[Gfs-users] Problem installing gfsview

[Marie-Jean Thoraval]

Dear all,

I cannot install gfsview anymore (gfsview-snapshot-110904). Here is the error I get after the command "$ sudo make install" (full message at the end):

"...
/home/thoravml/install/20110905/gfsview-snapshot-110904/libtool: line 8950: mpicc: command not found
libtool: install: error: relink `libgfsview2D.la' with the above command before installing it
make[2]: *** [install-pkglibLTLIBRARIES] Error 1
make[2]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/batch'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/batch'
make: *** [install-recursive] Error 1"

I was able to install a previous version (gfsview-snapshot-100923) (and it still works).
I also have a similar error with gfsview-snapshot-110122.

I am installing from source tarball, locally in "/home/thoravml/local/".
I am on Fedora 11.

$ gfsview2D -V
gfsview: 2D version 0.5.0

Thank you for your help.
Best regards,
Marie-Jean.

--

Marie-Jean Thoraval
PhD student, Physical Sciences and Engineering
King Abdullah University of Science and Technology
Jeddah, Saudi Arabia
+966 2 808 21 61
+966 5 67 79 08 33
http://www.carva.org/marie-jean.thoraval

"$ sudo make install
Making install in gl2ps
make[1]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/gl2ps'
make[2]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/gl2ps'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/gl2ps'
make[1]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/gl2ps'
Making install in gl
make[1]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/gl'
make[2]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/gl'
test -z "/home/thoravml/local/lib" || /bin/mkdir -p "/home/thoravml/local/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libgfsgl2D.la libgfsgl3D.la '/home/thoravml/local/lib'
libtool: install: /usr/bin/install -c .libs/libgfsgl2D.so.0.0.0 /home/thoravml/local/lib/libgfsgl2D.so.0.0.0
libtool: install: (cd /home/thoravml/local/lib && { ln -s -f libgfsgl2D.so.0.0.0 libgfsgl2D.so.0 || { rm -f libgfsgl2D.so.0 && ln -s libgfsgl2D.so.0.0.0 libgfsgl2D.so.0; }; })
libtool: install: (cd /home/thoravml/local/lib && { ln -s -f libgfsgl2D.so.0.0.0 libgfsgl2D.so || { rm -f libgfsgl2D.so && ln -s libgfsgl2D.so.0.0.0 libgfsgl2D.so; }; })
libtool: install: /usr/bin/install -c .libs/libgfsgl2D.lai /home/thoravml/local/lib/libgfsgl2D.la
libtool: install: /usr/bin/install -c .libs/libgfsgl3D.so.0.0.0 /home/thoravml/local/lib/libgfsgl3D.so.0.0.0
libtool: install: (cd /home/thoravml/local/lib && { ln -s -f libgfsgl3D.so.0.0.0 libgfsgl3D.so.0 || { rm -f libgfsgl3D.so.0 && ln -s libgfsgl3D.so.0.0.0 libgfsgl3D.so.0; }; })
libtool: install: (cd /home/thoravml/local/lib && { ln -s -f libgfsgl3D.so.0.0.0 libgfsgl3D.so || { rm -f libgfsgl3D.so && ln -s libgfsgl3D.so.0.0.0 libgfsgl3D.so; }; })
libtool: install: /usr/bin/install -c .libs/libgfsgl3D.lai /home/thoravml/local/lib/libgfsgl3D.la
libtool: install: /usr/bin/install -c .libs/libgfsgl2D.a /home/thoravml/local/lib/libgfsgl2D.a
libtool: install: chmod 644 /home/thoravml/local/lib/libgfsgl2D.a
libtool: install: ranlib /home/thoravml/local/lib/libgfsgl2D.a
libtool: install: /usr/bin/install -c .libs/libgfsgl3D.a /home/thoravml/local/lib/libgfsgl3D.a
libtool: install: chmod 644 /home/thoravml/local/lib/libgfsgl3D.a
libtool: install: ranlib /home/thoravml/local/lib/libgfsgl3D.a
libtool: finish: PATH="/usr/bin:/bin:/sbin" ldconfig -n /home/thoravml/local/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/thoravml/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/gl'
make[1]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/gl'
Making install in batch
make[1]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/batch'
make[2]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/batch'
test -z "/home/thoravml/local/bin" || /bin/mkdir -p "/home/thoravml/local/bin"
  /bin/sh ../libtool   --mode=install /usr/bin/install -c gfsview-batch2D gfsview-batch3D '/home/thoravml/local/bin'
libtool: install: /usr/bin/install -c .libs/gfsview-batch2D /home/thoravml/local/bin/gfsview-batch2D
libtool: install: /usr/bin/install -c .libs/gfsview-batch3D /home/thoravml/local/bin/gfsview-batch3D
test -z "/home/thoravml/local/lib/gerris" || /bin/mkdir -p "/home/thoravml/local/lib/gerris"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libgfsview2D.la libgfsview3D.la '/home/thoravml/local/lib/gerris'
libtool: install: warning: relinking `libgfsview2D.la'
libtool: install: (cd /home/thoravml/install/20110905/gfsview-snapshot-110904/batch; /bin/sh /home/thoravml/install/20110905/gfsview-snapshot-110904/libtool  --tag CC --mode=relink mpicc -DFTT_2D=1 -pthread -I/home/thoravml/local/include -I/home/thoravml/local//include -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -g -O2 -Wall -Werror-implicit-function-declaration -Wmissing-prototypes -Wmissing-declarations -pipe -std=c99 -D_XOPEN_SOURCE=500 -no-undefined -release 0.0.1 -export-dynamic -module -o libgfsview2D.la -rpath /home/thoravml/local/lib/gerris libgfsview2D_la-module.lo -lrender2D )
libtool: relink: warning: `/home/thoravml/local/lib/libgts.la' seems to be moved
libtool: relink: mpicc -shared  -fPIC -DPIC  .libs/libgfsview2D_la-module.o  -Wl,--whole-archive /home/thoravml/install/20110905/gfsview-snapshot-110904/batch/.libs/librender2D.a -Wl,--no-whole-archive  -Wl,-rpath -Wl,/home/thoravml/local/lib -Wl,-rpath -Wl,/home/thoravml/local//lib -Wl,-rpath -Wl,/usr/lib64 -L../gl2ps -L../gl -L/home/thoravml/local/lib -lgfsgl2D -L/home/thoravml/local//lib -lgfs2D -lgts -lgthread-2.0 -lrt -lgmodule-2.0 -lglib-2.0 -lOSMesa -L/usr/lib64 -lGL -L/usr/X11R6/lib -lm -lXext -lX11 -ldl -lGLU  -pthread -O2   -pthread -Wl,-soname -Wl,libgfsview2D-0.0.1.so -o .libs/libgfsview2D-0.0.1.so
/home/thoravml/install/20110905/gfsview-snapshot-110904/libtool: line 8950: mpicc: command not found
libtool: install: error: relink `libgfsview2D.la' with the above command before installing it
make[2]: *** [install-pkglibLTLIBRARIES] Error 1
make[2]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/batch'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/batch'
make: *** [install-recursive] Error 1"

[Stephane Popinet]

Hi Marie-Jean,

As indicated clearly here:

> mpicc: command not found

The makefile cannot find the 'mpicc' command which is part of MPI.
First try to redo:

% sh autogen.sh --prefix=...
% make

if this still gives the error message above, check your installation
of MPI and/or disable the parallel version (--disable-mpi).

Note also that you should try to update your versions of
gerris/gfsview more often than once a year!

cheers

Stephane

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[Marie-Jean Thoraval]

Dear Stephane,

* The first try gave the same result.
(% sh autogen.sh --prefix=...
% make)

* The installation finished with the option "--disable-mpi"

* I have tried also to do the installation without "--disable-mpi", but instead of "$ sudo make install" at the end, I have done "$ make install". The installation also finished in a similar way as with the option "--disable-mpi" (result at the end). I don't know why the "sudo" makes a difference.

* With both versions (with or without "--disable-mpi") I am able to run the interactive viewer and the batch version. I am able to open simulation files, and generated ppm images with the batch version.

* However, when I export in gnuplot format, the gnuplot files are different. Previously, I had something like:

-0.0217348 0.499878 0.00100053
-0.0217348 0.500001 0.00100053

-0.0217348 0.499756 0.00100053
-0.0217348 0.499878 0.00100053

-0.0217348 0.499634 0.00100053
-0.0217348 0.499756 0.00100053
...,

but now I get:

-0.0224609 1.19219e-07 0.00100053
-0.0224609 0.00195323 0.00100053
-0.0224609 0.00390637 0.00100053
-0.0224609 0.00585952 0.00100053
-0.0224609 0.00781266 0.00100053
-0.0224609 0.00976581 0.00100053
...

The size of the new gnuplot file is approximately half the size of the previous version I had.

* From the interactive viewer: now the option "res = 1" and "res = 0" both give the full resolution for the gnuplot files.

* However, generating the gnuplot files from the batch viewer (with the same gfv file) gives different results: the resolution is much lower. The script I am using is the following:

(for k in `seq 0 1 9`; do
if [ -e "file$k.gfs" ]; then
cat file$k.gfs
echo "Save file$k.gnu { format = Gnuplot }"
fi
done ) | gfsview-batch2D t.gfv

Should it give the same result as with the interactive viewer? This would be very useful for me.

Or is it a problem with my installation?

Best regards,
Marie-Jean.

"$ make install

libtool: finish: PATH="/home/thoravml/local/bin:/usr/lib64/qt-3.3/bin:/usr/lib64/mpich2/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/Gerris:/home/Gerris:/sbin" ldconfig -n /home/thoravml/local/lib

libtool: relink: warning: `/home/thoravml/local/lib/libftgl.la' seems to be moved
libtool: relink: mpicc -shared  .libs/libgfsview2D_la-module.o  -Wl,--whole-archive /home/thoravml/install/20110905/gfsview-snapshot-110904/batch/.libs/librender2D.a -Wl,--no-whole-archive  -Wl,-rpath -Wl,/home/thoravml/local/lib -Wl,-rpath -Wl,/home/thoravml/local//lib -L/home/thoravml/install/20110905/gfsview-snapshot-110904/gl2ps -L/home/thoravml/install/20110905/gfsview-snapshot-110904/gl -L/home/thoravml/local/lib -lgfsgl2D -L/home/thoravml/local//lib -L/usr/X11R6/lib -L/usr/lib64 -lgfs2D -lgts -lgthread-2.0 -lrt -lgmodule-2.0 -lglib-2.0 -lftgl -lfreetype -lOSMesa -lGL -lm -lXext -lX11 -ldl -lGLU  -pthread   -pthread -Wl,-soname -Wl,libgfsview2D-0.0.1.so -o .libs/libgfsview2D-0.0.1.so
libtool: install: /usr/bin/install -c .libs/libgfsview2D-0.0.1.soT /home/thoravml/local/lib/gerris/libgfsview2D-0.0.1.so
libtool: install: (cd /home/thoravml/local/lib/gerris && { ln -s -f libgfsview2D-0.0.1.so libgfsview2D.so || { rm -f libgfsview2D.so && ln -s libgfsview2D-0.0.1.so libgfsview2D.so; }; })
libtool: install: /usr/bin/install -c .libs/libgfsview2D.lai /home/thoravml/local/lib/gerris/libgfsview2D.la
libtool: install: warning: relinking `libgfsview3D.la'
libtool: install: (cd /home/thoravml/install/20110905/gfsview-snapshot-110904/batch; /bin/sh /home/thoravml/install/20110905/gfsview-snapshot-110904/libtool  --tag CC --mode=relink mpicc -pthread -I/home/thoravml/local/include -I/home/thoravml/local//include -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -g -O2 -Wall -Werror-implicit-function-declaration -Wmissing-prototypes -Wmissing-declarations -pipe -std=c99 -D_XOPEN_SOURCE=500 -no-undefined -release 0.0.1 -export-dynamic -module -o libgfsview3D.la -rpath /home/thoravml/local/lib/gerris libgfsview3D_la-module.lo -lrender3D )

libtool: relink: warning: `/home/thoravml/local/lib/libgts.la' seems to be moved

libtool: relink: warning: `/home/thoravml/local/lib/libftgl.la' seems to be moved
libtool: relink: mpicc -shared  .libs/libgfsview3D_la-module.o  -Wl,--whole-archive /home/thoravml/install/20110905/gfsview-snapshot-110904/batch/.libs/librender3D.a -Wl,--no-whole-archive  -Wl,-rpath -Wl,/home/thoravml/local/lib -Wl,-rpath -Wl,/home/thoravml/local//lib -L/home/thoravml/install/20110905/gfsview-snapshot-110904/gl2ps -L/home/thoravml/install/20110905/gfsview-snapshot-110904/gl -L/home/thoravml/local/lib -lgfsgl3D -L/home/thoravml/local//lib -L/usr/X11R6/lib -L/usr/lib64 -lgfs3D -lgts -lgthread-2.0 -lrt -lgmodule-2.0 -lglib-2.0 -lftgl -lfreetype -lOSMesa -lGL -lm -lXext -lX11 -ldl -lGLU  -pthread   -pthread -Wl,-soname -Wl,libgfsview3D-0.0.1.so -o .libs/libgfsview3D-0.0.1.so
libtool: install: /usr/bin/install -c .libs/libgfsview3D-0.0.1.soT /home/thoravml/local/lib/gerris/libgfsview3D-0.0.1.so
libtool: install: (cd /home/thoravml/local/lib/gerris && { ln -s -f libgfsview3D-0.0.1.so libgfsview3D.so || { rm -f libgfsview3D.so && ln -s libgfsview3D-0.0.1.so libgfsview3D.so; }; })
libtool: install: /usr/bin/install -c .libs/libgfsview3D.lai /home/thoravml/local/lib/gerris/libgfsview3D.la
libtool: install: /usr/bin/install -c .libs/libgfsview2D.a /home/thoravml/local/lib/gerris/libgfsview2D.a
libtool: install: chmod 644 /home/thoravml/local/lib/gerris/libgfsview2D.a
libtool: install: ranlib /home/thoravml/local/lib/gerris/libgfsview2D.a
libtool: install: /usr/bin/install -c .libs/libgfsview3D.a /home/thoravml/local/lib/gerris/libgfsview3D.a
libtool: install: chmod 644 /home/thoravml/local/lib/gerris/libgfsview3D.a
libtool: install: ranlib /home/thoravml/local/lib/gerris/libgfsview3D.a
libtool: finish: PATH="/home/thoravml/local/bin:/usr/lib64/qt-3.3/bin:/usr/lib64/mpich2/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/Gerris:/home/Gerris:/sbin" ldconfig -n /home/thoravml/local/lib/gerris

----------------------------------------------------------------------
Libraries have been installed in:

   /home/thoravml/local/lib/gerris

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[2]: Nothing to be done for `install-data-am'.

make[2]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/batch'

make[1]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/batch'

Making install in view
make[1]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view'
make  install-recursive
make[2]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view'
Making install in desktop
make[3]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view/desktop'
make[4]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view/desktop'
make[4]: Nothing to be done for `install-exec-am'.
test -z "/home/thoravml/local/share/applications" || /bin/mkdir -p "/home/thoravml/local/share/applications"
 /usr/bin/install -c -m 644 gfsview2D.desktop gfsview3D.desktop gfsview.desktop '/home/thoravml/local/share/applications'
test -z "/home/thoravml/local/share/icons/hicolor/48x48/mimetypes" || /bin/mkdir -p "/home/thoravml/local/share/icons/hicolor/48x48/mimetypes"
 /usr/bin/install -c -m 644 application-gfsview.png application-gfsview-2D.png application-gfsview-3D.png '/home/thoravml/local/share/icons/hicolor/48x48/mimetypes'
test -z "/home/thoravml/local/share/mime/packages" || /bin/mkdir -p "/home/thoravml/local/share/mime/packages"
 /usr/bin/install -c -m 644 gfsview.xml '/home/thoravml/local/share/mime/packages'
make[4]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view/desktop'
make[3]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view/desktop'
make[3]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view'
make[4]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view'

test -z "/home/thoravml/local/bin" || /bin/mkdir -p "/home/thoravml/local/bin"

  /bin/sh ../libtool   --mode=install /usr/bin/install -c gfsview2D gfsview3D '/home/thoravml/local/bin'
libtool: install: /usr/bin/install -c .libs/gfsview2D /home/thoravml/local/bin/gfsview2D
libtool: install: /usr/bin/install -c .libs/gfsview3D /home/thoravml/local/bin/gfsview3D

test -z "/home/thoravml/local/bin" || /bin/mkdir -p "/home/thoravml/local/bin"

 /usr/bin/install -c gfsview '/home/thoravml/local/bin'
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view'
make[3]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view'
make[2]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view'
make[1]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/view'
Making install in debian
make[1]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/debian'
make[2]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/debian'

make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.

make[2]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/debian'
make[1]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904/debian'
make[1]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904'
make[2]: Entering directory `/home/thoravml/install/20110905/gfsview-snapshot-110904'

make[2]: Nothing to be done for `install-exec-am'.

if test -d ./pixmaps; then \
      /bin/sh /home/thoravml/install/20110905/gfsview-snapshot-110904/install-sh -d /home/thoravml/local/share/gfsview/pixmaps; \
      for pixmap in ./pixmaps/*; do \
        if test -f $pixmap; then \
          /usr/bin/install -c -m 644 $pixmap /home/thoravml/local/share/gfsview/pixmaps; \
        fi \
      done \
    fi; \
    if test -d ./fonts; then \
      /bin/sh /home/thoravml/install/20110905/gfsview-snapshot-110904/install-sh -d /home/thoravml/local/share/gfsview/fonts; \
      for font in ./fonts/*; do \
        if test -f $font; then \
          /usr/bin/install -c -m 644 $font /home/thoravml/local/share/gfsview/fonts; \
        fi \
      done \
    fi
make[2]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904'
make[1]: Leaving directory `/home/thoravml/install/20110905/gfsview-snapshot-110904'"

2011/9/5 Stephane Popinet <s.po...@niwa.co.nz>

[Stephane Popinet]

> * I have tried also to do the installation without "--disable-mpi", but
> instead of "$ sudo make install" at the end, I have done "$ make install".
> The installation also finished in a similar way as with the option
> "--disable-mpi" (result at the end). I don't know why the "sudo" makes a
> difference.

Neither do I, it must be something peculiar to the way your system is
configured.

> * However, when I export in gnuplot format, the gnuplot files are different.

> ...
> The size of the new gnuplot file is approximately half the size of the
> previous version I had.

Yes, this is due to this patch:

2011-05-27 Stephane Popinet <popinet at users.sf.net>
* Isolines are now continuous (in 2D only)

> * However, generating the gnuplot files from the batch viewer (with the same
> gfv file) gives different results: the resolution is much lower. The script
> I am using is the following:
> (for k in `seq 0 1 9`; do
> if [ -e "file$k.gfs" ]; then
> cat file$k.gfs
> echo "Save file$k.gnu { format = Gnuplot }"
> fi
> done ) | gfsview-batch2D t.gfv
> Should it give the same result as with the interactive viewer? This would be
> very useful for me.

Yes it should. I will look at it.

cheers

Stephane

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[Marie-Jean Thoraval]

Dear Stephane,

I have some problems when I try to export as gnuplot format large files.
* I open a large file (644 Mb, maximum level = 16) with the interactive viewer and a gfv file (option res = 1 in the "View" section). This gfv file shows the full result (zoomed out), with only isolines of T. Then I go to "File -> Save", write the name "test.gnu", and then press "Save". The viewer immediately closes. I get the following message on the terminal:

"
[5] 5434
[4]   Segmentation fault      gfsview2D file.gfs t.gfv
"

* The problem is not limited to one file, since it happens for different simulation files.
* I am able to save as ppm image from the same files (gfs and gfv).
* The computer I am using has 23.4 Gb of memory. I don't know if memory can be an issue here.
* When the file is open in the viewer, I go to "View -> Preferences -> Advanced -> Resolution", I put 0 instead of 1, and when I press "Enter", the viewer stops in a similar way.
* If I change the gfv file to "res = 0", the viewer opens and immediatly closes with the same error: "[2]+  Segmentation fault      gfsview2D file.gfs t.gfv"
* If I zoom in, I am able to save smaller regions of the same file. The largest file I was able to save was 3.2 Mb, containing 109296 lines. Then expending the view (zooming slightly out) results in the same error (closing the viewer and segmentation fault error message).
* I installed a previous version of the viewer (gfsview-snapshot-110122). I am able to save successfully the gnuplot file from the previous version with the same files (gfs and gfv). I am able to switch to the option "res = 0" without crashing the viewer (only very slow). It is also possible to save the gnuplot file with the "res = 0" option (gnuplot file is 7.3 Mb in the old format, 368688 lines).
* All the tests above are working fine when looking at smaller files with similar parameters with the new version of the viewer.

Therefore, it is a problem with this new version of the viewer (after gfsview-snapshot-110122), related to large files.
Thank you for your help. Please tell me if you need more information, or if you want one large file to reproduce the error.
Best regards,
Marie-Jean.

2011/9/7 Stephane Popinet <s.po...@niwa.co.nz>

[Stephane Popinet]

> "File -> Save", write the name "test.gnu", and then press "Save". The viewer
> immediately closes. I get the following message on the terminal:
> "
> [5] 5434
> [4]   Segmentation fault      gfsview2D file.gfs t.gfv

Could you please do the following:

% ulimit -c unlimited
% whatever is required to produce the "segmentation fault" above

then you should have a 'core' file in the directory (or 'core.14534'
where 14534 is the id of the process). This is what the 'ulimit'
command tells the system to do i.e. produce core files arbitrarily
big. The core file is a dump of the memory used by the process when it
crashed. This allows to do 'post-mortem debbuging'. The core file is
not human-readable but a debugger such as gdb will know what do with
it.

To use gdb do

% gdb gfsview2D core
gdb> where

which will tell you where in the code the 'segmentation fault'
occurred. Just cut and paste the gdb output and send it to me. thanks.

Stephane

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[Marie-Jean Thoraval]

I have followed the procedure you have described. It generates a core file but the size of the file is zero.

"
$ gdb gfsview2D core.7921
GNU gdb (GDB) Fedora (6.8.50.20090302-40.fc11)
Copyright (C) 2009 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
"/home/thoravml/core.7921" is not a core dump: File format not recognized
(gdb) where
No stack.
(gdb)
"

Thanks and regards,
Marie-Jean.

2011/9/13 Stephane Popinet <s.po...@niwa.co.nz>

[Stephane Popinet]

> I have followed the procedure you have described. It generates a core file
> but the size of the file is zero.

hmm, are you sure it is zero?

What does:

% ulimit -c

return?

[Marie-Jean Thoraval]

I have tried again. It returns again zero.
$ ulimit -c
returns "unlimited".

2011/9/14 Stephane Popinet <s.po...@niwa.co.nz>:

[Marie-Jean Thoraval]

The email below was too long, so I post a shorter version:

Dear Stephane,

I have just installed a virtual Ubuntu 10.04 to identify the problem above.
The problem is the same on this new installation (standard Ubuntu installation with the latest versions).
The procedure you gave now returns a result: the "core" file is 3.4G. I have tried to monitor the memory during the crash, and it always stays lower than 30%. It stays at 24.7% during some time, jumps above 28% just before the crash and then crashes.
"
$ gdb gfsview2D core
GNU gdb (GDB) 7.1-ubuntu
Copyright (C) 2010 Free Software Foundation, Inc.

License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.

This GDB was configured as "x86_64-linux-gnu".

For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...

Reading symbols from /usr/bin/gfsview2D...(no debugging symbols found)...done.
[New Thread 2381]

warning: Can't read pathname for load map: Input/output error.
Error while mapping shared library sections:
/tmp/gfsxxSgfM: No such file or directory.
Reading symbols from /usr/lib/libgfsgl2D.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libgfsgl2D.so.0
Reading symbols from /usr/lib/libgfs2D-1.3.so.2...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libgfs2D-1.3.so.2
Reading symbols from /usr/lib/libgts-0.7.so.5...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libgts-0.7.so.5
Reading symbols from /usr/lib/libftgl.so.2...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libftgl.so.2
Reading symbols from /usr/lib/libgtkglext-x11-1.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libgtkglext-x11-1.0.so.0
Reading symbols from /usr/lib/libgdkglext-x11-1.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libgdkglext-x11-1.0.so.0
Reading symbols from /usr/lib/libGLU.so.1...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libGLU.so.1
Reading symbols from /usr/lib/mesa/libGL.so.1...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/mesa/libGL.so.1
Reading symbols from /usr/lib/libXmu.so.6...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libXmu.so.6
Reading symbols from /usr/lib/libXt.so.6...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libXt.so.6
Reading symbols from /usr/lib/libSM.so.6...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libSM.so.6
Reading symbols from /usr/lib/libICE.so.6...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libICE.so.6
Reading symbols from /usr/lib/libgtk-x11-2.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libgtk-x11-2.0.so.0
Reading symbols from /usr/lib/libpangox-1.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libpangox-1.0.so.0
Reading symbols from /usr/lib/libX11.so.6...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libX11.so.6
Reading symbols from /usr/lib/libgdk-x11-2.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libgdk-x11-2.0.so.0
Reading symbols from /usr/lib/libatk-1.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libatk-1.0.so.0
Reading symbols from /usr/lib/libpangoft2-1.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libpangoft2-1.0.so.0
Reading symbols from /usr/lib/libgdk_pixbuf-2.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libgdk_pixbuf-2.0.so.0
Reading symbols from /lib/libm.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib/libm.so.6
Reading symbols from /usr/lib/libpangocairo-1.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libpangocairo-1.0.so.0
Reading symbols from /usr/lib/libcairo.so.2...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libcairo.so.2
...
Reading symbols from /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
Reading symbols from /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
Reading symbols from /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
Reading symbols from /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
Reading symbols from /usr/lib/openmpi/lib/openmpi/mca_dpm_orte.so...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/openmpi/lib/openmpi/mca_dpm_orte.so
Reading symbols from /usr/lib/dri/swrast_dri.so...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/dri/swrast_dri.so
Reading symbols from /usr/lib/gtk-2.0/2.10.0/loaders/libpixbufloader-png.so...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/gtk-2.0/2.10.0/loaders/libpixbufloader-png.so
Reading symbols from /usr/lib/pango/1.6.0/modules/pango-basic-fc.so...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/pango/1.6.0/modules/pango-basic-fc.so
Symbol file not found for /tmp/gfsxxSgfM
Core was generated by `gfsview2D gouttes-bin-0.003.gfs t.gfv'.
Program terminated with signal 11, Segmentation fault.
#0  0x00007f98c4fbf745 in ?? () from /usr/lib/libgfs2D-1.3.so.2
(gdb) where
#0  0x00007f98c4fbf745 in ?? () from /usr/lib/libgfs2D-1.3.so.2
#1  0x00007f98c4fbfaed in ?? () from /usr/lib/libgfs2D-1.3.so.2
#2  0x00007f98c4fbfaed in ?? () from /usr/lib/libgfs2D-1.3.so.2
#3  0x00007f98c4fbfaed in ?? () from /usr/lib/libgfs2D-1.3.so.2
#4  0x00007f98c4fbfe05 in gfs_cell_corner_interpolator () from /usr/lib/libgfs2D-1.3.so.2
#5  0x00007f98c4fc0133 in gfs_cell_corner_value () from /usr/lib/libgfs2D-1.3.so.2
#6  0x00007f98c5262195 in ?? () from /usr/lib/libgfsgl2D.so.0
#7  0x00007f98c52622ac in ?? () from /usr/lib/libgfsgl2D.so.0
#8  0x00007f98c5262444 in ?? () from /usr/lib/libgfsgl2D.so.0
#9  0x00007f98c5262444 in ?? () from /usr/lib/libgfsgl2D.so.0
#10 0x00007f98c5262444 in ?? () from /usr/lib/libgfsgl2D.so.0
#11 0x00007f98c5262444 in ?? () from /usr/lib/libgfsgl2D.so.0
#12 0x00007f98c5262444 in ?? () from /usr/lib/libgfsgl2D.so.0
#13 0x00007f98c5262444 in ?? () from /usr/lib/libgfsgl2D.so.0
#14 0x00007f98c5262444 in ?? () from /usr/lib/libgfsgl2D.so.0
#15 0x00007f98c5262444 in ?? () from /usr/lib/libgfsgl2D.so.0
#16 0x00007f98c5262444 in ?? () from /usr/lib/libgfsgl2D.so.0
#17 0x00007f98c5262444 in ?? () from /usr/lib/libgfsgl2D.so.0
#18 0x00007f98c5262444 in ?? () from /usr/lib/libgfsgl2D.so.0
...
---Type <return> to continue, or q <return> to quit---
..."

It is the same as far I have seen.

Best regards,
Marie-Jean.

[Stephane Popinet]

Hi Marie-Jean,

>> Reading symbols from /usr/bin/gfsview2D...(no debugging symbols
>> found)...done.

There is a problem there. How did you install GfsView? as you can see
it does not include "debugging symbols" i.e. symbols indicating the
correspondance between the executable code and the source code. This
explains why you get lines like:

#0 0x00007f98c4fbf745 in ?? () from /usr/lib/libgfs2D-1.3.so.2

where "??" should contain the position in the source code where the
call occured (this is what we are after).

To fix this you need to install gerris and gfsview from source (which
will include the "-g" option of the compiler which will generate
executables with debugging symbols).

cheers

[Marie-Jean Thoraval]

Dear Stephane,

Yes, the previous result was for the gerris installation described here: http://gfs.sourceforge.net/wiki/index.php/Ubuntu/Debian_installation.
I have made a new local installation on the virtual Ubuntu 10.04 following: http://gfs.sourceforge.net/wiki/index.php/Installing_from_source.

The local installation also shows the same problem ("Segmentation fault"):

"
$ gdb gfsview2D core
GNU gdb (GDB) 7.1-ubuntu
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...

Reading symbols from /home/thoravml/local/bin/gfsview2D...done.
[New Thread 22334]

warning: Can't read pathname for load map: Input/output error.
Error while mapping shared library sections:

/tmp/gfskh2pQF: No such file or directory.
Reading symbols from /home/thoravml/local/lib/libgfsgl2D.so.0...done.
Loaded symbols for /home/thoravml/local/lib/libgfsgl2D.so.0
Reading symbols from /home/thoravml/local/lib/libgfs2D-1.3.so.2...done.
Loaded symbols for /home/thoravml/local/lib/libgfs2D-1.3.so.2
Reading symbols from /home/thoravml/local/lib/libgts-0.7.so.5...done.
Loaded symbols for /home/thoravml/local/lib/libgts-0.7.so.5

Reading symbols from /usr/lib/libftgl.so.2...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libftgl.so.2
Reading symbols from /usr/lib/libgtkglext-x11-1.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libgtkglext-x11-1.0.so.0
Reading symbols from /usr/lib/libgdkglext-x11-1.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/libgdkglext-x11-1.0.so.0

Reading symbols from /lib/libpng12.so.0...(no debugging symbols found)...done.
Loaded symbols for /lib/libpng12.so.0
...

Reading symbols from /usr/lib/gtk-2.0/2.10.0/loaders/libpixbufloader-png.so...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/gtk-2.0/2.10.0/loaders/libpixbufloader-png.so
Reading symbols from /usr/lib/pango/1.6.0/modules/pango-basic-fc.so...(no debugging symbols found)...done.
Loaded symbols for /usr/lib/pango/1.6.0/modules/pango-basic-fc.so

Symbol file not found for /tmp/gfskh2pQF

Core was generated by `gfsview2D gouttes-bin-0.003.gfs t.gfv'.
Program terminated with signal 11, Segmentation fault.

#0  do_path (cell=0x3f242ba8, i=2, n=0x7ffffe0e44b0, d=0x7f06162b8728, max_level=-1, centered=0, inter=0x7ffffe0e4550) at fluid.c:2895
2895        d1[l] = path[i][j][l] < 0 ? FTT_OPPOSITE_DIRECTION (d[- path[i][j][l] - 1]) :
(gdb) where
#0  do_path (cell=0x3f242ba8, i=2, n=0x7ffffe0e44b0, d=0x7f06162b8728, max_level=-1, centered=0, inter=0x7ffffe0e4550) at fluid.c:2895
#1  0x00007f0615e082ad in do_path (cell=<value optimized out>, i=<value optimized out>, n=0x7ffffe0e44b0, d=0x7f06162b8728, max_level=<value optimized out>, centered=<value optimized out>, inter=0x7ffffe0e4550) at fluid.c:2903
#2  0x00007f0615e082ad in do_path (cell=<value optimized out>, i=<value optimized out>, n=0x7ffffe0e44b0, d=0x7f06162b8728, max_level=<value optimized out>, centered=<value optimized out>, inter=0x7ffffe0e4550) at fluid.c:2903
#3  0x00007f0615e082ad in do_path (cell=<value optimized out>, i=<value optimized out>, n=0x7ffffe0e44b0, d=0x7f06162b8728, max_level=<value optimized out>, centered=<value optimized out>, inter=0x7ffffe0e4550) at fluid.c:2903
#4  0x00007f0615e085c5 in gfs_cell_corner_interpolator (cell=0x3f242b68, d=0x7f06162b8728, max_level=-1, centered=0, inter=0x7ffffe0e4550) at fluid.c:2963
#5  0x00007f0615e088f3 in gfs_cell_corner_value (cell=0x3f242ba8, d=0x2, v=0x1c81f30, max_level=-32619344) at fluid.c:3008
#6  0x00007f06160aba35 in vertex_isoline (cell=0x3f242b68, d=0x7f06162b8728, gl=0xbcc64300, v=0x7ffffe0e4720) at gfsgl2D.h:690
#7  0x00007f06160abb4c in follow_isoline (cell=0x3f242b68, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:725
#8  0x00007f06160abce4 in follow_isoline (cell=0x3f242ba8, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
#9  0x00007f06160abce4 in follow_isoline (cell=0x3f243288, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
#10 0x00007f06160abce4 in follow_isoline (cell=0x3f2432c8, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
#11 0x00007f06160abce4 in follow_isoline (cell=0x3f243778, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
#12 0x00007f06160abce4 in follow_isoline (cell=0x3f2437b8, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
#13 0x00007f06160abce4 in follow_isoline (cell=0x3f2440c8, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
#14 0x00007f06160abce4 in follow_isoline (cell=0x3f244108, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
#15 0x00007f06160abce4 in follow_isoline (cell=0x3f2445b8, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
...
"

I have now the lines:
"Reading symbols from /home/thoravml/local/bin/gfsview2D...done." and
"Reading symbols from /home/thoravml/local/lib/libgfs2D-1.3.so.2...done."

Best regards,
Marie-Jean.

2011/9/15 Stephane Popinet <s.po...@niwa.co.nz>

[Stephane Popinet]

> I have now the lines:
> "Reading symbols from /home/thoravml/local/bin/gfsview2D...done." and
> "Reading symbols from /home/thoravml/local/lib/libgfs2D-1.3.so.2...done."

yes and also:

#0 do_path (cell=0x3f242ba8, i=2, n=0x7ffffe0e44b0, d=0x7f06162b8728,
max_level=-1, centered=0, inter=0x7ffffe0e4550) at fluid.c:2895
2895 d1[l] = path[i][j][l] < 0 ? FTT_OPPOSITE_DIRECTION (d[-
path[i][j][l] - 1]) :

which tells you that the "segmentation fault" occurred at line 2895 of
file fluid.c. These lines are also important:

#9 0x00007f06160abce4 in follow_isoline (cell=0x3f243288, start=0,
gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756

how many lines with follow_isoline do you have?

cheers

Stephane

------------------------------------------------------------------------------
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[Marie-Jean Thoraval]

Here is the end of the output of "where":
"
#50359 0x00007f06160abce4 in follow_isoline (cell=0x155a2908, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
#50360 0x00007f06160abce4 in follow_isoline (cell=0x155a2948, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
#50361 0x00007f06160abce4 in follow_isoline (cell=0x155a3188, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
#50362 0x00007f06160abce4 in follow_isoline (cell=0x155a31c8, start=0, gl=0xbcc64300, val=<value optimized out>) at gfsgl2D.h:756
#50363 0x00007f06160b35a3 in gl_boundary_isoline (cell=0x155a31c8, gl=0xbcc64300) at gfsgl2D.h:835
#50364 0x00007f06160b227a in cell_traverse_visible_condition_no_check (root=0x155a31c8, par=0x7ffffeae1e90) at gfsgl.c:540
#50365 0x00007f06160b2265 in cell_traverse_visible_condition_no_check (root=<value optimized out>, par=0x7ffffeae1e90) at gfsgl.c:548
#50366 0x00007f06160b2265 in cell_traverse_visible_condition_no_check (root=<value optimized out>, par=0x7ffffeae1e90) at gfsgl.c:548
#50367 0x00007f06160b2265 in cell_traverse_visible_condition_no_check (root=<value optimized out>, par=0x7ffffeae1e90) at gfsgl.c:548
#50368 0x00007f06160b2265 in cell_traverse_visible_condition_no_check (root=<value optimized out>, par=0x7ffffeae1e90) at gfsgl.c:548
#50369 0x00007f06160b2265 in cell_traverse_visible_condition_no_check (root=<value optimized out>, par=0x7ffffeae1e90) at gfsgl.c:548
#50370 0x00007f06160b2265 in cell_traverse_visible_condition_no_check (root=<value optimized out>, par=0x7ffffeae1e90) at gfsgl.c:548
#50371 0x00007f06160b2265 in cell_traverse_visible_condition_no_check (root=<value optimized out>, par=0x7ffffeae1e90) at gfsgl.c:548
#50372 0x00007f06160b2265 in cell_traverse_visible_condition_no_check (root=<value optimized out>, par=0x7ffffeae1e90) at gfsgl.c:548
#50373 0x00007f06160b2265 in cell_traverse_visible_condition_no_check (root=<value optimized out>, par=0x7ffffeae1e90) at gfsgl.c:548
#50374 0x00007f06160b2470 in cell_traverse_visible_condition (root=0x149addf0, par=0x7ffffeae1e90) at gfsgl.c:571
#50375 0x00007f0615e2fd63 in domain_foreach (c=<value optimized out>, func=0x7f06160b2480 <box_traverse_visible_condition>, data=0x7ffffeae1e90) at domain.c:580
#50376 0x00007f06160a5012 in gfs_gl_cell_traverse_visible_condition (gl=<value optimized out>, f=<value optimized out>, condition=<value optimized out>,
    datacon=0x7f06162b8728, func=0xffffffff, data=0x0) at gfsgl.c:620



#50377 0x00007f06160a50ea in gfs_gl_cell_traverse_visible_iso (gl=0x3f242ba8, f=0x2, min=<value optimized out>, max=<value optimized out>, level=0,
    func=0xffffffff, data=0x0) at gfsgl.c:2293
#50378 0x00007f06160ab623 in gl_isoline_draw (gl=0xbcc64300, f=0x7ffffeae1fa0) at gfsgl2D.h:870
#50379 0x0000000000438c46 in gfk_gl_view_draw (view=<value optimized out>, format=<value optimized out>) at gfkgl.c:4093
#50380 0x000000000042d4a1 in expose (widget=<value optimized out>, event=<value optimized out>) at main.c:154
#50381 0x00007f0613bfa178 in ?? () from /usr/lib/libgtk-x11-2.0.so.0
#50382 0x00007f06117445de in g_closure_invoke () from /usr/lib/libgobject-2.0.so.0
#50383 0x00007f0611758598 in ?? () from /usr/lib/libgobject-2.0.so.0

---Type <return> to continue, or q <return> to quit---

#50384 0x00007f06117598b9 in g_signal_emit_valist () from /usr/lib/libgobject-2.0.so.0
#50385 0x00007f061175a033 in g_signal_emit () from /usr/lib/libgobject-2.0.so.0
#50386 0x00007f0613d110bf in ?? () from /usr/lib/libgtk-x11-2.0.so.0
#50387 0x00007f0613bf38a1 in gtk_main_do_event () from /usr/lib/libgtk-x11-2.0.so.0
#50388 0x00007f061330b94a in ?? () from /usr/lib/libgdk-x11-2.0.so.0
#50389 0x00007f06133083db in ?? () from /usr/lib/libgdk-x11-2.0.so.0
#50390 0x00007f061330a251 in gdk_window_process_all_updates () from /usr/lib/libgdk-x11-2.0.so.0
#50391 0x00007f0613b75591 in ?? () from /usr/lib/libgtk-x11-2.0.so.0
#50392 0x00007f06132e6db6 in ?? () from /usr/lib/libgdk-x11-2.0.so.0
#50393 0x00007f0610e868c2 in g_main_context_dispatch () from /lib/libglib-2.0.so.0
#50394 0x00007f0610e8a748 in ?? () from /lib/libglib-2.0.so.0
#50395 0x00007f0610e8ac55 in g_main_loop_run () from /lib/libglib-2.0.so.0
#50396 0x00007f0613bf3bb7 in gtk_main () from /usr/lib/libgtk-x11-2.0.so.0
#50397 0x000000000042c5f5 in main (argc=3, argv=0x7ffffeae2ba8) at main.c:763
(gdb)
"

Therefore, 50356 lines with "follow_isoline".

2011/9/15 Stephane Popinet <s.po...@niwa.co.nz>

[Stephane Popinet]

> Therefore, 50356 lines with "follow_isoline".

OK that explains the crash then. follow_isoline() is calling itself
recursively 50356 times and the stack runs out of memory.

To check that this is the case, try:

% ulimit -s

on my system I get 8192

then do

% ulimit -s 4096

and re-crash the code. If the hypothesis above is correct the code
should now crash after only 50356 / 2 calls to follow_isoline().

There are mostly two reasons this could happen:

1- you do really have an isoline which crosses (more than) 50356
cells. In this case, the algorithm needs to be modified to be able to
handle isolines which cross more than ~50000 cells (this can vary
depending on the size of the memory stack on different systems).

2- there is a bug in the algorithm and it loops endlessly around the
same (closed) isoline. This case should be handled properly by the
current algorithm but there could be a bug.

What do you think? Is 1- plausible for your particular simulation file?

[Marie-Jean Thoraval]

Dear Stephane,

% ulimit -s
returns also 8192
I have done % ulimit -s 4096.
After recrashing the code, I don't get 50356 / 2 calls to follow_isoline() but 30181.
A rough estimate of the number of cells crossing the interface gives 110000 > 50000. A simulation at lower refinement starts at around 55000. The viewer do not crash at the beginning of the computation, but later when the interface length increases. So the hypothesis 1 sounds consistent.

Best regards,
Marie-Jean.

2011/9/16 Stephane Popinet <s.po...@niwa.co.nz>

[Stephane Popinet]

Hi Marie-Jean,

Could you please apply the attached patch to a clean checkout of gfsview i.e.

% darcs get http://gerris.dalembert.upmc.fr/darcs/gfsview-stable
% cd gfsview-stable
% darcs apply /tmp/isopatch
% sh autogen.sh --prefix=...
% make && make install

and retry to generate very long isolines. The patch removes the
useless function recursion and should fix the problem. Please also
check that the isolines generated look OK.

Once I get your confirmation, I will push the patch to gfsview-devel.

cheers

Stephane

[Marie-Jean Thoraval]

Dear Stephane,

I have followed your instruction and the patch is working.
I have made a first installation with darcs without the patch, and I had the segmentation fault error again.
Then I added the patch and installed again. I didn't have the error anymore.

The isolines look ok. I have tried to export in gnuplot format to plot it, and it also looks good. The file generated is 3.6M.
However, the other issue still appears. If I do the command "$ gerris2D -e "GfsOutputView test.gnu { format = Gnuplot } t.gfv" file.gfs > /dev/null", it still gives a different result than with the interactive viewer (27K instead of 3.6M). I don't know if this is related to gfsview.

Thank you very much for fixing this problem.
Best regards,
Marie-Jean.

2011/9/19 Stephane Popinet <s.po...@niwa.co.nz>

[Stephane Popinet]

> I have followed your instruction and the patch is working.
> I have made a first installation with darcs without the patch, and I had the
> segmentation fault error again.
> Then I added the patch and installed again. I didn't have the error anymore.

Great, thanks for your help in tracking the bug.

> However, the other issue still appears. If I do the command "$ gerris2D -e
> "GfsOutputView test.gnu { format = Gnuplot } t.gfv" file.gfs > /dev/null",
> it still gives a different result than with the interactive viewer (27K
> instead of 3.6M). I don't know if this is related to gfsview.

Yes, this is a different bug. I can reproduce it here. I will have a look.

cheers

Stephane

------------------------------------------------------------------------------
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[Marie-Jean Thoraval]

Dear Stephane,

When I download the gfsview tarball from http://gfs.sourceforge.net/wiki/index.php/Download, I get gfsview-snapshot-110913.
The fix is added on the log at 110919. Is the gfsview tarball updated?

Best regards,
Marie-Jean.

2011/9/19 Stephane Popinet <s.po...@niwa.co.nz>

> I have followed your instruction and the patch is working.

[Stephane Popinet]

Hi Marie-Jean,

> When I download the gfsview tarball from
> http://gfs.sourceforge.net/wiki/index.php/Download, I get
> gfsview-snapshot-110913.
> The fix is added on the log at 110919. Is the gfsview tarball updated?

To make sure, you can look at the 'ChangeLog' file in the tarball. As
you can see, the recent patch is not in this tarball. So the tarball
has not been updated (this should be done automatically). I will check
what happened. Thanks for reporting the problem.

Stephane

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2