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Old   July 23, 2014, 02:25
Default foam-extend_3.1 decompose and pyfoam warning
  #1
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Baris (Heewa)
Join Date: Jan 2013
Location: Japan
Posts: 123
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Hi to everybody,

I am using foam-extend 3.1 and ubuntu version 12.04. After installation 3.1, when i tried to decompose my case although it gives following warning it makes decomposition:

HTML Code:
Create mesh for region region0

Calculating distribution of cells
--> FOAM Warning : 
    From function dlLibraryTable::open(const fileName& functionLibName)
    in file db/dlLibraryTable/dlLibraryTable.C at line 85
    could not load libmetisDecomp.so: cannot open shared object file: No such file or directory
--> FOAM Warning : 
    From function decompositionMethod::loadExternalLibraries()
    in file decompositionMethod/decompositionMethod.C at line 453
    Loading of decomposition library libmetisDecomp.so unsuccesful. Some decomposition methods may not be  available
--> FOAM Warning : 
    From function dlLibraryTable::open(const fileName& functionLibName)
    in file db/dlLibraryTable/dlLibraryTable.C at line 85
    could not load libparMetisDecomp.so: cannot open shared object file: No such file or directory
--> FOAM Warning : 
    From function decompositionMethod::loadExternalLibraries()
    in file decompositionMethod/decompositionMethod.C at line 453
    Loading of decomposition library libparMetisDecomp.so unsuccesful. Some decomposition methods may not be  available
Selecting decompositionMethod simple

Finished decomposition in 0.25 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Calculating processor boundary addressing

Distributing points to processors

Constructing processor meshes

Processor 0
    Number of cells = 11668
    Number of faces shared with processor 1 = 11850
    Number of faces shared with processor 4 = 104
    Number of processor patches = 2
    Number of processor faces = 11954
    Number of boundary faces = 11898

Processor 1
    Number of cells = 20171
    Number of faces shared with processor 0 = 11850
    Number of faces shared with processor 2 = 1605
    Number of faces shared with processor 5 = 296
    Number of processor patches = 3
    Number of processor faces = 13751
    Number of boundary faces = 2282

Processor 2
    Number of cells = 16737
    Number of faces shared with processor 1 = 1605
    Number of faces shared with processor 3 = 1190
    Number of faces shared with processor 6 = 263
    Number of faces shared with processor 5 = 22
    Number of faces shared with processor 7 = 6
    Number of processor patches = 5
    Number of processor faces = 3086
    Number of boundary faces = 6942

Processor 3
    Number of cells = 16510
    Number of faces shared with processor 2 = 1190
    Number of faces shared with processor 7 = 348
    Number of processor patches = 2
    Number of processor faces = 1538
    Number of boundary faces = 6888

Processor 4
    Number of cells = 13049
    Number of faces shared with processor 5 = 11874
    Number of faces shared with processor 0 = 104
    Number of faces shared with processor 8 = 155
    Number of processor patches = 3
    Number of processor faces = 12133
    Number of boundary faces = 12051

Processor 5
    Number of cells = 19115
    Number of faces shared with processor 4 = 11874
    Number of faces shared with processor 1 = 296
    Number of faces shared with processor 6 = 1559
    Number of faces shared with processor 2 = 22
    Number of faces shared with processor 9 = 232
    Number of faces shared with processor 8 = 50
    Number of processor patches = 6
    Number of processor faces = 14033
    Number of boundary faces = 2193

Processor 6
    Number of cells = 16566
    Number of faces shared with processor 5 = 1559
    Number of faces shared with processor 2 = 263
    Number of faces shared with processor 7 = 1157
    Number of faces shared with processor 10 = 242
    Number of faces shared with processor 9 = 1
    Number of faces shared with processor 11 = 3
    Number of processor patches = 6
    Number of processor faces = 3225
    Number of boundary faces = 6844

Processor 7
    Number of cells = 16356
    Number of faces shared with processor 3 = 348
    Number of faces shared with processor 6 = 1157
    Number of faces shared with processor 2 = 6
    Number of faces shared with processor 11 = 320
    Number of processor patches = 4
    Number of processor faces = 1831
    Number of boundary faces = 6795

Processor 8
    Number of cells = 24098
    Number of faces shared with processor 4 = 155
    Number of faces shared with processor 9 = 10882
    Number of faces shared with processor 5 = 50
    Number of faces shared with processor 10 = 102
    Number of processor patches = 4
    Number of processor faces = 11189
    Number of boundary faces = 13084

Processor 9
    Number of cells = 9528
    Number of faces shared with processor 8 = 10882
    Number of faces shared with processor 5 = 232
    Number of faces shared with processor 10 = 1626
    Number of faces shared with processor 6 = 1
    Number of processor patches = 4
    Number of processor faces = 12741
    Number of boundary faces = 1943

Processor 10
    Number of cells = 15511
    Number of faces shared with processor 6 = 242
    Number of faces shared with processor 9 = 1626
    Number of faces shared with processor 11 = 1318
    Number of faces shared with processor 8 = 102
    Number of processor patches = 4
    Number of processor faces = 3288
    Number of boundary faces = 6414

Processor 11
    Number of cells = 15948
    Number of faces shared with processor 7 = 320
    Number of faces shared with processor 10 = 1318
    Number of faces shared with processor 6 = 3
    Number of processor patches = 3
    Number of processor faces = 1641
    Number of boundary faces = 6795

Number of processor faces = 45205
Max number of processor patches = 6
Max number of faces between processors = 14033

Processor 0: field transfer
Processor 1: field transfer
Processor 2: field transfer
Processor 3: field transfer
Processor 4: field transfer
Processor 5: field transfer
Processor 6: field transfer
Processor 7: field transfer
Processor 8: field transfer
Processor 9: field transfer
Processor 10: field transfer
Processor 11: field transfer

End.
Then to check this warning i run the foamIstallation and it gives following error:

HTML Code:
Executing /home/baris/foam/foam-extend-3.1/bin/foamInstallationTest:


Checking basic setup...
-------------------------------------------------------------------------------
Shell:              bash
Host:               baris-desktop
OS:                 Linux version 3.2.0-29-generic
-------------------------------------------------------------------------------


Checking main foam-extend env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid      Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /home/baris/foam                         yes       yes
$WM_PROJECT_USER_DIR /home/baris/foam/baris-3.1               no        no
$WM_THIRD_PARTY_DIR  ...aris/foam/foam-extend-3.1/ThirdParty  yes       yes
-------------------------------------------------------------------------------


Checking the foam-extend env variables set on the PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid Path Crit
-------------------------------------------------------------------------------
$WM_PROJECT_DIR      /home/baris/foam/foam-extend-3.1         yes  yes  yes

$FOAM_APPBIN         ...3.1/applications/bin/linux64GccDPOpt  yes  yes  yes
$FOAM_SITE_APPBIN    ...is/foam/site/3.1/bin/linux64GccDPOpt  yes  yes  no
$FOAM_USER_APPBIN    ...3.1/applications/bin/linux64GccDPOpt  no        no
$WM_DIR              /home/baris/foam/foam-extend-3.1/wmake   yes  yes  yes
-------------------------------------------------------------------------------


Checking the foam-extend env variables set on the LD_LIBRARY_PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid Path Crit
-------------------------------------------------------------------------------
$FOAM_LIBBIN         .../foam-extend-3.1/lib/linux64GccDPOpt  yes  yes  yes
$FOAM_SITE_LIBBIN    ...is/foam/site/3.1/lib/linux64GccDPOpt  yes  yes  no
$FOAM_USER_LIBBIN    ...s/foam/baris-3.1/lib/linux64GccDPOpt  no        no
$MPI_ARCH_PATH       ...nmpi-1.6.5/platforms/linux64GccDPOpt  yes  yes  yes
-------------------------------------------------------------------------------


Third party software
-------------------------------------------------------------------------------
Software Version   Location 
-------------------------------------------------------------------------------
WARNING: gcc version does not match gcc supplied with this release of foam-extend
         Supplied version: 4.3.3
         User version    : 4.6.3
         Minimum required: 4.3.1

gcc      4.6.3    
WARNING:  Conflicting installations:
          foam-extend settings        : /bin/gcc
          current path             : /usr/bin/gcc
          CRITICAL ERROR

gzip     1.4       /bin/gzip                                                
tar      1.26      /bin/tar                                                 
icoFoam            ...am-extend-3.1/applications/bin/linux64GccDPOpt/icoFoam
-------------------------------------------------------------------------------


Summary
-------------------------------------------------------------------------------
Base configuration ok.

The foam installation contains 1 critical error(s).

Review the output for warning messages and consult 
the installation guide for trouble shooting.

done.
Could someone help to me how can i correct this error?

On the other hand, when i also tried to run parallel by using pyfoam it gives attached warning, but it is going to run. I am a bit confused about it. So, also about this if someone have idea i will be appreciated.

thanks a lot.

B
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Old   July 23, 2014, 16:44
Default
  #2
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Bernhard Gschaider
Join Date: Mar 2009
Posts: 3,915
Rep Power: 40
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Quote:
Originally Posted by shipman View Post
Hi to everybody,

I am using foam-extend 3.1 and ubuntu version 12.04. After installation 3.1, when i tried to decompose my case although it gives following warning it makes decomposition:

HTML Code:
Create mesh for region region0

Calculating distribution of cells
--> FOAM Warning : 
    From function dlLibraryTable::open(const fileName& functionLibName)
    in file db/dlLibraryTable/dlLibraryTable.C at line 85
    could not load libmetisDecomp.so: cannot open shared object file: No such file or directory
--> FOAM Warning : 
    From function decompositionMethod::loadExternalLibraries()
    in file decompositionMethod/decompositionMethod.C at line 453
    Loading of decomposition library libmetisDecomp.so unsuccesful. Some decomposition methods may not be  available
--> FOAM Warning : 
    From function dlLibraryTable::open(const fileName& functionLibName)
    in file db/dlLibraryTable/dlLibraryTable.C at line 85
    could not load libparMetisDecomp.so: cannot open shared object file: No such file or directory
--> FOAM Warning : 
    From function decompositionMethod::loadExternalLibraries()
    in file decompositionMethod/decompositionMethod.C at line 453
    Loading of decomposition library libparMetisDecomp.so unsuccesful. Some decomposition methods may not be  available
Selecting decompositionMethod simple

Finished decomposition in 0.25 s

Calculating original mesh data

Could someone help to me how can i correct this error?

On the other hand, when i also tried to run parallel by using pyfoam it gives attached warning, but it is going to run. I am a bit confused about it. So, also about this if someone have idea i will be appreciated.

thanks a lot.

B
Have a look at your output: it is only a warning and says
Code:
Loading of decomposition library libmetisDecomp.so unsuccesful. Some decomposition methods may not be  available
Seems like metis and parMetis from the ThirdParty-directory did not compile correctly and therefor these decomposition methods were not compiled. But this doesn't concern you as you're using simple.
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Old   July 24, 2014, 03:28
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  #3
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Baris (Heewa)
Join Date: Jan 2013
Location: Japan
Posts: 123
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Hi Bernhard,

Thank you for the information. Could you also tell me how can i correctly compile the metis and parMetis from the ThirdParty-directory.

Also, do you have any idea about my 2nd (after runing the foamIstallation and it gives error) and 3rd (pyfoam warning) problems?

Thanks in advance.

Baris
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Old   July 24, 2014, 08:14
Default
  #4
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Bernhard Gschaider
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Quote:
Originally Posted by shipman View Post
Hi Bernhard,

Thank you for the information. Could you also tell me how can i correctly compile the metis and parMetis from the ThirdParty-directory.
I'll have to ask you to look elsewhere
a) I have no information whatsoever about your system
b) most probably somebody else already had the problem. Search the Board
c) my time is limited and I currently focus on swak4foam and pyFoam because I think there are few people here on the board with my expertise on these two. Installation-issues there are more people

Quote:
Originally Posted by shipman View Post
Also, do you have any idea about my 2nd (after runing the foamIstallation and it gives error) and 3rd (pyfoam warning) problems?
Same for your second question.

Third question: please don't post screenshots of terminal output. It is hard to read and it is not searchable. From the blury pixels it looks like it is only a warning. Basically it found a string, tried to interpret it as a number and fails. Instead of failing it just informed you. To get to the heart of the matter I'd have to type it from your screenshot, hope that I didn't misstype it and try on my machine. Which I refuse to do. See c) above (first 4 words)
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