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HelyxOS problem while reading an STL file

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Old   October 7, 2012, 07:32
Default HelyxOS problem while reading an STL file
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Oleksy Armas
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Hello all!

I have problems with HelyxOS....Do you know how to fix such problem...


I have put in terminal command (recommended by wyldcat) for VTK issue:

Code:
ln -s $MPI_ARCH_PATH/lib/libmpi.so $MPI_ARCH_PATH/lib/libmpi.so.0
After this, VTK worked good (I have made BOX on view , but after STL file loaded HELYX-OS crashed...

It crashes after every attempt to load an STL ASCII File

Code:
ubuntu@ubuntu:~/Desktop/Engys/HelyxOS/v1.0.0$ ./helyxOS.sh 
java -Xms128m -Xmx1024m -jar ./lib/HelyxOS.jar
vtkHybridJava NOT loaded: /home/ubuntu/Desktop/Engys/HelyxOS/v1.0.0/ext/libvtkHybridJava.so.5.10.0: libmpi.so.1: nie można otworzyć pliku obiektu dzielonego: Nie ma takiego pliku ani katalogu
java.lang.UnsatisfiedLinkError: /home/ubuntu/Desktop/Engys/HelyxOS/v1.0.0/ext/libvtkHybridJava.so.5.10.0: libmpi.so.1: nie można otworzyć pliku obiektu dzielonego: Nie ma takiego pliku ani katalogu
    at java.lang.ClassLoader$NativeLibrary.load(Native Method)
    at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1807)
    at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1732)
    at java.lang.Runtime.loadLibrary0(Runtime.java:823)
    at java.lang.System.loadLibrary(System.java:1028)
    at eu.engys.helyx.vtk.VTKUtil.loadLibrary(VTKUtil.java:96)
    at eu.engys.helyx.vtk.VTKUtil.LoadAllNativeLibraries(VTKUtil.java:72)
    at eu.engys.helyx.gui.Launcher.main(Launcher.java:44)
Make sure the search path is correct: 
/home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/server:/home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64:/home/ubuntu/Desktop/Engys/HelyxOS/jre/../lib/amd64:./ext:./../jre/lib/amd64/xawt:/opt/paraviewopenfoam3120/lib/paraview-3.12:/opt/openfoam211/platforms/linux64GccDPOpt/lib/openmpi-system:/opt/ThirdParty-2.1.1/platforms/linux64GccDPOpt/lib/openmpi-system:/usr/lib/openmpi/lib:/home/ubuntu/OpenFOAM/ubuntu-2.1.1/platforms/linux64GccDPOpt/lib:/opt/site/2.1.1/platforms/linux64GccDPOpt/lib:/opt/openfoam211/platforms/linux64GccDPOpt/lib:/opt/ThirdParty-2.1.1/platforms/linux64GccDPOpt/lib:/opt/openfoam211/platforms/linux64GccDPOpt/lib/dummy:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
ubuntu@ubuntu:~/Desktop/Engys/HelyxOS/v1.0.0$ sudo ln -s $MPI_ARCH_PATH/lib64/libmpi.so $MPI_ARCH_PATH/lib64/libmpi.so.0
ln: tworzenie dowiązania symbolicznego `/usr/lib/openmpi/lib64/libmpi.so.0': Nie ma takiego pliku ani katalogu
ubuntu@ubuntu:~/Desktop/Engys/HelyxOS/v1.0.0$ sudo ln -s $MPI_ARCH_PATH/lib64/libmpi.so $MPI_ARCH_PATH/lib64/libmpi.so.1
ln: tworzenie dowiązania symbolicznego `/usr/lib/openmpi/lib64/libmpi.so.1': Nie ma takiego pliku ani katalogu
ubuntu@ubuntu:~/Desktop/Engys/HelyxOS/v1.0.0$ sudo ln -s $MPI_ARCH_PATH/lib64/libmpi.so $MPI_ARCH_PATH/lib64/libmpi.so.1
ln: tworzenie dowiązania symbolicznego `/usr/lib/openmpi/lib64/libmpi.so.1': Nie ma takiego pliku ani katalogu
ubuntu@ubuntu:~/Desktop/Engys/HelyxOS/v1.0.0$ ln -s $MPI_ARCH_PATH/lib/libmpi.so $MPI_ARCH_PATH/lib/libmpi.so.1
ln: tworzenie dowiązania symbolicznego `/usr/lib/openmpi/lib/libmpi.so.1': Brak dostępu
ubuntu@ubuntu:~/Desktop/Engys/HelyxOS/v1.0.0$ sudo ln -s $MPI_ARCH_PATH/lib/libmpi.so $MPI_ARCH_PATH/lib/libmpi.so.1
ubuntu@ubuntu:~/Desktop/Engys/HelyxOS/v1.0.0$ ./helyxOS.sh 
java -Xms128m -Xmx1024m -jar ./lib/HelyxOS.jar
WRITE: blockMeshDict -> /home/ubuntu/Desktop/NC/newCase/system/blockMeshDict
WRITE: snappyHexMeshDict -> /home/ubuntu/Desktop/NC/newCase/system/snappyHexMeshDict
WRITE: controlDict -> /home/ubuntu/Desktop/NC/newCase/system/controlDict
WRITE: fvSchemes -> /home/ubuntu/Desktop/NC/newCase/system/fvSchemes
WRITE: fvSolution -> /home/ubuntu/Desktop/NC/newCase/system/fvSolution
WRITE: decomposeParDict -> /home/ubuntu/Desktop/NC/newCase/system/decomposeParDict
Stl.addBox(): box min [0.0, 0.0, 0.0], max [2.0, 2.0, 1.0]
VolumeRefinementBuilder.buildVolumeDictionary() 
box
{
    mode inside;
    levels 0;
}

STLUtils.copyToTriSurface() /home/ubuntu/Desktop/NC/newCase/constant/triSurface/lambo_gallardo_Poizia.stl
*** glibc detected *** java: double free or corruption (out): 0x00007fe5cdd1ea80 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x78a8f)[0x7fe5d5c19a8f]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x73)[0x7fe5d5c1d8e3]
/lib/x86_64-linux-gnu/libc.so.6(fclose+0x155)[0x7fe5d5c08235]
./ext/libvtkIO.so.5.10(_ZN12vtkSTLReader11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x2b6)[0x7fe5c5122f86]
./ext/libvtkFiltering.so.5.10(_ZN12vtkExecutive13CallAlgorithmEP14vtkInformationiPP20vtkInformationVectorS3_+0x55)[0x7fe5c7ef9515]
./ext/libvtkFiltering.so.5.10(_ZN23vtkDemandDrivenPipeline11ExecuteDataEP14vtkInformationPP20vtkInformationVectorS3_+0x4e)[0x7fe5c7eeca7e]
./ext/libvtkFiltering.so.5.10(_ZN23vtkDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x158)[0x7fe5c7eee4d8]
./ext/libvtkFiltering.so.5.10(_ZN32vtkStreamingDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x1ea)[0x7fe5c804b18a]
./ext/libvtkFiltering.so.5.10(_ZN23vtkDemandDrivenPipeline10UpdateDataEi+0x9e)[0x7fe5c7eec71e]
./ext/libvtkFiltering.so.5.10(_ZN32vtkStreamingDemandDrivenPipeline6UpdateEi+0xaf)[0x7fe5c804b99f]
[0x7fe5c8e06d6e]
======= Memory map: ========
40000000-40009000 r-xp 00000000 00:11 71346                              /home/ubuntu/Desktop/Engys/HelyxOS/jre/bin/java
40108000-4010a000 rwxp 00008000 00:11 71346                              /home/ubuntu/Desktop/Engys/HelyxOS/jre/bin/java
40e7f000-442d6000 rwxp 00000000 00:00 0                                  [heap]
bae00000-be770000 rwxp 00000000 00:00 0 
be770000-c0000000 rwxp 00000000 00:00 0 
c0000000-c5560000 rwxp 00000000 00:00 0 
c5560000-eaab0000 rwxp 00000000 00:00 0 
eaab0000-ed550000 rwxp 00000000 00:00 0 
ed550000-100000000 rwxp 00000000 00:00 0 
7fe5bd5be000-7fe5bd5bf000 rwxs 180183000 00:05 5655                      /dev/dri/card0
7fe5bd7a8000-7fe5bd994000 rwxs 1804cc000 00:05 5655                      /dev/dri/card0
7fe5bd994000-7fe5bdb80000 rwxs 180d4a000 00:05 5655                      /dev/dri/card0
7fe5bdb80000-7fe5bdf61000 rwxs 00000000 00:04 1736716                    /SYSV00000000 (deleted)
7fe5bdf61000-7fe5bdf77000 r-xp 00000000 00:11 96202                      /home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/libdcpr.so
7fe5bdf77000-7fe5be079000 ---p 00016000 00:11 96202                      /home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/libdcpr.so
7fe5be079000-7fe5be091000 rwxp 00018000 00:11 96202                      /home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/libdcpr.so
7fe5be44a000-7fe5be44d000 ---p 00000000 00:00 0 
7fe5be44d000-7fe5be54b000 rwxp 00000000 00:00 0 
7fe5be54b000-7fe5be54d000 rwxs 180348000 00:05 5655                      /dev/dri/card0
7fe5be54d000-7fe5be55d000 rwxs 180332000 00:05 5655                      /dev/dri/card0
7fe5be55e000-7fe5be55f000 rwxs 180320000 00:05 5655                      /dev/dri/card0
7fe5be562000-7fe5be563000 rwxs 18031c000 00:05 5655                      /dev/dri/card0
7fe5be565000-7fe5be566000 rwxs 180319000 00:05 5655                      /dev/dri/card0
7fe5be569000-7fe5be56a000 rwxs 180317000 00:05 5655                      /dev/dri/card0
7fe5be571000-7fe5be574000 ---p 00000000 00:00 0 
7fe5be574000-7fe5be672000 rwxp 00000000 00:00 0 
7fe5be672000-7fe5be699000 r-xp 00000000 00:11 1980                       /lib/x86_64-linux-gnu/libexpat.so.1.5.2
7fe5be699000-7fe5be899000 ---p 00027000 00:11 1980                       /lib/x86_64-linux-gnu/libexpat.so.1.5.2
7fe5be899000-7fe5be89b000 r-xp 00027000 00:11 1980                       /lib/x86_64-linux-gnu/libexpat.so.1.5.2
7fe5be89b000-7fe5be89c000 rwxp 00029000 00:11 1980                       /lib/x86_64-linux-gnu/libexpat.so.1.5.2
7fe5be89c000-7fe5be996000 r-xp 00000000 00:11 3389                       /usr/lib/dri/libglsl.so
7fe5be996000-7fe5beb95000 ---p 000fa000 00:11 3389                       /usr/lib/dri/libglsl.so
7fe5beb95000-7fe5beb9d000 r-xp 000f9000 00:11 3389                       /usr/lib/dri/libglsl.so
7fe5beb9d000-7fe5beb9f000 rwxp 00101000 00:11 3389                       /usr/lib/dri/libglsl.so
7fe5beb9f000-7fe5beba0000 rwxp 00000000 00:00 0 
7fe5beba0000-7fe5bedb8000 r-xp 00000000 00:11 3384                       /usr/lib/dri/libdricore.so
7fe5bedb8000-7fe5befb8000 ---p 00218000 00:11 3384                       /usr/lib/dri/libdricore.so
7fe5befb8000-7fe5befc2000 r-xp 00218000 00:11 3384                       /usr/lib/dri/libdricore.so
7fe5befc2000-7fe5befc5000 rwxp 00222000 00:11 3384                       /usr/lib/dri/libdricore.so
7fe5befc5000-7fe5befd5000 rwxp 00000000 00:00 0 
7fe5befd5000-7fe5bf312000 r-xp 00000000 00:11 3371                       /usr/lib/dri/r600_dri.so
7fe5bf312000-7fe5bf512000 ---p 0033d000 00:11 3371                       /usr/lib/dri/r600_dri.so
7fe5bf512000-7fe5bf529000 r-xp 0033d000 00:11 3371                       /usr/lib/dri/r600_dri.so
7fe5bf529000-7fe5bf530000 rwxp 00354000 00:11 3371                       /usr/lib/dri/r600_dri.so
7fe5bf530000-7fe5bf57e000 rwxp 00000000 00:00 0 
7fe5bf57e000-7fe5bf581000 ---p 00000000 00:00 0 
7fe5bf581000-7fe5bf67f000 rwxp 00000000 00:00 0 
7fe5bf67f000-7fe5bf682000 ---p 00000000 00:00 0 
7fe5bf682000-7fe5bf780000 rwxp 00000000 00:00 0 
7fe5bf780000-7fe5bf783000 ---p 00000000 00:00 0 
7fe5bf783000-7fe5bf881000 rwxp 00000000 00:00 0 
7fe5bf881000-7fe5bf884000 ---p 00000000 00:00 0 
7fe5bf884000-7fe5bf982000 rwxp 00000000 00:00 0 
7fe5bf982000-7fe5bf989000 r-xp 00000000 00:11 96168                      /home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/libnio.so
7fe5bf989000-7fe5bfa88000 ---p 00007000 00:11 96168                      /home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/libnio.so
7fe5bfa88000-7fe5bfa8a000 rwxp 00006000 00:11 96168                      /home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/libnio.so
7fe5bfa8a000-7fe5bfa9d000 r-xp 00000000 00:11 96167                      /home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/libnet.so
7fe5bfa9d000-7fe5bfb9e000 ---p 00013000 00:11 96167                      /home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/libnet.so
7fe5bfb9e000-7fe5bfba1000 rwxp 00014000 00:11 96167                      /home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/libnet.so
7fe5bfba1000-7fe5bfba4000 ---p 00000000 00:00 0 
7fe5bfba4000-7fe5bfca2000 rwxp 00000000 00:00 0 
7fe5bfca2000-7fe5bfca5000 ---p 00000000 00:00 0 
7fe5bfca5000-7fe5bfda3000 rwxp 00000000 00:00 0 
7fe5bfda3000-7fe5bfde1000 r-xp 00000000 00:11 96556                      /home/ubuntu/Desktop/Engys/HelyxOS/v1.0.0/ext/libvtkParallelJava.so.5.10.0
7fe5bfde1000-7fe5bfee1000 ---p 0003e000 00:11 96556                      /home/ubuntu/Desktop/Engys/HelyxOS/v1.0.0/ext/libvtkParallelJava.so.5.10.0
7fe5bfee1000-7fe5bfee2000 rwxp 0003e000 00:11 96556                      /home/ubuntu/Desktop/Engys/HelyxOS/v1.0.0/ext/libvtkParallelJava.so.5.10.0
7fe5bfee2000-7fe5bfee5000 ---p 00000000 00:00 0 
7fe5bfee5000-7fe5bffe3000 rwxp 00000000 00:00 0 
7fe5bffe3000-7fe5bffe6000 ---p 00000000 00:00 0 
7fe5bffe6000-7fe5c00e4000 rwxp 00000000 00:00 0 
7fe5c00e4000-7fe5c015d000 r-xp 00000000 00:11 96176                      /home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/libfontmanager.so
7fe5c015d000-7fe5c025c000 ---p 00079000 00:11 96176                      /home/ubuntu/Desktop/Engys/HelyxOS/jre/lib/amd64/libfontmanager.so./helyxOS.sh: line 124: 18069 Przerwane               (core dumped) ${JAVA} ${LOCALEFLAG} ${JFLAG} ${XFLAG} ${HELYXJAR} ${HELYXARG} ${VERBOSITY_LEVEL} $@ 1>&2
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Old   October 9, 2012, 06:37
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Daniel P. Combest
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chegdan will become famous soon enoughchegdan will become famous soon enough
can you load your STL file in Paraview?
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Old   October 14, 2012, 15:28
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Krzysztof Wołosz
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Hello and Welcome in my first post in the forum.

I have also a problem during the STL ASCII import into the Helyx OS. The crash looks the same as mentioned above. And answering the Dan's question: Yes, I can load the STL file in the Paraview and everything looks good.
Some answers may be given when the file presented in the example http://www.youtube.com/watch?v=yJbFnFzDLqo
could be available (ahmed_body.stl).

Regards

Christopher

Quote:
Originally Posted by chegdan View Post
can you load your STL file in Paraview?
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Old   October 15, 2012, 07:06
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Quote:
Originally Posted by kjw View Post
Hello and Welcome in my first post in the forum.

I have also a problem during the STL ASCII import into the Helyx OS. The crash looks the same as mentioned above. And answering the Dan's question: Yes, I can load the STL file in the Paraview and everything looks good.
Some answers may be given when the file presented in the example http://www.youtube.com/watch?v=yJbFnFzDLqo
could be available (ahmed_body.stl).

Regards

Christopher
What is the result of the command

Code:
locale
and also, what is the character in your STL file that is used to separate the decimal numbers i.e. is it 3.14159 or 3,14159?
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Old   October 16, 2012, 04:01
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Krzysztof Wołosz
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Good question was the answer. I had polish locales set and when I changed it to english everything is correct and works fine.

Regards

Quote:
Originally Posted by chegdan View Post
What is the result of the command

Code:
locale
and also, what is the character in your STL file that is used to separate the decimal numbers i.e. is it 3.14159 or 3,14159?
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Old   October 16, 2012, 06:58
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chegdan will become famous soon enoughchegdan will become famous soon enough
Excellent! This happens to be a VTK problem that is not completely fixed in the VTK distribution. Another possible solution is to change your decimal separator to a "," in your STL file instead of changing your language settings.

Quote:
Originally Posted by kjw View Post
Good question was the answer. I had polish locales set and when I changed it to english everything is correct and works fine.

Regards
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