[Gfs-users] problem after updating to ubuntu 11

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Juvénal Dufaur

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May 10, 2011, 4:36:48 AM5/10/11
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Hello

I was on ubuntu 10.10 and I updated to ubuntu 11.
gfsview doesn't work anymore. I have the following error message in my terminal if for example i try to run the example tangaroa.gfs (see below).
I have recompiled gts gerris and gfs already with ./configure, make, make install but it doesn't seem to make any changes.


Thanks for any help.

J.Dufaur

error message:

  [juvenal-DH55PJ:01102] *** Process received signal ***
[juvenal-DH55PJ:01102] Signal: Floating point exception (8)
[juvenal-DH55PJ:01102] Signal code: Floating point divide-by-zero (3)
[juvenal-DH55PJ:01102] Failing at address: 0x7f9d06a7af35
[juvenal-DH55PJ:01102] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfc60) [0x7f9d0c896c60]
[juvenal-DH55PJ:01102] [ 1] /usr/lib/gtk-2.0/2.10.0/engines/libmurrine.so(+0x7f35) [0x7f9d06a7af35]
[juvenal-DH55PJ:01102] [ 2] /usr/lib/gtk-2.0/2.10.0/engines/libmurrine.so(+0x1bb00) [0x7f9d06a8eb00]
[juvenal-DH55PJ:01102] [ 3] /usr/lib/gtk-2.0/2.10.0/engines/libmurrine.so(+0x103c3) [0x7f9d06a833c3]
[juvenal-DH55PJ:01102] [ 4] /usr/lib/libgtk-x11-2.0.so.0(+0x145588) [0x7f9d10e0b588]
[juvenal-DH55PJ:01102] [ 5] /usr/lib/libgtk-x11-2.0.so.0(+0x138578) [0x7f9d10dfe578]
[juvenal-DH55PJ:01102] [ 6] /usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0(g_closure_invoke+0x15c) [0x7f9d0ed0a81c]
[juvenal-DH55PJ:01102] [ 7] /usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0(+0x1fe1f) [0x7f9d0ed1be1f]
[juvenal-DH55PJ:01102] [ 8] /usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0(g_signal_emit_valist+0x5a9) [0x7f9d0ed24fa9]
[juvenal-DH55PJ:01102] [ 9] /usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0(g_signal_emit+0x7f) [0x7f9d0ed2541f]
[juvenal-DH55PJ:01102] [10] /usr/lib/libgtk-x11-2.0.so.0(+0x2544d1) [0x7f9d10f1a4d1]
[juvenal-DH55PJ:01102] [11] /usr/lib/libgtk-x11-2.0.so.0(gtk_main_do_event+0x55d) [0x7f9d10dfcd9d]
[juvenal-DH55PJ:01102] [12] /usr/lib/libgdk-x11-2.0.so.0(+0x437dc) [0x7f9d1050f7dc]
[juvenal-DH55PJ:01102] [13] /usr/lib/libgdk-x11-2.0.so.0(+0x4378b) [0x7f9d1050f78b]
[juvenal-DH55PJ:01102] [14] /usr/lib/libgdk-x11-2.0.so.0(+0x3e73b) [0x7f9d1050a73b]
[juvenal-DH55PJ:01102] [15] /usr/lib/libgdk-x11-2.0.so.0(gdk_window_process_all_updates+0x129) [0x7f9d1050c929]
[juvenal-DH55PJ:01102] [16] /usr/lib/libgtk-x11-2.0.so.0(+0xb9761) [0x7f9d10d7f761]
[juvenal-DH55PJ:01102] [17] /usr/lib/libgdk-x11-2.0.so.0(+0x1dc46) [0x7f9d104e9c46]
[juvenal-DH55PJ:01102] [18] /lib/x86_64-linux-gnu/libglib-2.0.so.0(g_main_context_dispatch+0x1dd) [0x7f9d0da8ebcd]
[juvenal-DH55PJ:01102] [19] /lib/x86_64-linux-gnu/libglib-2.0.so.0(+0x433a8) [0x7f9d0da8f3a8]
[juvenal-DH55PJ:01102] [20] /lib/x86_64-linux-gnu/libglib-2.0.so.0(g_main_loop_run+0x172) [0x7f9d0da8f9f2]
[juvenal-DH55PJ:01102] [21] /usr/lib/libgtk-x11-2.0.so.0(gtk_main+0xa7) [0x7f9d10dfbaf7]
[juvenal-DH55PJ:01102] [22] gfsview3D(main+0x34b) [0x42c2eb]
[juvenal-DH55PJ:01102] [23] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff) [0x7f9d0c511eff]
[juvenal-DH55PJ:01102] [24] gfsview3D() [0x40d249]
[juvenal-DH55PJ:01102] *** End of error message ***
FFmpeg version 0.6.2-4:0.6.2-1ubuntu1, Copyright (c) 2000-2010 the Libav developers
  built on Mar 22 2011 15:55:04 with gcc 4.5.2
  configuration: --extra-version=4:0.6.2-1ubuntu1 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-vaapi --enable-gpl --enable-postproc --enable-swscale --enable-x11grab --enable-libdc1394 --enable-shared --disable-static
  libavutil     50.15. 1 / 50.15. 1
  libavcodec    52.72. 2 / 52.72. 2
  libavformat   52.64. 2 / 52.64. 2
  libavdevice   52. 2. 0 / 52. 2. 0
  libavfilter    1.19. 0 /  1.19. 0
  libswscale     0.11. 0 /  0.11. 0
  libpostproc   51. 2. 0 / 51. 2. 0
[image2pipe @ 0x989440]Could not find codec parameters (Video: ppm)
[image2pipe @ 0x989440]Estimating duration from bitrate, this may be inaccurate
pipe:: could not find codec parameters
Solid volume fraction
    min:  7.832e-10 avg:  5.343e-01 |  3.347e-01 max:  1.000e+00 n:      11866
Total merged solid volume fraction
    min:  1.093e-01 avg:  1.020e+00 |  4.135e-01 max:  4.114e+00 n:       8440
Number of cells merged per merged cell
    min:          2 avg:      2.438 |      1.110 max:         20 n:       3963
Number of "thin" cells removed:          2
step:       0 t:      0.00000000 dt:  2.030869e-04 cpu:      1.27000000 real:      1.28883600
Balance summary: 1 PE
  domain   min:     33944 avg:     33944         |       0 max:     33944
Approximate projection
    niter:    5
    residual.bias:   -5.104e-18 -1.308e-06
    residual.first:   1.199e-01  1.263e-05    6.2
    residual.second:  2.898e-01  3.271e-05    6.2
    residual.infty:   7.988e-01  6.098e-04    4.2


Stephane Popinet

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May 12, 2011, 1:10:47 PM5/12/11
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Hi Juvenal,

> I was on ubuntu 10.10 and I updated to ubuntu 11.
> gfsview doesn't work anymore.

I suppose you were still using the gerris/gfsview packages made for
ubuntu 10.10.

I have just released the packages for ubuntu 11.04. See:

http://gfs.sourceforge.net/wiki/index.php/Ubuntu/Debian_installation

Change your repositories (remove 10.10 and add 11.04), update your
packages and see if this fixes your problem.
I suspect it will not. As you can see in your error messages, this is
not strictly a problem with gfsview but a bug of libmurrine.so? which
triggers a floating-point exception. You should report the bug on the
ubuntu forums.

If the problem persists, we will try to find a workaround.

cheers

Stephane

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Juvénal Dufaur

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May 16, 2011, 6:05:26 AM5/16/11
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Hello Stephane

Thanks for your answer.

I have changed my repositorie from the source tarballs (when I do it from the link you sent me I never achieve to install Gerris) I hope this is ok.
GTS works, and Gerris runs but I still have the same error as you predicted.

Here is the error message:

[juvenal-DH55PJ:05895] *** Process received signal ***
[juvenal-DH55PJ:05895] Signal: Floating point exception (8)
[juvenal-DH55PJ:05895] Signal code: Floating point divide-by-zero (3)
[juvenal-DH55PJ:05895] Failing at address: 0x7fe22dc8ef35
[juvenal-DH55PJ:05895] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfc60) [0x7fe233aaac60]
[juvenal-DH55PJ:05895] [ 1] /usr/lib/gtk-2.0/2.10.0/engines/libmurrine.so(+0x7f35) [0x7fe22dc8ef35]
[juvenal-DH55PJ:05895] [ 2] /usr/lib/gtk-2.0/2.10.0/engines/libmurrine.so(+0x1bb00) [0x7fe22dca2b00]
[juvenal-DH55PJ:05895] [ 3] /usr/lib/gtk-2.0/2.10.0/engines/libmurrine.so(+0x103c3) [0x7fe22dc973c3]
[juvenal-DH55PJ:05895] [ 4] /usr/lib/libgtk-x11-2.0.so.0(+0x145588) [0x7fe238020588]
[juvenal-DH55PJ:05895] [ 5] /usr/lib/libgtk-x11-2.0.so.0(+0x138578) [0x7fe238013578]
[juvenal-DH55PJ:05895] [ 6] /usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0(g_closure_invoke+0x15c) [0x7fe235f1f81c]
[juvenal-DH55PJ:05895] [ 7] /usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0(+0x1fe1f) [0x7fe235f30e1f]
[juvenal-DH55PJ:05895] [ 8] /usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0(g_signal_emit_valist+0x5a9) [0x7fe235f39fa9]
[juvenal-DH55PJ:05895] [ 9] /usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0(g_signal_emit+0x7f) [0x7fe235f3a41f]
[juvenal-DH55PJ:05895] [10] /usr/lib/libgtk-x11-2.0.so.0(+0x2544d1) [0x7fe23812f4d1]
[juvenal-DH55PJ:05895] [11] /usr/lib/libgtk-x11-2.0.so.0(gtk_main_do_event+0x55d) [0x7fe238011d9d]
[juvenal-DH55PJ:05895] [12] /usr/lib/libgdk-x11-2.0.so.0(+0x437dc) [0x7fe2377247dc]
[juvenal-DH55PJ:05895] [13] /usr/lib/libgdk-x11-2.0.so.0(+0x4378b) [0x7fe23772478b]
[juvenal-DH55PJ:05895] [14] /usr/lib/libgdk-x11-2.0.so.0(+0x3e73b) [0x7fe23771f73b]
[juvenal-DH55PJ:05895] [15] /usr/lib/libgdk-x11-2.0.so.0(gdk_window_process_all_updates+0x129) [0x7fe237721929]
[juvenal-DH55PJ:05895] [16] /usr/lib/libgtk-x11-2.0.so.0(+0xb9761) [0x7fe237f94761]
[juvenal-DH55PJ:05895] [17] /usr/lib/libgdk-x11-2.0.so.0(+0x1dc46) [0x7fe2376fec46]
[juvenal-DH55PJ:05895] [18] /lib/x86_64-linux-gnu/libglib-2.0.so.0(g_main_context_dispatch+0x1dd) [0x7fe234ca2bcd]
[juvenal-DH55PJ:05895] [19] /lib/x86_64-linux-gnu/libglib-2.0.so.0(+0x433a8) [0x7fe234ca33a8]
[juvenal-DH55PJ:05895] [20] /lib/x86_64-linux-gnu/libglib-2.0.so.0(g_main_loop_run+0x172) [0x7fe234ca39f2]
[juvenal-DH55PJ:05895] [21] /usr/lib/libgtk-x11-2.0.so.0(gtk_main+0xa7) [0x7fe238010af7]
[juvenal-DH55PJ:05895] [22] gfsview3D(main+0x34b) [0x42c2eb]
[juvenal-DH55PJ:05895] [23] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff) [0x7fe233725eff]
[juvenal-DH55PJ:05895] [24] gfsview3D() [0x40d249]
[juvenal-DH55PJ:05895] *** End of error message ***


Thanks

J. Dufaur




2011/5/12 Stephane Popinet <s.po...@niwa.co.nz>

Stephane Popinet

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May 16, 2011, 6:32:05 AM5/16/11
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Hi Juvenal,

> I have changed my repositorie from the source tarballs (when I do it from
> the link you sent me I never achieve to install Gerris) I hope this is ok.

Do you mean that following these instructions:

http://gfs.sourceforge.net/wiki/index.php/Ubuntu/Debian_installation

doesn't work? What's happening?

> GTS works, and Gerris runs but I still have the same error as you predicted.

OK. This is a bug in Ubuntu (I suspect it has to do with all the stuff
they did to make the new Ubuntu look "pretty"). The workaround is to
turn off floating-point exceptions in Gerris. I will see what I can
do.

Juvénal Dufaur

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May 16, 2011, 7:05:50 AM5/16/11
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Hi again

Yes when I follow the instructions of this link I have never achieved to install Gerris. I reckon the system doesn't really like adding lines to the source.list file (not sure though).

Cheers and thanks for your message. I will wait for your instructions.

Juvenal



2011/5/16 Stephane Popinet <s.po...@niwa.co.nz>

Stephane Popinet

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May 16, 2011, 7:19:42 AM5/16/11
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> Yes when I follow the instructions of this link I have never achieved to
> install Gerris. I reckon the system doesn't really like adding lines to the
> source.list file (not sure though).

Could you please try again and tell me exactly where things go wrong.
This should work if you follow the instructions.

Juvénal Dufaur

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May 16, 2011, 11:31:49 AM5/16/11
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Hello

I don't want to do it adding lines to the source.list because once it froze my computer and I had to reinstall the all system. I have used the synaptic manager though and it works fine.
Hope this is ok.

Cheers

Juvenal

2011/5/16 Stephane Popinet <s.po...@niwa.co.nz>
> Yes when I follow the instructions of this link I have never achieved to

Kian Mehravaran

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May 17, 2011, 1:42:57 PM5/17/11
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I had the same problem despite compiling from source. Solution: login as classic gnome, it gets rid of the new ubuntu pretty-ness :)

--- On Mon, 5/16/11, Juvénal Dufaur <jdu...@gmail.com> wrote:
-----Inline Attachment Follows-----


------------------------------------------------------------------------------
Achieve unprecedented app performance and reliability
What every C/C++ and Fortran developer should know.
Learn how Intel has extended the reach of its next-generation tools
to help boost performance applications - inlcuding clusters.
http://p.sf.net/sfu/intel-dev2devmay

-----Inline Attachment Follows-----

Juvénal Dufaur

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May 20, 2011, 9:42:52 AM5/20/11
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Hello Kian

Thanks for the advice. I logged in with ubuntu classic, no effects, and every thing works now.

Cheers

Juvenal

2011/5/17 Kian Mehravaran <key...@yahoo.com>
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