00035000 03:02 864979     /lib/libssl.so.0.9.7f
> 00a2a000-00a41000 r-xp 00000000 03:02 105050  
> /usr/lib/libgssapi_krb5.so.2.2
> 00a41000-00a42000 rwxp 00017000 03:02 105050  
> /usr/lib/libgssapi_krb5.so.2.2
> 00cee000-00d11000 r-xp 00000000 03:02 111383      
> /usr/lib/libk5crypto.so.3.0
> 00d11000-00d12000 rwxp 00023000 03:02 111383      
> /usr/lib/libk5crypto.so.3.0
> 00d14000-00d16000 r-xp 00000000 03:02 106698  
> /usr/lib/libkrb5support.so.0.0
> 00d16000-00d17000 rwxp 00001000 03:02 106698  
> /usr/lib/libkrb5support.so.0.0
> 00d64000-00ddb000 r-xp 00000000 03:02 201832  
> /usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/
> make_sparse.oct
> 00ddb000-00ddd000 rwxp 00077000 03:02 201832  
> /usr/libexec/octave/2.1.71/site/oct/i686-pc-linux-gnu/octave-forge/
> make_sparse.oct
> 02bdb000-02f92000 r-xp 00000000 03:02 99339      
> /usr/lib/liblapack.so.3.0.3
> 02f92000-02f95000 rwxp 003b7000 03:02 99339      
> /usr/lib/liblapack.so.3.0.3
> 02f95000-03099000 rwxp 02f95000 00:00 0
> 0309b000-03675000 r-xp 00000000 03:02 128643  
> /usr/lib/octave-2.1.71/liboctave.so.2.1.71
> 03675000-03681000 rwxp 005da000 03:02 128643  
> /usr/lib/octave-2.1.71/liboctave.so.2.1.71
> 03681000-03682000 rwxp 03681000 00:00 0
> 03dc0000-03dfe000 r-xp 00000000 03:02 109746      
> /usr/lib/libncurses.so.5.4
> 03dfe000-03e07000 rwxp 0003d000 03:02 109746      
> /usr/lib/libncurses.so.5.4
> 03e09000-0457d000 r-xp 00000000 03:02 128644  
> /usr/lib/octave-2.1.71/liboctinterp.so.2.1.71
> 0457d000-04599000 rwxp 00773000 03:02 128644  
> /usr/lib/octave-2.1.71/liboctinterp.so.2.1.71
> 04599000-0459b000 rwxp 04599000 00:00 0
> 0460f000-04707000 r-xp 00000000 03:02 867431      
> /lib/libcrypto.so.0.9.7f
> 04707000-04719000 rwxp 000f8000 03:02 867431      
> /lib/libcrypto.so.0.9.7f
> 04719000-0471c000 rwxp 04719000 00:00 0
> 064f8000-0662c000 r-xp 00000000 03:02 107290      
> /usr/lib/libhdf5.so.0.0.0
> 0662c000-0662f000 rwxp 00134000 03:02 107290      
> /usr/lib/libhdf5.so.0.0.0
> 08048000-08049000 r-xp 00000000 03:02 99342      /usr/bin/octave-2.1.71
> 08049000-0804d000 rw-p 00000000 03:02 99342      /usr/bin/octave-2.1.71
> 09152000-09d2a000 rw-p 09152000 00:00 0          [heap]
> b6c00000-b6c21000 rw-p b6c00000 00:00 0
> b6c21000-b6d00000 ---p b6c21000 00:00 0
> b6de6000-b7c4c000 rw-p b6de6000 00:00 0
> b7c4c000-b7c4d000 r--p 00edd000 03:02 107632  
> /usr/lib/locale/locale-archive
> b7c4d000-b7c7e000 r--p 00e5c000 03:02 107632  
> /usr/lib/locale/locale-archive
> b7c7e000-b7e7e000 r--p 00000000 03:02 107632  
> /usr/lib/locale/locale-archive
> b7e7e000-b7fe1000 rw-p b7e7e000 00:00 0
> b7ffb000-b7ffc000 rw-p b7ffb000 00:00 0
> bfee7000-bfefc000 rw-p bfee7000 00:00 0          [stack]
> panic: Aborted -- stopping myself...
> attempting to save variables to `octave-core'...
> save to `octave-core' complete
> Abort
>
> --
> Orion Poplawski
> System Administrator                   303-415-9701 x222
> Colorado Research Associates/NWRA      FAX: 303-415-9702
> 3380 Mitchell Lane, Boulder CO 80301   http://www.co-ra.com
> function [grid,xg,yg]=make_grid(minx,maxx,miny,maxy,dx,dy)
>
> xg=minx:dx:maxx;
> yg=maxy:-dy:miny;
>
> k=0;
> for x=xg
>    for y=yg
>       k=k+1;
>       grid(k,1)=x;
>       grid(k,2)=y;
>    end
> end
>
> %%% function MedBhm_preproc.m
>
> %**************************************************
> %**** Make grids for atm
> %**************************************************
>
> [grdxyA,xgA,ygA]=make_grid(14.000,37.000,30.000,46.0000,.25,.25);
> nxA=length(xgA)-2;
> nyA=length(ygA)-2;
>
> MtilB=make_MtilB_sparse(nxA,nyA);
> %%% function MedBhm_preproc.m
>
> %**************************************************
> %**** Make grids for atm
> %**************************************************
>
> [grdxyA,xgA,ygA]=make_grid(14.000,37.000,30.000,46.0000,.25,.25);
> nx=length(xgA)-2;
> ny=length(ygA)-2;
>
> Nx=nx+2;
> Ny=ny+2;
> N=Nx*Ny;
> n=nx*ny;
> NB=2*Nx+2*Ny-4;
>
> MtilB=sparse(NB,N);
>
> for k=1:Ny
>    MtilB(k,k)=1;
>    MtilB(Ny+Nx-2+k,N+1-k)=1;
> end
>
> for i=1:nx
>    MtilB(Ny+i,Ny*(i+1))=1;
>    MtilB(NB+1-i,(Ny*i)+1)=1;
> end
>
> function MtilB=make_MtilB_sparse(nx,ny)
>
> Nx=nx+2;
> Ny=ny+2;
> N=Nx*Ny;
> n=nx*ny;
> NB=2*Nx+2*Ny-4;
>
> MtilB=sparse(NB,N);
>
> for k=1:Ny
>    MtilB(k,k)=1;
>    MtilB(Ny+Nx-2+k,N+1-k)=1;
> end
>
> for i=1:nx
>    MtilB(Ny+i,Ny*(i+1))=1;
>    MtilB(NB+1-i,(Ny*i)+1)=1;
> end
>



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Re: [OctDev] Panic in sparse matrix code

Quentin Spencer
Paul Kienzle wrote:

> Is 2.9.x octave available for Fedora?  It has replacement code for
> the  octave-forge sparse functions and the octave-forge functions are
> no  longer supported [though you are welcome to provide patches if
> you  want].


2.9.3 can is available in the Fedora development tree. I don't plan to
move 2.9.x into the main FC-4 tree until it is considered stable (though
of course it really is pretty stable in practice).

-Quentin



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Re: [OctDev] Panic in sparse matrix code

David Bateman-3
In reply to this post by Orion Poplawski
Orion Poplawski wrote:

> Running octave 2.1.71 with octave-forge-2005-06.13 on Fedora Core 4.
> With the attached files:
>
> octave test.m
>
> runs ok.
>
> octave test2.m
>
> aborts with the following.  test is basically test2 with the function
> call folded into the main code.  The code is matlab code I'm trying to
> run in octave that I haven't explored very much.

Just for information, on the latest octave CVS (pretty similar to
2.9.3), test2.m ran without problem and gave the results

octave:2> whos

*** currently compiled functions:

  Prot Name                   Size                     Bytes  Class
  ==== ====                   ====                     =====  =====
   rwd make_MtilB_sparse     -1x-1                         0  user-defined function
   rwd make_grid             -1x-1                         0  user-defined function

Total is 2 elements using 0 bytes

*** local user variables:

  Prot Name            Size                     Bytes  Class
  ==== ====            ====                     =====  =====
   rwd MtilB         312x6045                   27928  sparse matrix
   rw- __nargin__      1x1                          8  scalar
   rwd grdxyA       6045x2                      96720  matrix
   rwd nxA             1x1                          8  scalar
   rwd nyA             1x1                          8  scalar
   rwd xgA             1x93                        24  range
   rwd ygA             1x65                        24  range

Total is 12563 elements using 124720 bytes


I have no idea what the results are supposed to be, but this appears to
work..

Cheers
David

--
David Bateman                                [hidden email]
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Re: [OctDev] Panic in sparse matrix code

Orion Poplawski
In reply to this post by Quentin Spencer
Quentin Spencer wrote:
>
> 2.9.3 can is available in the Fedora development tree. I don't plan to
> move 2.9.x into the main FC-4 tree until it is considered stable (though
> of course it really is pretty stable in practice).

Quentin -

    Would you mind producing some octave-2.9.3 rpms for FC4?  I've been
trying to build the stuff in extras/devel on FC4 and running into
problems, particularly with some blas issues.

- Orion


--
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System Administrator                   303-415-9701 x222
Colorado Research Associates/NWRA      FAX: 303-415-9702
3380 Mitchell Lane, Boulder CO 80301   http://www.co-ra.com


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Re: [OctDev] Panic in sparse matrix code

Quentin Spencer
Orion Poplawski wrote:

> Quentin Spencer wrote:
>
>>
>> 2.9.3 can is available in the Fedora development tree. I don't plan
>> to move 2.9.x into the main FC-4 tree until it is considered stable
>> (though of course it really is pretty stable in practice).
>
>
> Quentin -
>
>    Would you mind producing some octave-2.9.3 rpms for FC4?  I've been
> trying to build the stuff in extras/devel on FC4 and running into
> problems, particularly with some blas issues.


I think your problems are caused by the fact that Fedora's lapack was
recently modified to split blas and lapack into -devel packages, which
it previously hadn't done. Installing those should solve your problems.
I'll modify the spec files to update the build requirements, and build
an octave-2.9.3 rpm, however you may be able to build your own before I
can finish mine (unless I uncover other problems).

-Quentin



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Re: [OctDev] Panic in sparse matrix code

Orion Poplawski
In reply to this post by Paul Kienzle-3
Paul Kienzle wrote:
> Is 2.9.x octave available for Fedora?  It has replacement code for the  
> octave-forge sparse functions and the octave-forge functions are no  
> longer supported [though you are welcome to provide patches if you  want].
>
> - Paul

Is it possible to prevent octave-forge sparse code from overriding the
octave builtins?  I installed octave 2.9.3 and the sparse code worked.
Then I installed octave-forge on top and now I'm getting the same error
in the octave-forge sparse matrix code as before.

--
Orion Poplawski
System Administrator                   303-415-9701 x222
Colorado Research Associates/NWRA      FAX: 303-415-9702
3380 Mitchell Lane, Boulder CO 80301   http://www.co-ra.com


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Re: [OctDev] Panic in sparse matrix code

Stéfan van der Walt
On Wed, Sep 28, 2005 at 02:08:09PM -0600, Orion Poplawski wrote:

> Paul Kienzle wrote:
> >Is 2.9.x octave available for Fedora?  It has replacement code for the  
> >octave-forge sparse functions and the octave-forge functions are no  
> >longer supported [though you are welcome to provide patches if you  want].
> >
> >- Paul
>
> Is it possible to prevent octave-forge sparse code from overriding the
> octave builtins?  I installed octave 2.9.3 and the sparse code worked.
> Then I installed octave-forge on top and now I'm getting the same error
> in the octave-forge sparse matrix code as before.

You can prevent certain parts of octave-forge from being installed by
putting a "NOINSTALL" file in the appropriate.directory
(i.e. main/sparse).

Regards
Stéfan


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Re: [OctDev] Panic in sparse matrix code

Orion Poplawski
Stefan van der Walt wrote:
>
> You can prevent certain parts of octave-forge from being installed by
> putting a "NOINSTALL" file in the appropriate.directory
> (i.e. main/sparse).
>

Perhaps it is time to start putting NOINSTALL in those directories that
are no longer needed in 2.9.X?  A quick look seems to point to
main/sparse and main/cell.  Others?


--
Orion Poplawski
System Administrator                   303-415-9701 x222
Colorado Research Associates/NWRA      FAX: 303-415-9702
3380 Mitchell Lane, Boulder CO 80301   http://www.co-ra.com


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Re: [OctDev] Panic in sparse matrix code

David Bateman-3
Orion Poplawski wrote:

> Stefan van der Walt wrote:
>
>>
>> You can prevent certain parts of octave-forge from being installed by
>> putting a "NOINSTALL" file in the appropriate.directory
>> (i.e. main/sparse).
>>
>
> Perhaps it is time to start putting NOINSTALL in those directories
> that are no longer needed in 2.9.X?  A quick look seems to point to
> main/sparse and main/cell.  Others?
>
>
Don't put it in main/cell as cell2mat.m is not in octave yet, though as
it is a core function of matlab I imagine it soon will be.. In fact
there are some iterative functions in main/sparse that are not in octave
but are still useful, so I'd even be careful about putting NOINSTALL in
main/sparse. The correct solution is probably to completely decruft
octave-forge for a 2.9.x tree, including removing functions merged with
octave. Make a specific 2.9.x octave-forge release then use Soren's
packaging system to start to breaking octave-forge apart into seperate
packages...

Cheers
David

--
David Bateman                                [hidden email]
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