intro story D-Flow FM

 

D-Flow Flexible Mesh

D-Flow Flexible Mesh (D-Flow FM) is the new software engine for hydrodynamical simulations on unstructured grids in 1D-2D-3D. Together with the familiar curvilinear meshes from Delft3D 4, the unstructured grid can consist of triangles, pentagons (etc.) and 1D channel networks, all in one single mesh. It combines proven technology from the hydrodynamic engines of Delft3D 4 and SOBEK 2 and adds flexible administration, resulting in:

  • Easier 1D-2D-3D model coupling, intuitive setup of boundary conditions and meteorological forcings (amongst others).
  • More flexible 2D gridding in delta regions, river junctions, harbours, intertidal flats and more.
  • High performance by smart use of multicore architectures, and grid computing clusters.
An overview of the current developments can be found here.
 
The D-Flow FM - team would be delighted if you would participate in discussions on the generation of meshes, the specification of boundary conditions, the running of computations, and all kinds of other relevant topics. Feel free to share your smart questions and/or brilliant solutions! 

 

=======================================================
We have launched a new website (still under construction so expect continuous improvements) and a new forum dedicated to Delft3D Flexible Mesh.

Please follow this link to the new forum: 
/web/delft3dfm/forum

Post your questions, issues, suggestions, difficulties related to our Delft3D Flexible Mesh Suite on the new forum.

=======================================================

** PLEASE TAG YOUR POST! **

 

 

Sub groups
D-Flow Flexible Mesh
DELWAQ
Cohesive sediments & muddy systems

 


Message Boards

Flow only Bug? "glibc detected"..

Shawn Harrison, modified 7 Years ago.

Flow only Bug? "glibc detected"..

Padawan Posts: 70 Join Date: 6/25/12 Recent Posts
I have compiled on linux (Ubuntu 11.10 32b) the D3D v5.00.06.1662 trunk..

It works great for most things.. However, I cannot get it to run a simple FLOW model. It works fine for FLOW-WAVE coupling, Morph, and many other example problems included. It does not work for the 01_standard example. Also, I cannot get it to run any simple FLOW only model.

The error that is reported is:


   Starting Delft3D-FLOW computation ...
Executing "/opt/delft3d/intel/flow/bin/d_hydro.exe TMP_config_flow2d3d_13629.xml" ...
--------------------------------------------------------------------------------
       Deltares, FLOW2D3D Version 5.00.06.1662, Jun 29 2012, 17:14:35
       libflow2d3d.so entry Flow2D3D::Run
--------------------------------------------------------------------------------

Part I    - Initialisation Time Dep. Data module...   
            runid : f34
Part II   - Creating intermediate files...            
Part III  - Initialisation of the Execution module... 
Part IV   - Reading complete MD-file...                     
Part V    - Initialisation & checking input...             
Part VI   - Initialisation & checking second part...       
Part VII  - Initialisation output...                        

ERROR: *** glibc detected *** /opt/delft3d/intel/flow/bin/d_hydro.exe: free(): invalid next size (fast): 0x09ea3548 ***

Then it dumps a bunch of backtrace and memory map lines to the terminal.

Any ideas what might be wrong? Do I need to recompile a more recent version?
Could it be possible that the 01_standard example mdf file has an error which keeps it from launching?

Thanks,
Shawn
Qinghua Ye, modified 7 Years ago.

RE: Flow only Bug? "glibc detected"..

Jedi Council Member Posts: 612 Join Date: 3/2/11 Recent Posts
Hi, Shawn,

I am trying to reproduce the problem. At the same time, if you could update your code to latest and try it, it would be nice.

Regards,

Qinghua
Shawn Harrison, modified 7 Years ago.

RE: Flow only Bug? "glibc detected"..

Padawan Posts: 70 Join Date: 6/25/12 Recent Posts
Hi Qinghua,
Thank you for your reply. Ok.. so I just updated to the latest trunk (1698) and tried running the simple FLOW example (examples/01_standard/). Again.. the same error. See below.

BTW, this version of the trunk was way smoother to prepare-configure-make-install.. No problems with the dolcli --> don't need to erase " src/dolcli \ src/dolprint" in trunk/src/utils_lgpl_delftonline/Makefile.am.

Thanks.



shawn@GRIZZLE:~/delft3trunk/examples/01_standard$ deltares_hydro.tcl config_flow2d3d.ini

Executing "/usr/local/bin/d_hydro.exe TMP_config_flow2d3d_29065.xml" ...
--------------------------------------------------------------------------------
       Deltares, FLOW2D3D Version 5.00.07.1698, Jul 12 2012, 11:09:38
       libflow2d3d.so entry Flow2D3D::Run
--------------------------------------------------------------------------------

Part I    - Initialisation Time Dep. Data module...   
            runid : f34
Part II   - Creating intermediate files...            
Part III  - Initialisation of the Execution module... 
Part IV   - Reading complete MD-file...                     
Part V    - Initialisation & checking input...             
Part VI   - Initialisation & checking second part...       
Part VII  - Initialisation output...                        
*** glibc detected *** /usr/local/bin/d_hydro.exe: free(): invalid next size (fast): 0x08d33d88 ***
======= Backtrace: =========
/lib/i386-linux-gnu/libc.so.6(+0x6ff22)[0x17ff22]
/lib/i386-linux-gnu/libc.so.6(+0x70bc2)[0x180bc2]
/lib/i386-linux-gnu/libc.so.6(cfree+0x6d)[0x183cad]
/usr/local/lib/libflow2d3d.so(__d3dpublish_MOD_publishgdp+0x114d)[0x1339a4d]
/usr/local/lib/libflow2d3d.so(tricom_init_+0x1767)[0x1017977]
/usr/local/lib/libflow2d3d.so(__mod_trisim_MOD_trisim_init+0x598)[0x101f488]
/usr/local/lib/libflow2d3d.so(trisim_+0xb4)[0x101ea34]
/usr/local/lib/libflow2d3d.so(_ZN8Flow2D3D3RunEv+0x19f)[0xfd8dff]
/usr/local/bin/d_hydro.exe[0x8049f03]
/usr/local/bin/d_hydro.exe[0x804925c]
/lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x129113]
/usr/local/bin/d_hydro.exe[0x8049391]
======= Memory map: ========
00110000-00288000 r-xp 00000000 08:01 18874520   /lib/i386-linux-gnu/libc-2.13.so
00288000-0028a000 r--p 00178000 08:01 18874520   /lib/i386-linux-gnu/libc-2.13.so
0028a000-0028b000 rw-p 0017a000 08:01 18874520   /lib/i386-linux-gnu/libc-2.13.so
0028b000-0028e000 rw-p 00000000 00:00 0
0028e000-0038d000 r-xp 00000000 08:01 29368553   /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0
0038d000-0038e000 r--p 000fe000 08:01 29368553   /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0
0038e000-0038f000 rw-p 000ff000 08:01 29368553   /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0
0038f000-00390000 rw-p 00000000 00:00 0
00390000-00402000 r-xp 00000000 08:01 29365598   /usr/lib/i386-linux-gnu/libquadmath.so.0.0.0
00402000-00403000 r--p 00071000 08:01 29365598   /usr/lib/i386-linux-gnu/libquadmath.so.0.0.0
00403000-00404000 rw-p 00072000 08:01 29365598   /usr/lib/i386-linux-gnu/libquadmath.so.0.0.0
004a5000-004c3000 r-xp 00000000 08:01 18874517   /lib/i386-linux-gnu/ld-2.13.so
004c3000-004c4000 r--p 0001d000 08:01 18874517   /lib/i386-linux-gnu/ld-2.13.so
004c4000-004c5000 rw-p 0001e000 08:01 18874517   /lib/i386-linux-gnu/ld-2.13.so
00785000-007ab000 r-xp 00000000 08:01 18875317   /lib/i386-linux-gnu/libexpat.so.1.5.2
007ab000-007ac000 ---p 00026000 08:01 18875317   /lib/i386-linux-gnu/libexpat.so.1.5.2
007ac000-007ae000 r--p 00026000 08:01 18875317   /lib/i386-linux-gnu/libexpat.so.1.5.2
007ae000-007af000 rw-p 00028000 08:01 18875317   /lib/i386-linux-gnu/libexpat.so.1.5.2
00a06000-00a22000 r-xp 00000000 08:01 18875322   /lib/i386-linux-gnu/libgcc_s.so.1
00a22000-00a23000 r--p 0001b000 08:01 18875322   /lib/i386-linux-gnu/libgcc_s.so.1
00a23000-00a24000 rw-p 0001c000 08:01 18875322   /lib/i386-linux-gnu/libgcc_s.so.1
00a76000-00a89000 r-xp 00000000 08:01 29754160   /usr/local/lib/libDelftOnline.so.0.0.0
00a89000-00a8a000 r--p 00013000 08:01 29754160   /usr/local/lib/libDelftOnline.so.0.0.0
00a8a000-00a8b000 rw-p 00014000 08:01 29754160   /usr/local/lib/libDelftOnline.so.0.0.0
00ac6000-00ba4000 r-xp 00000000 08:01 29365627   /usr/lib/i386-linux-gnu/libstdc++.so.6.0.16
00ba4000-00ba5000 ---p 000de000 08:01 29365627   /usr/lib/i386-linux-gnu/libstdc++.so.6.0.16
00ba5000-00ba9000 r--p 000de000 08:01 29365627   /usr/lib/i386-linux-gnu/libstdc++.so.6.0.16
00ba9000-00baa000 rw-p 000e2000 08:01 29365627   /usr/lib/i386-linux-gnu/libstdc++.so.6.0.16
00baa000-00bb1000 rw-p 00000000 00:00 0
00db7000-00ddf000 r-xp 00000000 08:01 18874524   /lib/i386-linux-gnu/libm-2.13.so
00ddf000-00de0000 r--p 00028000 08:01 18874524   /lib/i386-linux-gnu/libm-2.13.so
00de0000-00de1000 rw-p 00029000 08:01 18874524   /lib/i386-linux-gnu/libm-2.13.so
00e02000-00e19000 r-xp 00000000 08:01 18878445   /lib/i386-linux-gnu/libpthread-2.13.so
00e19000-00e1a000 r--p 00016000 08:01 18878445   /lib/i386-linux-gnu/libpthread-2.13.so
00e1a000-00e1b000 rw-p 00017000 08:01 18878445   /lib/i386-linux-gnu/libpthread-2.13.so
00e1b000-00e1d000 rw-p 00000000 00:00 0
00e2e000-00e31000 r-xp 00000000 08:01 18874523   /lib/i386-linux-gnu/libdl-2.13.so
00e31000-00e32000 r--p 00002000 08:01 18874523   /lib/i386-linux-gnu/libdl-2.13.so
00e32000-00e33000 rw-p 00003000 08:01 18874523   /lib/i386-linux-gnu/libdl-2.13.so
00f8f000-00f90000 r-xp 00000000 00:00 0          [vdso]
00f90000-0149e000 r-xp 00000000 08:01 29761378   /usr/local/lib/libflow2d3d.so.0.0.0
0149e000-014a3000 r--p 0050d000 08:01 29761378   /usr/local/lib/libflow2d3d.so.0.0.0
014a3000-014ac000 rw-p 00512000 08:01 29761378   /usr/local/lib/libflow2d3d.so.0.0.0
014ac000-03ae9000 rw-p 00000000 00:00 0
08048000-0804d000 r-xp 00000000 08:01 29761394   /usr/local/bin/d_hydro.exe
0804d000-0804e000 r--p 00004000 08:01 29761394   /usr/local/bin/d_hydro.exe
0804e000-0804f000 rw-p 00005000 08:01 29761394   /usr/local/bin/d_hydro.exe
0804f000-08067000 rw-p 00000000 00:00 0
08d32000-0913e000 rw-p 00000000 00:00 0          [heap]
b7600000-b7621000 rw-p 00000000 00:00 0
b7621000-b7700000 ---p 00000000 00:00 0
b7736000-b7775000 rw-p 00000000 00:00 0
b7786000-b7788000 rw-p 00000000 00:00 0
bfb71000-bfb92000 rw-p 00000000 00:00 0          [stack]

ERROR: child killed: SIGABRT
       - Starting "d_hydro.exe" may give more information:
         - Run "deltares_hydro.exe <INI-inputfile> -keepXML".
         - Run "d_hydro.exe TMP_config_flow2d3d_<processId>.xml".
Qinghua Ye, modified 7 Years ago.

RE: Flow only Bug? "glibc detected".. (Answer)

Jedi Council Member Posts: 612 Join Date: 3/2/11 Recent Posts
dear Shawn,

We don't have this problem with our Redhat santos system. So we cannot reproduce the error.

However, we checked the code based the error message you provided and got the following file updated. Would you do the following:

1. download the attached d3dpublish.f90.
2. replace this new version in your download dir and compile again.
3. rerun the examples again.

Let us know the results. Thanks,

Qinghua
Shawn Harrison, modified 7 Years ago.

RE: Flow only Bug? "glibc detected"..

Padawan Posts: 70 Join Date: 6/25/12 Recent Posts
That worked great Qinghua!
The FLOW model example now works.. (examples/01_standard/)

Proof attached below:

For some reason, the FLOW-WAVE example doesn't run.. The wave model is never launched. I will look into it - I'm not sure if it is some problem with my install (e.g. library paths) or the TRUNK version.

Thanks Heaps!
Shawn





shawn@GRIZZLE:~/delft3trunk/examples/01_standard$ deltares_hydro.tcl config_flow2d3d.ini

Executing "/usr/local/bin/d_hydro.exe TMP_config_flow2d3d_28163.xml" ...
--------------------------------------------------------------------------------
       Deltares, FLOW2D3D Version 5.00.07.1698, Jul 12 2012, 14:22:23
       libflow2d3d.so entry Flow2D3D::Run
--------------------------------------------------------------------------------

Part I    - Initialisation Time Dep. Data module...   
            runid : f34
Part II   - Creating intermediate files...            
Part III  - Initialisation of the Execution module... 
Part IV   - Reading complete MD-file...                     
Part V    - Initialisation & checking input...             
Part VI   - Initialisation & checking second part...       
Part VII  - Initialisation output...                        
Part VIII - Start Simulation...                            

  Time to finish   0s,    0.0% completed, time steps left  300
  Time to finish   1s,    0.3% completed, time steps left  299
  Time to finish   1s,    0.7% completed, time steps left  298
  Time to finish   1s,    1.0% completed, time steps left  297
...
  Time to finish   0s,   98.3% completed, time steps left  5
  Time to finish   0s,   98.7% completed, time steps left  4
  Time to finish   0s,   99.0% completed, time steps left  3
  Time to finish   0s,   99.3% completed, time steps left  2
  Time to finish   0s,   99.7% completed, time steps left  1


------------------------------------------------------------------------------
  FINISHED    Delft3D-FLOW
              runid      : f34
              date, time : 2012-07-12, 14:27:23
    0 errors and     0 warnings
returning to main program from domain f34
------------------------------------------------------------------------------
D_Hydro [1342096043.796822] <anonymous> >> d_hydro shutting down normally
Shawn Harrison, modified 7 Years ago.

RE: Flow only Bug? "glibc detected"..

Padawan Posts: 70 Join Date: 6/25/12 Recent Posts
For some reason, the FLOW-WAVE example doesn't run.. The wave model is never launched. I will look into it - I'm not sure if it is some problem with my install (e.g. library paths) or the TRUNK version.


Actually, If I put the binaries into the GUI installation and use from the GUI, then the FLOW-WAVE example works..