[Helyx OS] Helyx-OS (GUI for SnappyHexMesh

wyldckat · September 15, 2012, 10:51

@Stefano: Mmm... OK, this was spotted sometime ago, where it couldn't find "libmpi.so.0". Now it complains about "libmpi.so.1"

Try step #5:

Quote:

Originally Posted by http://sourceforge.net/p/helyx-os/wiki/DownloadAndInstallation/

If you receive an error loading VTK libraries, with the accompanying

Code:

libmpi.so.0: cannot open shared object file: No such file or directory

then this error can be fixed by

Code:

ln -s $MPI_ARCH_PATH/lib/libmpi.so $MPI_ARCH_PATH/lib/libmpi.so.0

and in some, the 64 bit distribution will require instead

Code:

ln -s $MPI_ARCH_PATH/lib64/libmpi.so $MPI_ARCH_PATH/lib64/libmpi.so.0

But instead of "libmpi.so.0", use "libmpi.so.1".

Best regards,
Bruno

stez · September 15, 2012, 12:47

Ok now libraries works, but it still can't open STL files, always the same error.
So I tried to generate the mesh with the older version, import it in the newer and run a simulation (I was looking for a working "rotating wall" simulation).
It generates wrong boundary conditions, "omega" should be "constant" instead of "uniform", so it gives error.
Since the error show up after some seconds, I tried the trick to be faster than the solver to modify the "0/U" file before it could read that field, and then it works (with simpleFoam), but it is not a good way to get it work.
I tried the same trick with DES but then it gives other errors with some patch, that I can't understand.

I have looked into HelyxOS dictData folder to see if there was some dict containing the wrong "omega" definition and fix it, but I didn't find any

wyldckat · September 16, 2012, 04:50

Hi Stefano,

Quote:

Originally Posted by stez

Ok now libraries works, but it still can't open STL files, always the same error.

I went back to your other posts and I can't figure it out... what is the exact error message you're getting?

Because, AFAIK, most of the other problems you're having should be fixed in the current version! At least from what I briefly saw in the bug reports.

Best regards,
Bruno

stez · September 16, 2012, 05:42

Hi Bruno,

I've attached screenshots of the errors.
One is related to STL import.
The second to "omega" definition.
The last two are related to the DES error i said in previous post.

About the bug of moving wall, the old report was about the text field in the GUI (scalar field when a vector one was required), AFAIK.

Thank you for the support.

wyldckat · September 16, 2012, 07:29

Hi Stefano,

OK, for each image:

The bad character seems to either be a space, tab or line break. Therefore, look for:
- spaces in names or trailing spaces in names.
- tab characters going around anywhere in the code.
- Bad line breaks can occur if you created the STL file in Windows/Mac or modified it in Windows/Mac or even if you copied the names from a Windows/Mac program, where the bad line break came along for the copy-paste ride.
In the "omega" line, "uniform" should either be removed or replaced with "constant", as discussed here: http://www.openfoam.org/mantisbt/view.php?id=444
A fix for this is to... I can't figure it out
It should be possible to fix in HelyxOS' "dictData/" folder, but I can't figure out how this BC is coming to existence...
and 4. - that boundary condition simply doesn't exist on OpenFOAM 2.1! Or at least I can't find it...

Best regards,
Bruno

stez · September 16, 2012, 10:03

I'll check STL later. About image 3-4, the patch ffmaxy is the outlet of a small "wind tunnel", if this info could be useful.

wyldckat · September 16, 2012, 11:47

About 3 and 4: what I meant was that the boundary condition "nutTurbulentIntensityLengthScaleInlet" does not exist in OpenFOAM 2.1.1/x and by I've looked at, neither does in 1.6-ext.

plucas · September 19, 2012, 23:36

Hello Bruno,

I am getting an error when trying to mesh my .stl file. I have meshed it fine using just snappyHexMesh, but I am always looking at trying new software. I got HELYX-OS running, but I haven't got passed the meshing stage. Any help would be awesome! The picture of the error is shown in the picture below.

Thanks,
Paul

chegdan · September 20, 2012, 11:58

@Stez and @wyldkat
1) The issue with the rotatingWallVelocity has been added as a bug on sourceforge.
2) the nutTurbulentIntensityLengthScaleInlet issue has been listed as a bug to be fixed. To get around this, fixedValue can be used to define nuTilda instead. Sourceforge Tickets

@Paul Can you give more information how you received this error? Maybe provide the .stl or an example?

plucas · September 20, 2012, 21:53

Quote:

Originally Posted by chegdan

@Paul Can you give more information how you received this error? Maybe provide the .stl or an example?

I just got helyxOS working after fixing the vtk libraries. I setup the preprocessing like they showed on the youtube video using basic mesh to see if I could get it working. The blockMesh setup is shown in the picture below.

The surface refinement is shown below.

The mesh screen is now shown below.

After I hit mesh, the error pops up.

The .stl is too large to upload.

thomas_schumacher · September 24, 2012, 06:21

Hi,
not sure it is related to that, but try to place your material point further up. At the moment it sits directly on the lower surface of your blockMesh. Maybe this creates problems. Use z=2m for example.

Thomas

plucas · September 24, 2012, 07:21

Quote:

Originally Posted by thomas_schumacher

Hi,
not sure it is related to that, but try to place your material point further up. At the moment it sits directly on the lower surface of your blockMesh. Maybe this creates problems. Use z=2m for example.

Thomas

Thanks, I will give that a try when I get home from work.

plucas · September 25, 2012, 10:08

Quote:

Originally Posted by thomas_schumacher

Hi,
not sure it is related to that, but try to place your material point further up. At the moment it sits directly on the lower surface of your blockMesh. Maybe this creates problems. Use z=2m for example.

Thomas

I tried this last night and I got the same error. Any other suggestions?

vinz · September 28, 2012, 09:37

Hi everybody,

HelyxOs is working fine for me.
However I wanted to have a look at the software and I tried to import the sources into eclipse.
I've got some problems to run it from eclipse so I would like to know if some of them managed to do it?

stez · September 28, 2012, 14:19

Hi
I think I've found another bug..
I'm working with .stl made with Blender. When I load them in HelyxOS the generated patch name in dict files is [filename]ExportedfromBlender-263(sub17). With this name nothing works (error sounds like it could not locate that patch name in some dict files), but if i delete the -263(sub17) part from the patch name in the "boundaries" file it works. Strange thing is that Openfoam works without problem with the complete name.. Is it related to HelyxOS?

chegdan · September 29, 2012, 10:47

Quote:

Originally Posted by stez

Hi
I think I've found another bug..
I'm working with .stl made with Blender. When I load them in HelyxOS the generated patch name in dict files is [filename]ExportedfromBlender-263(sub17). With this name nothing works (error sounds like it could not locate that patch name in some dict files), but if i delete the -263(sub17) part from the patch name in the "boundaries" file it works. Strange thing is that Openfoam works without problem with the complete name.. Is it related to HelyxOS?

Comment Edited : I am going through to try and reproduce this issue, but I am unable to do so. I have an STL file with the name, ExportedfromBlender-263(sub17).stl and everything is imported into HelyxOS fine and meshes as expected. Also, it really should be ok to have a file with a minus sign in it... Can you give some more details on how to reproduce this?

Right now its on the sourceforge ticket tracker but it needs some more detail. Otherwise, thanks for pointing this one out.

dark lancer · October 5, 2012, 15:52

hi
i have downloaded helyxos but its 64bit and I have not found for 32 bit because my linux is 32 bit and
When I launch helyx (./helyxOS.sh) I get the following message.
[hadi@hadi v1.0.0]$ ./helyxOS.sh
java -Xms128m -Xmx512m -jar ./lib/HelyxOS.jar
./helyxOS.sh: line 124: ./../jre/bin/java: cannot execute binary file

chegdan · October 8, 2012, 07:07

Quote:

Originally Posted by dark lancer

hi
i have downloaded helyxos but its 64bit and I have not found for 32 bit because my linux is 32 bit and
When I launch helyx (./helyxOS.sh) I get the following message.
[hadi@hadi v1.0.0]$ ./helyxOS.sh
java -Xms128m -Xmx512m -jar ./lib/HelyxOS.jar
./helyxOS.sh: line 124: ./../jre/bin/java: cannot execute binary file

HelyxOS is 64 bit, so you will have to recompile it for 32 bit to get it working for you.

dark lancer · October 9, 2012, 08:33

Quote:

Originally Posted by chegdan

HelyxOS is 64 bit, so you will have to recompile it for 32 bit to get it working for you.

How can I recompile it to 32 bit?

pgeremia · October 10, 2012, 05:39

@plucas: currently there is a bug affecting the automatic block mesh option whereas everything should run fine if you use the user defined option. However, if you have set block mesh to automatic type, just save the case, re-open the case and set the block mesh type to user-defined option which should be automatically filled for you by Helyx-OS. Can you double-check please?

@dark lancer: there are no installation/compilations instructions available for 32bit as we currently don't support Helyx-OS on 32bit. However, there are some examples (e.g. http://www.cfd-online.com/Forums/ope...tml#post375991) of successfull installations on 32bit systems. The main idea is to use the system VTK libraries as well as the system vtk.jar file to replace the 64bit ones available in Helyx-OS before you compile Helyx-OS, but this depends on the OS you have and thus there is no general guidelines I can provide.

September 16, 2012, 07:29		#45
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,981 Blog Entries: 45 Rep Power: 128	Hi Stefano, OK, for each image: The bad character seems to either be a space, tab or line break. Therefore, look for: spaces in names or trailing spaces in names. tab characters going around anywhere in the code. Bad line breaks can occur if you created the STL file in Windows/Mac or modified it in Windows/Mac or even if you copied the names from a Windows/Mac program, where the bad line break came along for the copy-paste ride. In the "omega" line, "uniform" should either be removed or replaced with "constant", as discussed here: http://www.openfoam.org/mantisbt/view.php?id=444 A fix for this is to... I can't figure it out It should be possible to fix in HelyxOS' "dictData/" folder, but I can't figure out how this BC is coming to existence... and 4. - that boundary condition simply doesn't exist on OpenFOAM 2.1! Or at least I can't find it... Best regards, Bruno __________________ OpenFOAM: FAQ \| Getting started Forum: How to get help, to post code/output and forum guide Read this before sending me PM

September 16, 2012, 11:47		#47
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,981 Blog Entries: 45 Rep Power: 128	About 3 and 4: what I meant was that the boundary condition "nutTurbulentIntensityLengthScaleInlet" does not exist in OpenFOAM 2.1.1/x and by I've looked at, neither does in 1.6-ext. __________________ OpenFOAM: FAQ \| Getting started Forum: How to get help, to post code/output and forum guide Read this before sending me PM

September 20, 2012, 11:58	rotatingWallVelocity Definition	#49
chegdan Senior Member Daniel P. Combest Join Date: Mar 2009 Location: St. Louis, USA Posts: 621 Rep Power: 0	@Stez and @wyldkat 1) The issue with the rotatingWallVelocity has been added as a bug on sourceforge. 2) the nutTurbulentIntensityLengthScaleInlet issue has been listed as a bug to be fixed. To get around this, fixedValue can be used to define nuTilda instead. Sourceforge Tickets @Paul Can you give more information how you received this error? Maybe provide the .stl or an example? Last edited by chegdan; September 20, 2012 at 12:23. Reason: more info

September 24, 2012, 06:21		#51
thomas_schumacher New Member Thomas Schumacher Join Date: Mar 2009 Posts: 2 Rep Power: 0	Hi, not sure it is related to that, but try to place your material point further up. At the moment it sits directly on the lower surface of your blockMesh. Maybe this creates problems. Use z=2m for example. Thomas plucas likes this.

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September 15, 2012, 12:47		#42
stez New Member stefano pieretti Join Date: Aug 2012 Posts: 12 Rep Power: 14	Ok now libraries works, but it still can't open STL files, always the same error. So I tried to generate the mesh with the older version, import it in the newer and run a simulation (I was looking for a working "rotating wall" simulation). It generates wrong boundary conditions, "omega" should be "constant" instead of "uniform", so it gives error. Since the error show up after some seconds, I tried the trick to be faster than the solver to modify the "0/U" file before it could read that field, and then it works (with simpleFoam), but it is not a good way to get it work. I tried the same trick with DES but then it gives other errors with some patch, that I can't understand. I have looked into HelyxOS dictData folder to see if there was some dict containing the wrong "omega" definition and fix it, but I didn't find any

September 16, 2012, 10:03		#46
stez New Member stefano pieretti Join Date: Aug 2012 Posts: 12 Rep Power: 14	I'll check STL later. About image 3-4, the patch ffmaxy is the outlet of a small "wind tunnel", if this info could be useful.

September 19, 2012, 23:36		#48
plucas Senior Member Anonymous Join Date: Dec 2011 Location: USA Posts: 108 Rep Power: 15	Hello Bruno, I am getting an error when trying to mesh my .stl file. I have meshed it fine using just snappyHexMesh, but I am always looking at trying new software. I got HELYX-OS running, but I haven't got passed the meshing stage. Any help would be awesome! The picture of the error is shown in the picture below. Thanks, Paul

September 28, 2012, 09:37		#54
vinz Senior Member Vincent RIVOLA Join Date: Mar 2009 Location: France Posts: 283 Rep Power: 18	Hi everybody, HelyxOs is working fine for me. However I wanted to have a look at the software and I tried to import the sources into eclipse. I've got some problems to run it from eclipse so I would like to know if some of them managed to do it?

September 28, 2012, 14:19		#55
stez New Member stefano pieretti Join Date: Aug 2012 Posts: 12 Rep Power: 14	Hi I think I've found another bug.. I'm working with .stl made with Blender. When I load them in HelyxOS the generated patch name in dict files is [filename]ExportedfromBlender-263(sub17). With this name nothing works (error sounds like it could not locate that patch name in some dict files), but if i delete the -263(sub17) part from the patch name in the "boundaries" file it works. Strange thing is that Openfoam works without problem with the complete name.. Is it related to HelyxOS?

October 5, 2012, 15:52		#57
dark lancer Member hadi abdollahzadeh Join Date: Aug 2012 Location: Iran-yasouj Posts: 59 Rep Power: 14	hi i have downloaded helyxos but its 64bit and I have not found for 32 bit because my linux is 32 bit and When I launch helyx (./helyxOS.sh) I get the following message. [hadi@hadi v1.0.0]$ ./helyxOS.sh java -Xms128m -Xmx512m -jar ./lib/HelyxOS.jar ./helyxOS.sh: line 124: ./../jre/bin/java: cannot execute binary file

October 10, 2012, 05:39		#60
pgeremia New Member Paolo Geremia Join Date: Aug 2012 Posts: 11 Rep Power: 14	@plucas: currently there is a bug affecting the automatic block mesh option whereas everything should run fine if you use the user defined option. However, if you have set block mesh to automatic type, just save the case, re-open the case and set the block mesh type to user-defined option which should be automatically filled for you by Helyx-OS. Can you double-check please? @dark lancer: there are no installation/compilations instructions available for 32bit as we currently don't support Helyx-OS on 32bit. However, there are some examples (e.g. http://www.cfd-online.com/Forums/ope...tml#post375991) of successfull installations on 32bit systems. The main idea is to use the system VTK libraries as well as the system vtk.jar file to replace the 64bit ones available in Helyx-OS before you compile Helyx-OS, but this depends on the OS you have and thus there is no general guidelines I can provide.