CFD Online Logo CFD Online URL
www.cfd-online.com
[Sponsors]
Home > Forums > OpenFOAM Native Meshers: snappyHexMesh and Others

Helyx Doesnt load my stl geometry

Register Blogs Members List Search Today's Posts Mark Forums Read

Like Tree1Likes
  • 1 Post By chegdan

Reply
 
LinkBack Thread Tools Display Modes
Old   June 20, 2013, 09:47
Default Helyx Doesnt load my stl geometry
  #1
New Member
 
patrick okolo
Join Date: Nov 2011
Posts: 14
Rep Power: 5
pitpat231 is on a distinguished road
pls help me out, i installed HelyxOS using the procedures i saw on the Engys website. my problem now is that my helyx does not load (show) my stl geometry. pls i need help.
pitpat231 is offline   Reply With Quote

Old   June 20, 2013, 10:51
Default
  #2
Senior Member
 
chegdan's Avatar
 
Daniel P. Combest
Join Date: Mar 2009
Location: St. Louis, USA
Posts: 535
Rep Power: 18
chegdan will become famous soon enough
More information is helpful in order to solve this
  1. Is your STL in binary or ASCII format?
    HELYX-OS only accepts ASCII formatted STL files. You can convert between a binary STL (.obj) and an ASCII (.stl) via the command
    Code:
    surfaceConvert inputFile.obj outputFile.stl
  2. What is the decimal separator in your STL file, a "," or a "."? What are your language settings? i.e. what is your locale on the machine?
    If you have a language that uses "," as a decimal separator but your .stl file uses a "." instead then this could be a cause but HELYX-OS will provide an error to let you know this is the issue.
  3. Any error messages with the install? Does it complain about a VTK error? If so then its a problem with your libmpi.so discussed here
  4. What system are you using and how did you install OpenFOAM (via .deb, precompiled source, you compiled OpenFOAM, etc.)?
    In general, problems that users encounter with the precompiled versions of OpenFOAM and are linked to the libmpi.so issue in (3)
__________________
Dan

Find me on twitter @dancombest and LinkedIn
chegdan is offline   Reply With Quote

Old   June 21, 2013, 09:59
Default
  #3
New Member
 
patrick okolo
Join Date: Nov 2011
Posts: 14
Rep Power: 5
pitpat231 is on a distinguished road
thanks, i can now load stl geometry, but now i encounter the following problem wen i run a case in helyx. i use a intel corei7 personal laptop.



MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
mpirun has exited due to process rank 3 with PID 3555 on
node chijioke-W240HU-W250HUQ exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
[chijioke-W240HU-W250HUQ:03550] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[chijioke-W240HU-W250HUQ:03550] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages




pls any help on how i can solve this?????
thanks in advance.
pitpat231 is offline   Reply With Quote

Old   June 22, 2013, 18:27
Default
  #4
Senior Member
 
chegdan's Avatar
 
Daniel P. Combest
Join Date: Mar 2009
Location: St. Louis, USA
Posts: 535
Rep Power: 18
chegdan will become famous soon enough
We need to do a few test to see if there is a problem with your MPI install

1: See if we are pointing to your MPI Install
What is the result of the command

Code:
echo $MPI_ARCH_PATH
when you run that in a bash terminal? If nothing comes up then we have a problem. If something comes up in the terminal, let me know what it is if you make it to the end of this post and its still not clear what the problem is. Continue to step 2.

2: Can you run a case in parallel without HELYX-OS?

Assuming you have setup your $FOAM_RUN directory correctly and you are capable of running on 4 processors then we can test on some tutorials. To test this please copy the following into your terminal one-by-one

Code:
cd $FOAM_RUN/tutorials/multiphase/interFoam/laminar/damBreak
blockMesh >blockMesh.log 2>&1
cp 0/alpha1.org 0/alpha1
decomposePar >decomposePar.log 2>&1
mpirun -np 4 interFoam -parallel > interFoam.log 2>&1
and see if you are able to run a parallel case without HELYX-OS.

If you get an error on the first command saying that there is no such directory, then you need to go to 3. If you have an MPI_ABORT error when the last command is run, then its something with your MPI and not with HELYX-OS.

3: setting up your $FOAM_RUN correctly

copy the tutorials to your $FOAM_RUN directory with

Code:
mkdir -p $FOAM_RUN
cd $FOAM_RUN
cp -r $WM_PROJECT_DIR/tutorials $FOAM_RUN
and then start over with the previous steps with running the test case in parallel (part 2).

4: Report Back
Report back on errors that you are receiving and also with some information about your system like operating system and whether its 32 bit or 64 and if you compiled OpenFOAM or installed it from a .deb package. Also, is there a VtkError folder created in your home directory or where you launched HELYX-OS?
wyldckat likes this.
__________________
Dan

Find me on twitter @dancombest and LinkedIn

Last edited by chegdan; June 23, 2013 at 18:17. Reason: grammar
chegdan is offline   Reply With Quote

Old   June 24, 2013, 10:08
Default
  #5
New Member
 
patrick okolo
Join Date: Nov 2011
Posts: 14
Rep Power: 5
pitpat231 is on a distinguished road
@Chegdan.

for process 1. when i put the command echo $MPI_ARCH_PATH, i got the following; /usr/lib/openmpi

for process 2. ; after inputing the commands one after the other, it all ran well with no errors. no error report at all.

When i initially launch my Helyx the following report shows on my terminal, even though the helyx still opens;

java -Xms128m -Xmx1024m -XX:OnError="/home/chijioke/OpenFOAM/Engys/HelyxOS/v1.0.1/bin/collectInfo.run" -jar /home/chijioke/OpenFOAM/Engys/HelyxOS/v1.0.1/lib/HelyxOS.jar HelyxOS 2>&1 | tee /home/chijioke/OpenFOAM/Engys/HelyxOS/v1.0.1/helyxEE.log

pls wat next??? thanks
pitpat231 is offline   Reply With Quote

Old   June 24, 2013, 10:49
Default
  #6
Senior Member
 
chegdan's Avatar
 
Daniel P. Combest
Join Date: Mar 2009
Location: St. Louis, USA
Posts: 535
Rep Power: 18
chegdan will become famous soon enough
That line

Code:
java -Xms128m -Xmx1024m -XX:OnError="/home/chijioke/OpenFOAM/Engys/HelyxOS/v1.0.1/bin/collectInfo.run" -jar /home/chijioke/OpenFOAM/Engys/HelyxOS/v1.0.1/lib/HelyxOS.jar HelyxOS 2>&1 | tee /home/chijioke/OpenFOAM/Engys/HelyxOS/v1.0.1/helyxEE.log
is not an error so you are fine. Do you have a file in your home directory (or where you launch HELYX-OS) called

Code:
vtkError.txt
When you run a case in parallel and get an error?
__________________
Dan

Find me on twitter @dancombest and LinkedIn
chegdan is offline   Reply With Quote

Old   April 25, 2014, 23:03
Default
  #7
atg
Member
 
Karl
Join Date: Jan 2011
Posts: 36
Rep Power: 6
atg is on a distinguished road
I am having some issues getting HelyxOS 2.0.1 to run in parallel on ubuntu 12.04.

Code:
echo $MPI_ARCH_PATH
yields /usr/lib/openmpi

Tutorials run fine in parallel outside of Helyx as described by chegdan above. pitzDaily converges just fine on multiple processors.

HelyxOS itself seems to launch fine, load old cases, etc.

I can run checkmesh and blockmesh in Helyx and get an OK.

decomposePar seems to work, but then the meshing run ends with the following appearing in the little terminal window within HelyxOS:

Code:
End.

mpirun:  Symbol  'orte_plm' has different size in shared object, consider re-linking
mpirun:  symbol lookup error: mpirun: undefined symbol: orte_cmd_basename
I'm not sure where to start with this. I noticed my bashrc in home/openFoam-2.2.2/etc had WM_MPLIB set to "OPENMPI" instead of "SYSTEMOPENMPI", so I thought that might be the problem. But after changing it to SYSTEMOPENMPI and re-sourcing in the terminal, restarting helyx and reloading the case, the same message resulted and the case would not run.

Anybody have any thoughts? I must have done something to OF while compiling that Helyx does not like. But OF seems perfectly happy otherwise.

Also, is there any way to capture the text from the little terminal within Helyx? It would have saved me some typing!

Thanks for any suggestions! And sorry to bother on a Friday night!
Karl

Quote:
Originally Posted by pitpat231 View Post
@Chegdan.

for process 1. when i put the command echo $MPI_ARCH_PATH, i got the following; /usr/lib/openmpi

for process 2. ; after inputing the commands one after the other, it all ran well with no errors. no error report at all.

When i initially launch my Helyx the following report shows on my terminal, even though the helyx still opens;

java -Xms128m -Xmx1024m -XX:OnError="/home/chijioke/OpenFOAM/Engys/HelyxOS/v1.0.1/bin/collectInfo.run" -jar /home/chijioke/OpenFOAM/Engys/HelyxOS/v1.0.1/lib/HelyxOS.jar HelyxOS 2>&1 | tee /home/chijioke/OpenFOAM/Engys/HelyxOS/v1.0.1/helyxEE.log

pls wat next??? thanks
atg is offline   Reply With Quote

Old   April 27, 2014, 21:51
Default
  #8
Senior Member
 
chegdan's Avatar
 
Daniel P. Combest
Join Date: Mar 2009
Location: St. Louis, USA
Posts: 535
Rep Power: 18
chegdan will become famous soon enough
Is there a way you have multiple installs of OpenFOAM 2.2.2 on your machine and HELYX-OS is pointing to one that it shouldn't? You may have one version sourced in your .bashrc (say $HOME/OpenFOAM/OpenFOAM-2.2.2) and HELYX-OS is pointing to another one in say /opt/openfoam222.
__________________
Dan

Find me on twitter @dancombest and LinkedIn
chegdan is offline   Reply With Quote

Old   April 27, 2014, 22:09
Default
  #9
atg
Member
 
Karl
Join Date: Jan 2011
Posts: 36
Rep Power: 6
atg is on a distinguished road
Quote:
Originally Posted by chegdan View Post
Is there a way you have multiple installs of OpenFOAM 2.2.2 on your machine and HELYX-OS is pointing to one that it shouldn't? You may have one version sourced in your .bashrc (say $HOME/OpenFOAM/OpenFOAM-2.2.2) and HELYX-OS is pointing to another one in say /opt/openfoam222.
Thanks chegdan - I do have 2.3.0 and 2.2.2 installed, but they are both in my home directory. Nothing in /opt. It is a fresh ubuntu install but the home folder is old. I did discard my old openfoam directories and install both 2.2.2 and 2.3.0 from freshly extracted tar files. I could easily discard 2.3.0 or both and build again. I may just try that and see what happens, but I wish I understood the problem better so I can avoid repeating it.

Karl
atg is offline   Reply With Quote

Reply

Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are On
Pingbacks are On
Refbacks are On


Similar Threads
Thread Thread Starter Forum Replies Last Post
External mesh crawls into car model. Holes in STL model? MadsR OpenFOAM Native Meshers: snappyHexMesh and Others 8 October 26, 2013 10:21
Multi region meshing & recovering the original patch names fluidpath OpenFOAM Native Meshers: snappyHexMesh and Others 4 May 19, 2013 19:13
Boundary conditions on patches, from a stl file. emirust OpenFOAM Native Meshers: snappyHexMesh and Others 4 October 23, 2012 09:05
Mesh a geometry without stl file eysteinn OpenFOAM Native Meshers: snappyHexMesh and Others 0 May 5, 2011 10:15
Problem meshing an imported geometry Alicia Open Source Meshers: Gmsh, Netgen, CGNS, ... 0 March 30, 2010 04:53


All times are GMT -4. The time now is 10:07.