CFD Online Logo CFD Online URL
www.cfd-online.com
[Sponsors]
Home > Forums > Software User Forums > SU2 > SU2 Installation

Errors when installing cgns library

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

Reply
 
LinkBack Thread Tools Search this Thread Display Modes
Old   January 12, 2015, 00:05
Default Errors when installing cgns library
  #1
New Member
 
Yan Bochao
Join Date: Aug 2014
Posts: 14
Rep Power: 10
wruudf is on a distinguished road
I'm trying to install SU2 in Macbook Yosemite and failed for lots of times. The latest one is when I was trying to install CGNS library with cmake and get errors below:[ 7%] Building C object src/CMakeFiles/cgns_shared.dir/cgio_ftoc.c.o
Linking C shared library libcgns.dylib
Undefined symbols for architecture x86_64:
"_H5Aclose", referenced from:
_get_str_att in ADFH.c.o
_set_str_att in ADFH.c.o
_ADFH_Create in ADFH.c.o
_new_str_att in ADFH.c.o
_ADFH_Database_Close in ADFH.c.o
"_H5Acreate2", referenced from:
_ADFH_Create in ADFH.c.o
_new_str_att in ADFH.c.o
"_H5Aget_type", referenced from:
_get_str_att in ADFH.c.o
_set_str_att in ADFH.c.o
"_H5Aiterate2", referenced from:
_get_str_att in ADFH.c.o
_set_str_att in ADFH.c.o
"_H5Aopen_name", referenced from:
_get_str_att in ADFH.c.o
_set_str_att in ADFH.c.o
"_H5Aread", referenced from:
_get_str_att in ADFH.c.o
"_H5Awrite", referenced from:
_set_str_att in ADFH.c.o
_ADFH_Create in ADFH.c.o
_new_str_att in ADFH.c.o
"_H5Dclose", referenced from:
_new_str_data in ADFH.c.o
_fix_dimensions in ADFH.c.o
_ADFH_Database_Get_Format in ADFH.c.o
_ADFH_Database_Close in ADFH.c.o
_ADFH_Is_Link in ADFH.c.o
_ADFH_Link_Size in ADFH.c.o
_ADFH_Get_Number_of_Dimensions in ADFH.c.o
...
"_H5Dcreate2", referenced from:
_new_str_data in ADFH.c.o
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5Dget_space", referenced from:
_fix_dimensions in ADFH.c.o
_ADFH_Is_Link in ADFH.c.o
_ADFH_Link_Size in ADFH.c.o
_ADFH_Get_Number_of_Dimensions in ADFH.c.o
_ADFH_Get_Dimension_Values in ADFH.c.o
_ADFH_Read_Block_Data in ADFH.c.o
_ADFH_Read_Data in ADFH.c.o
...
"_H5Dget_type", referenced from:
_ADFH_Read_Block_Data in ADFH.c.o
_ADFH_Read_Data in ADFH.c.o
_ADFH_Read_All_Data in ADFH.c.o
_ADFH_Write_Block_Data in ADFH.c.o
_ADFH_Write_Data in ADFH.c.o
_ADFH_Write_All_Data in ADFH.c.o
"_H5Dopen2", referenced from:
_fix_dimensions in ADFH.c.o
_ADFH_Database_Get_Format in ADFH.c.o
_ADFH_Is_Link in ADFH.c.o
_ADFH_Link_Size in ADFH.c.o
_ADFH_Get_Number_of_Dimensions in ADFH.c.o
_ADFH_Get_Dimension_Values in ADFH.c.o
_ADFH_Get_Link_Path in ADFH.c.o
...
"_H5Dread", referenced from:
_ADFH_Database_Get_Format in ADFH.c.o
_ADFH_Get_Link_Path in ADFH.c.o
_ADFH_Database_Version in ADFH.c.o
_ADFH_Read_Block_Data in ADFH.c.o
_ADFH_Read_Data in ADFH.c.o
_ADFH_Read_All_Data in ADFH.c.o
_ADFH_Write_Block_Data in ADFH.c.o
...
"_H5Dset_extent", referenced from:
_fix_dimensions in ADFH.c.o
"_H5Dwrite", referenced from:
_new_str_data in ADFH.c.o
_ADFH_Write_Block_Data in ADFH.c.o
_ADFH_Write_Data in ADFH.c.o
_ADFH_Write_All_Data in ADFH.c.o
"_H5Eset_auto2", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5Ewalk2", referenced from:
_walk_H5_error in ADFH.c.o
"_H5Fclose", referenced from:
_ADFH_Database_Close in ADFH.c.o
"_H5Fcreate", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5Fflush", referenced from:
_ADFH_Flush_to_Disk in ADFH.c.o
"_H5Fget_obj_count", referenced from:
_ADFH_Database_Close in ADFH.c.o
"_H5Fget_obj_ids", referenced from:
_ADFH_Database_Close in ADFH.c.o
"_H5Fis_hdf5", referenced from:
_ADFH_Database_Open in ADFH.c.o
_ADFH_Database_Valid in ADFH.c.o
_ADFH_Database_Delete in ADFH.c.o
"_H5Fopen", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5Gclose", referenced from:
_ADFH_Get_Label in ADFH.c.o
_ADFH_Delete in ADFH.c.o
_ADFH_Number_of_Children in ADFH.c.o
_ADFH_Get_Node_ID in ADFH.c.o
_parse_path in ADFH.c.o
_ADFH_Children_Names in ADFH.c.o
_ADFH_Children_IDs in ADFH.c.o
...
"_H5Gcreate2", referenced from:
_ADFH_Create in ADFH.c.o
"_H5Gget_objinfo", referenced from:
_ADFH_Move_Child in ADFH.c.o
_compare_children in ADFH.c.o
_ADFH_Delete in ADFH.c.o
_open_link in ADFH.c.o
_ADFH_Database_Close in ADFH.c.o
"_H5Giterate", referenced from:
_ADFH_Move_Child in ADFH.c.o
_ADFH_Put_Name in ADFH.c.o
_ADFH_Create in ADFH.c.o
_ADFH_Delete in ADFH.c.o
_delete_children in ADFH.c.o
_ADFH_Number_of_Children in ADFH.c.o
_ADFH_Database_Open in ADFH.c.o
...
"_H5Glink", referenced from:
_ADFH_Link in ADFH.c.o
"_H5Gmove", referenced from:
_ADFH_Move_Child in ADFH.c.o
_ADFH_Put_Name in ADFH.c.o
_ADFH_Database_Open in ADFH.c.o
"_H5Gopen2", referenced from:
_ADFH_Get_Label in ADFH.c.o
_ADFH_Number_of_Children in ADFH.c.o
_ADFH_Get_Node_ID in ADFH.c.o
_parse_path in ADFH.c.o
_open_link in ADFH.c.o
_ADFH_Children_Names in ADFH.c.o
_ADFH_Children_IDs in ADFH.c.o
...
"_H5Gunlink", referenced from:
_ADFH_Delete in ADFH.c.o
_delete_children in ADFH.c.o
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5Iget_name", referenced from:
_ADFH_Move_Child in ADFH.c.o
"_H5Lcreate_external", referenced from:
_ADFH_Link in ADFH.c.o
"_H5Lexists", referenced from:
_ADFH_Get_Dimension_Values in ADFH.c.o
_ADFH_Put_Dimension_Information in ADFH.c.o
_ADFH_Read_Data in ADFH.c.o
_ADFH_Write_Data in ADFH.c.o
"_H5Lget_val", referenced from:
_open_link in ADFH.c.o
"_H5Lis_registered", referenced from:
_open_link in ADFH.c.o
"_H5Literate", referenced from:
_ADFH_Children_Names in ADFH.c.o
_ADFH_Children_IDs in ADFH.c.o
"_H5Lunpack_elink_val", referenced from:
_open_link in ADFH.c.o
"_H5P_CLS_DATASET_CREATE_ID_g", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5P_CLS_FILE_ACCESS_ID_g", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5P_CLS_FILE_CREATE_ID_g", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5P_CLS_GROUP_CREATE_ID_g", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5P_CLS_LINK_ACCESS_ID_g", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5Pclose", referenced from:
_ADFH_Database_Open in ADFH.c.o
_ADFH_Database_Close in ADFH.c.o
"_H5Pcreate", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5Pset_deflate", referenced from:
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5Pset_libver_bounds", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5Pset_link_creation_order", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5Pset_nlinks", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5Sclose", referenced from:
_ADFH_Create in ADFH.c.o
_new_str_att in ADFH.c.o
_new_str_data in ADFH.c.o
_fix_dimensions in ADFH.c.o
_ADFH_Is_Link in ADFH.c.o
_ADFH_Link_Size in ADFH.c.o
_ADFH_Get_Number_of_Dimensions in ADFH.c.o
...
"_H5Screate", referenced from:
_new_str_att in ADFH.c.o
"_H5Screate_simple", referenced from:
_ADFH_Create in ADFH.c.o
_new_str_data in ADFH.c.o
_ADFH_Put_Dimension_Information in ADFH.c.o
_ADFH_Read_Data in ADFH.c.o
_ADFH_Write_Data in ADFH.c.o
"_H5Sget_select_npoints", referenced from:
_ADFH_Read_Data in ADFH.c.o
_ADFH_Write_Data in ADFH.c.o
"_H5Sget_simple_extent_dims", referenced from:
_fix_dimensions in ADFH.c.o
_ADFH_Get_Dimension_Values in ADFH.c.o
_ADFH_Read_Data in ADFH.c.o
_ADFH_Write_Data in ADFH.c.o
"_H5Sget_simple_extent_ndims", referenced from:
_ADFH_Get_Number_of_Dimensions in ADFH.c.o
_ADFH_Get_Dimension_Values in ADFH.c.o
_ADFH_Read_Data in ADFH.c.o
_ADFH_Write_Data in ADFH.c.o
"_H5Sget_simple_extent_npoints", referenced from:
_ADFH_Is_Link in ADFH.c.o
_ADFH_Link_Size in ADFH.c.o
_ADFH_Read_Block_Data in ADFH.c.o
_ADFH_Write_Block_Data in ADFH.c.o
"_H5Sselect_hyperslab", referenced from:
_ADFH_Read_Data in ADFH.c.o
_ADFH_Write_Data in ADFH.c.o
"_H5T_C_S1_g", referenced from:
_new_str_att in ADFH.c.o
"_H5T_IEEE_F32BE_g", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5T_IEEE_F32LE_g", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5T_IEEE_F64BE_g", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5T_IEEE_F64LE_g", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5T_NATIVE_DOUBLE_g", referenced from:
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5T_NATIVE_FLOAT_g", referenced from:
_ADFH_Database_Open in ADFH.c.o
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5T_NATIVE_INT32_g", referenced from:
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5T_NATIVE_INT64_g", referenced from:
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5T_NATIVE_INT_g", referenced from:
_ADFH_Create in ADFH.c.o
"_H5T_NATIVE_SCHAR_g", referenced from:
_new_str_data in ADFH.c.o
_ADFH_Database_Get_Format in ADFH.c.o
_ADFH_Put_Dimension_Information in ADFH.c.o
_ADFH_Get_Link_Path in ADFH.c.o
_ADFH_Database_Version in ADFH.c.o
"_H5T_NATIVE_UCHAR_g", referenced from:
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5T_NATIVE_UINT32_g", referenced from:
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5T_NATIVE_UINT64_g", referenced from:
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5Tclose", referenced from:
_get_str_att in ADFH.c.o
_set_str_att in ADFH.c.o
_new_str_att in ADFH.c.o
_ADFH_Database_Open in ADFH.c.o
_ADFH_Database_Close in ADFH.c.o
_ADFH_Put_Dimension_Information in ADFH.c.o
_ADFH_Read_Block_Data in ADFH.c.o
...
"_H5Tcopy", referenced from:
_new_str_att in ADFH.c.o
_ADFH_Database_Open in ADFH.c.o
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5Tequal", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5Tget_native_type", referenced from:
_ADFH_Read_Block_Data in ADFH.c.o
_ADFH_Read_Data in ADFH.c.o
_ADFH_Read_All_Data in ADFH.c.o
_ADFH_Write_Block_Data in ADFH.c.o
_ADFH_Write_Data in ADFH.c.o
_ADFH_Write_All_Data in ADFH.c.o
"_H5Tget_precision", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5Tget_size", referenced from:
_ADFH_Read_Block_Data in ADFH.c.o
_ADFH_Write_Block_Data in ADFH.c.o
"_H5Tset_precision", referenced from:
_ADFH_Put_Dimension_Information in ADFH.c.o
"_H5Tset_size", referenced from:
_new_str_att in ADFH.c.o
"_H5check_version", referenced from:
_ADFH_Database_Open in ADFH.c.o
"_H5garbage_collect", referenced from:
_ADFH_Database_Garbage_Collection in ADFH.c.o
"_H5get_libversion", referenced from:
_ADFH_Database_Open in ADFH.c.o
_ADFH_Library_Version in ADFH.c.o
"_H5open", referenced from:
_ADFH_Create in ADFH.c.o
_new_str_att in ADFH.c.o
_ADFH_Database_Open in ADFH.c.o
_new_str_data in ADFH.c.o
_ADFH_Database_Get_Format in ADFH.c.o
_ADFH_Put_Dimension_Information in ADFH.c.o
_ADFH_Get_Link_Path in ADFH.c.o
...
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [src/libcgns.3.2.dylib] Error 1
make[1]: *** [src/CMakeFiles/cgns_shared.dir/all] Error 2
make: *** [all] Error 2

The cmake settings are in the attachment.

The hdf5 library is already installed. I think it should be the link to the library didn't work, but I don't know how to figure it out and how to deal with it.
Attached Images
File Type: jpeg cmake.jpeg (57.8 KB, 7 views)
wruudf is offline   Reply With Quote

Old   January 16, 2015, 03:30
Default
  #2
Super Moderator
 
Thomas D. Economon
Join Date: Jan 2013
Location: Stanford, CA
Posts: 271
Rep Power: 13
economon is on a distinguished road
Hi,

Thanks for the question.. at the time of writing, we recommend using the CGNS library without HDF5 support. More specifically, please try compiling a static library (.a) of CGNS v3.1.4 (without HDF5) and then try linking to SU2 once again during your configure call. This is the configuration that we typically use. If you're still having issues, please let us know.

Hope this helps,

Thomas D. Economon
SU2 lead developer
economon is offline   Reply With Quote

Old   January 18, 2015, 22:40
Default
  #3
New Member
 
Yan Bochao
Join Date: Aug 2014
Posts: 14
Rep Power: 10
wruudf is on a distinguished road
Thanks for your reply. By ticking off the Enable_HDF5, the errors above was skipped. But an new error comes out.

Errors:

Undefined symbols for architecture x86_64:
"_glXChooseVisual", referenced from:
_OGLwinCmd in libtkogl.a(tkogl.c.o)
"_glXCreateContext", referenced from:
_OGLwinCmd in libtkogl.a(tkogl.c.o)
"_glXMakeCurrent", referenced from:
_OGLwinCmd in libtkogl.a(tkogl.c.o)
_OGLwinWidgetCmd in libtkogl.a(tkogl.c.o)
_OGLwinRedraw in libtkogl.a(tkogl.c.o)
"_glXQueryExtension", referenced from:
_Tkogl_Init in libtkogl.a(tkogl.c.o)
"_glXSwapBuffers", referenced from:
_OGLwinRedraw in libtkogl.a(tkogl.c.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [src/cgnstools/cgnsplot/plotwish] Error 1
make[1]: *** [src/cgnstools/cgnsplot/CMakeFiles/plotwish.dir/all] Error 2
make: *** [all] Error 2

Mac has an X11 already, and I also install the Xquartz and OpenGL.
wruudf is offline   Reply With Quote

Old   January 18, 2015, 22:41
Default
  #4
New Member
 
Yan Bochao
Join Date: Aug 2014
Posts: 14
Rep Power: 10
wruudf is on a distinguished road
Thanks for your reply. By ticking off the Enable_HDF5, the errors above was skipped. But an new error comes out.

Errors:

Undefined symbols for architecture x86_64:
"_glXChooseVisual", referenced from:
_OGLwinCmd in libtkogl.a(tkogl.c.o)
"_glXCreateContext", referenced from:
_OGLwinCmd in libtkogl.a(tkogl.c.o)
"_glXMakeCurrent", referenced from:
_OGLwinCmd in libtkogl.a(tkogl.c.o)
_OGLwinWidgetCmd in libtkogl.a(tkogl.c.o)
_OGLwinRedraw in libtkogl.a(tkogl.c.o)
"_glXQueryExtension", referenced from:
_Tkogl_Init in libtkogl.a(tkogl.c.o)
"_glXSwapBuffers", referenced from:
_OGLwinRedraw in libtkogl.a(tkogl.c.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [src/cgnstools/cgnsplot/plotwish] Error 1
make[1]: *** [src/cgnstools/cgnsplot/CMakeFiles/plotwish.dir/all] Error 2
make: *** [all] Error 2

Mac has an X11 already, and I also install the Xquartz and OpenGL.
Quote:
Originally Posted by economon View Post
Hi,

Thanks for the question.. at the time of writing, we recommend using the CGNS library without HDF5 support. More specifically, please try compiling a static library (.a) of CGNS v3.1.4 (without HDF5) and then try linking to SU2 once again during your configure call. This is the configuration that we typically use. If you're still having issues, please let us know.

Hope this helps,

Thomas D. Economon
SU2 lead developer
wruudf is offline   Reply With Quote

Old   January 19, 2015, 21:29
Default
  #5
Super Moderator
 
Thomas D. Economon
Join Date: Jan 2013
Location: Stanford, CA
Posts: 271
Rep Power: 13
economon is on a distinguished road
Hi Yan,

It looks like it is failing while build the extra CGNS tools, which aren't required for SU2. You might disable this part of the build (there should be a flag for that), and just build the static library (libcgns.a). This is the only thing that we link during the SU2 build.

Hope this helps,

Thomas D. Economon
SU2 lead developer
economon is offline   Reply With Quote

Old   January 20, 2015, 07:10
Default
  #6
New Member
 
Yan Bochao
Join Date: Aug 2014
Posts: 14
Rep Power: 10
wruudf is on a distinguished road
So I only need to compile the library without any CGNS tools or it's some specific tool that I should cancel?
Quote:
Originally Posted by economon View Post
Hi Yan,

It looks like it is failing while build the extra CGNS tools, which aren't required for SU2. You might disable this part of the build (there should be a flag for that), and just build the static library (libcgns.a). This is the only thing that we link during the SU2 build.

Hope this helps,

Thomas D. Economon
SU2 lead developer
wruudf is offline   Reply With Quote

Old   January 20, 2015, 17:11
Default
  #7
Super Moderator
 
Thomas D. Economon
Join Date: Jan 2013
Location: Stanford, CA
Posts: 271
Rep Power: 13
economon is on a distinguished road
Yep! Just the library is all that you need to link to SU2.
economon is offline   Reply With Quote

Old   January 21, 2015, 23:55
Default
  #8
New Member
 
Yan Bochao
Join Date: Aug 2014
Posts: 14
Rep Power: 10
wruudf is on a distinguished road
Quote:
Originally Posted by economon View Post
Yep! Just the library is all that you need to link to SU2.
Thx~! I finally install the SU2 successfully in parallel version.

And when I want to try running the start up tutorial, errors popped out again

command linearallel_computation.py -f inv_NACA0012.cfg -n 2

Errors:

Traceback (most recent call last):
File "/Users/Eric/Downloads/su2_test/bin/parallel_computation.py", line 117, in <module>
main()
File "/Users/Eric/Downloads/su2_test/bin/parallel_computation.py", line 62, in main
options.divide_grid )
File "/Users/Eric/Downloads/su2_test/bin/parallel_computation.py", line 94, in parallel_computation
info = SU2.run.CFD(config)
File "/Users/Eric/Downloads/su2_test/bin/SU2/run/interface.py", line 92, in CFD
the_Command = build_command( the_Command , processes )
File "/Users/Eric/Downloads/su2_test/bin/SU2/run/interface.py", line 255, in build_command
raise RuntimeError , 'could not find an mpi interface'
RuntimeError: could not find an mpi interface
wruudf is offline   Reply With Quote

Reply

Thread Tools Search this Thread
Search this Thread:

Advanced Search
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 Off
Pingbacks are On
Refbacks are On


Similar Threads
Thread Thread Starter Forum Replies Last Post
Building OpenFOAM1.7.0 from source ata OpenFOAM Installation 46 March 6, 2022 14:21
How to write k and epsilon before the abnormal end xiuying OpenFOAM Running, Solving & CFD 8 August 27, 2013 16:33
Upgraded from Karmic Koala 9.10 to Lucid Lynx10.04.3 bookie56 OpenFOAM Installation 8 August 13, 2011 05:03
IcoFoam parallel woes msrinath80 OpenFOAM Running, Solving & CFD 9 July 22, 2007 03:58
Could anybody help me see this error and give help liugx212 OpenFOAM Running, Solving & CFD 3 January 4, 2006 19:07


All times are GMT -4. The time now is 22:43.