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Old   August 14, 2013, 13:41
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  #101
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This error is associated with improper definition of WM_PROJECT_INST_DIR and WM_THIRD_PARTY_DIR.

if both

Code:
echo  $WM_PROJECT_INST_DIR
and

Code:
echo $WM_THIRD_PARTY_DIR
return a valid path then this error should not happen. I'm guessing that there may be a step that you may have missed. Did you do the

Code:
sudo apt-get install paraviewopenfoam3120
step? Also, see what

Code:
echo $WM_THIRD_PARTY_DIR
gives you.
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Last edited by chegdan; August 19, 2013 at 10:35.
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Old   August 14, 2013, 13:52
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on doing the first 2 commands

Quote:

izna@izna-MS-7592:~$ echo $WM_PROJECT_INST_DIR
/opt
izna@izna-MS-7592:~$ echo $WM_THIRD_PARTY_DIR
/opt/ThirdParty-2.2.1

paraview has been installed..

on doing the last command..
Quote:
izna@izna-MS-7592:~$ echo $WM_THIRD_PARTY_DIR
/opt/ThirdParty-2.2.1
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Old   August 14, 2013, 14:02
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Izna,

Alright, then we are looking at something similar to

Helyx-OS (GUI for SnappyHexMesh post 26 from Wyldckat

but with some differences. In HELYX-OS bin directory, find all the *.run scripts and add

Code:
. /opt/openfoam221/etc/bashrc
after the first line. See if this is a solution. Sometimes if you have multiple installations defined you will run into these problems.
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Old   August 14, 2013, 14:26
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IT WORKSSSSSSSSSSSSSSSSSSSSSSSSSSSS
Thanks a lot Dan. :*
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Old   August 29, 2013, 17:53
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Quote:
Originally Posted by chegdan View Post
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.
Ok I reproduced this error. Process for generating file is as follows:

1. Import stl to Blender
2. Divide surface into layers
3. Export each layer as a separate stl file
4. Import each stl file into HelyxOS. They receive the name of the stl file on the top level in the Surfaces list, with a sublayer indented beneath having the long "exported_from_blender" name automagically assigned
5. Set up number of layers and thickness on the sublayers of interest
6. Run the meshing command. Meshing goes fine until
7. Layer generation stalls with following error message for each stl/patch (note the name of the file it cannot find appears identical to the name listed in the "Valid patches are" section):

Code:
Mesh snapped in = 5630.23 s.
Layer thickness specified as final layer and expansion ratio.
--> FOAM Warning :
    From function polyBoundaryMesh::patchSet(const wordReList&, const bool, const bool) const
    in file meshes/polyMesh/polyBoundaryMesh/polyBoundaryMesh.C at line 777
    Cannot find any patch or group names matching bottom_Exported_from_Blender-2.68_(sub_0)
--> FOAM Warning :
    From function layerParameters::layerParameters(..)
    in file autoHexMesh/autoHexMeshDriver/layerParameters/layerParameters.C at line 286
    Reading "/home/karl/OpenFOAM/karl-2.2.x/run/newCase21i_1/processor0/../system/snappyHexMeshDict.addLayersControls.layers" from line 224 to line 239
    Layer specification for bottom_Exported_from_Blender-2.68_(sub_0) does not match any patch.
Valid patches are
18
(
ffminx
ffmaxx
ffminy
ffmaxy
ffminz
ffmaxz
far_Exported_from_Blender-2.68_(sub_0)
symmetry_Exported_from_Blender-2.68_(sub_0)
bottom_Exported_from_Blender-2.68_(sub_0)
top_Exported_from_Blender-2.68_(sub_0)
tip_Exported_from_Blender-2.68_(sub_0)
leading_Exported_from_Blender-2.68_(sub_0)
procBoundary0to15
procBoundary0to1
procBoundary0to16
procBoundary0to3
procBoundary0to18
procBoundary0to6
)
I have not tried the fix described above by stetz, but just wanted to confirm the error. System is starcluster Ubuntu 12.04 standard HVM AMI with 2.2.x and v1.0.3 helyx. Thanks for any thoughts. Maybe there is a maximum length? I will go back and edit the stl files so the first line matches the filename, reimport and see if that works.

Incidentally, a command line guide to running Helyx would be nice for those of us working across SSH connections. I set up the case on my home machine then put it on the server to run it, so all I need to do is load the case into helyx and initiate the "create mesh" (or run solver) steps. I guess I will study the terminal log files to figure out how to manage this from the command line.

--ADDENDUM--

Changing the name in the first line of each stl file to a simple short name e.g. "top" "bottom" "tip" etc. fixes this problem. Maybe something to do with the parentheses characters or something. Easy fix for those exporting blender files.

Last edited by atg; September 7, 2013 at 14:05. Reason: followup
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Old   September 19, 2013, 13:36
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Quote:
Changing the name in the first line of each stl file to a simple short name e.g. "top" "bottom" "tip" etc. fixes this problem. Maybe something to do with the parentheses characters or something. Easy fix for those exporting blender files.
This is exactly what I do when I use Blender. So getting rid of the text that says

Code:
Exported_from_Blender-blah.blah
in STL files and replacing it with nicer names is much better.
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Old   September 19, 2013, 13:39
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Just to inform everyone that there is a slight change in the buoyantBoussinesq*Foam using alphat instead of kappat that is defined in HELYX-OS. This was pointed out by JR22 at

Bug? Helyx-OS 1.0.3 for OpenFOAM-2.2.1 ?

and I posted a general workaround if someone is running into problems before the next release.
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Old   September 25, 2013, 11:05
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Hello guys, I just installed helyxOS on my ubuntu os v.12.04. But unfortunately as I am totally new to don't know from where it should be started. Also I have extracted all the files from the archive file.
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Old   September 25, 2013, 15:18
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Do you have OpenFOAM installed? Once you have a working installation of OpenFOAM-2.2.x then HELYX-OS should work with relative ease.

To install OpenFOAM-2.2.x I suggest the steps on the OpenFOAM.org site. From there its pretty much all copy paste if you read through slowly.
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Old   November 8, 2013, 20:28
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Hi all,

I'm not sure if this is the correct place to post but I cannot find a specific sub-forum for HelyxOS.

I am running xubuntu 12.04, openfoam2.2.2 and helyxos v1.02 on a 64bit machine.

Using the single core solver works fine, but I am running into trouble with parallel.

Creating the mesh and geometry and running works fine, and there is a definite speed-up with using multiple cores over a single core so this seems fine. After meshing when I go to re-open the folder to go through the solver properties, it asks for Serial or Parallel but is accompanied by this error:



Clicking serial only brings in part of the mesh, clicking parallel brings in the whole mesh as it should be.

When I put in my values for the solver and click start, the output logfile is:

Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.2.2                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.2.2-9240f8b967db
Exec   : simpleFoam -parallel -case /home/andrew/Helyx/p1
Date   : Nov 09 2013
Time   : 00:23:22
Host   : "andrew-pc"
PID    : 8600
Case   : /home/andrew/Helyx/p1
nProcs : 6
Slaves : 
5
(
"andrew-pc.8601"
"andrew-pc.8602"
"andrew-pc.8603"
"andrew-pc.8604"
"andrew-pc.8605"
)

Pstream initialized with:
    floatTransfer      : 0
    nProcsSimpleSum    : 0
    commsType          : nonBlocking
    polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Reading field p
Also for some reason the logfile stops recording there, and the rest is left in a terminal which I cannot seem to copy text from so have taken the screenshots of the output:





Many thanks if anyone has the time to take a look at this and suggest a solution

Andrew
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Old   November 9, 2013, 10:11
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Greetings Andrew,

Quote:
Originally Posted by AndrewMortimer View Post
I'm not sure if this is the correct place to post but I cannot find a specific sub-forum for HelyxOS.
Actually, the official forum is on their project: http://sourceforge.net/p/helyx-os/discussion/

Quote:
Originally Posted by AndrewMortimer View Post
I am running xubuntu 12.04, openfoam2.2.2 and helyxos v1.02 on a 64bit machine.
Mmm... v1.0.2... I'm guessing that you haven't seen that there is a patch for 1.0.2 and that the latest version is 1.0.3: http://sourceforge.net/projects/helyx-os/files/
My advice is to jump directly to 1.0.3, since the issues you are reporting probably have already been fixed.

Best regards,
Bruno
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Old   November 9, 2013, 14:39
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Hi Bruno,

Cheers for looking over the post, I'm afraid I mis-typed the version, and I am running v1.0.3 currently.

I will make a post on the project forum though, thanks for the link.

Andrew
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Old   November 11, 2013, 06:37
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I have the same problem. HelyxOS v1.0.3 does not make the p, U, k, etc files when running a parallel case that has been meshed in parallel.

How do you switch from a parallel to a serial case and vice versa?
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Old   November 29, 2013, 13:00
Default Helyx-OS 2.0.0
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Hi,

How do you reconstruct a Helyx parallel case after a run?

I have tried reconstructPar, but I get an Error message.



sture_ii@SturePCUbuntu:~/OpenFOAM/sture_ii-2.2.2/run/analyser/body03_00b/body03_00c$ reconstructPar -latestTime
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.2.2 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.2.2-9240f8b967db
Exec : reconstructPar -latestTime
Date : Nov 29 2013
Time : 17:53:24
Host : "SturePCUbuntu"
PID : 3823
Case : /home/sture_ii/OpenFOAM/sture_ii-2.2.2/run/analyser/body03_00b/body03_00c
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time



Reconstructing fields for mesh region0

Time = 1000

Reconstructing FV fields



--> FOAM FATAL ERROR:
Size of maps does not correspond to size of mesh for processor 0
faceProcAddressing : 123032 nFaces : 640997
cellProcAddressing : 39721 nCell : 203707
boundaryProcAddressing : 9 nFaces : 16

From function fvFieldReconstructor::fvFieldReconstructor
(
fvMesh&,
const PtrList<fvMesh>&,
const PtrList<labelIOList>&,
const PtrList<labelIOList>&,
const PtrList<labelIOList>&
)
in file fvFieldReconstructor.C at line 66.

FOAM exiting

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Old   November 29, 2013, 15:27
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Greetings Sture,

A bit more information would come in handy. More specifically, what was the case set-up you've made and the steps you've taken up to the point where you tried to use reconstructPar.

Best regards,
Bruno
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Old   November 30, 2013, 09:47
Default Helyx-OS 2.0.0
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Hi,

Thanks for your response!

I did:
  1. Set up a case with HelyxOS 2.0.0 in parallel on 6 processors
  2. Do the run
  3. Postprocess some in ParaView started from HelyxOS (then I can see a parallel case without reconstructing it)
  4. Close HelyxOS and ParaView
  5. Run preconstructPar (no qualifiers) from the case directory
  6. Then got the ERROR msg as above

If you need more info I will happily post it.

Rgds
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Old   November 30, 2013, 12:10
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Sture,

Have you reconstructed the serial mesh from your parallel generated mesh? You probably need to do something like

Code:
reconstructParMesh -constant -mergeTol 1e-6
or similar to reconstruct your mesh and then reconstructPar your latest times to map your fields to your reconstructed mesh. There is a thread which encounters the same error you are and does exactly this procedure

Parallel Computing decomposePar

Try that and see if it resolves your issue.
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Old   December 5, 2013, 16:46
Default Helyx OS 2.0.0
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It works like a charm in the new version.
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Old   February 13, 2014, 04:33
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I previously asked this on sourceforge but was redirected here: The gui looks great from the screenshots so I am keen to try it. I am running into problems installing the bin file on mac osx - during the install, at the select install directory prompt it doesn't seem to recognise any destination I give it. It always returns "destination doesn't exist". Any pointers would be greatly appreciated.

Cheers
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Old   February 20, 2014, 08:19
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Hello.

I'm getting started with OpenFOAM and find it convenient enough to use Helyx-OS to create mesh and manage cases. First I tried to create a mesh and encountered a problem. Official Helyx-OS v2.0.0 successfully read my STL geometry that contains many small elements (small holes on perforated plate). Base (block) mesh generates and snappyHexMesh then works (launched from Helyx-OS interface) but it's too coarse (it doesn't even "catch" the holes). Okay, I set Geometry => My geometry => Refinement => SURFACE => Min and Max levels (doesn't matter what levels, say 1 and 10). I click Create button and mesh is built. But no any refinement occures. And when I look at the Min and Max levels for surface refinement in Helyx-OS interface there are all zeroes. Why does it happen? How can I avoid this and apply surface refinement?
STL is large enough (50+ MiB) but if it matters I'll upload it with the whole test case.

Thanks for attension.
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