[MOAB-dev] building MOAB with CGNS support
Grindeanu, Iulian R.
iulian at mcs.anl.gov
Wed Sep 3 15:43:20 CDT 2014
cgns is missing from from your compile line
Do you use moab.make?
I mean, do you include moab.make from <moab_install>/lib/ in your makefile? And then use MOAB_LIBRARIES, etc?
After configuring moab, how does you moab.make look like ?
Iulian
________________________________________
From: Kanaev A.A. [kanaev at ibrae.ac.ru]
Sent: Wednesday, September 03, 2014 2:44 PM
To: Grindeanu, Iulian R.
Subject: RE: [MOAB-dev] building MOAB with CGNS support
Actually i also can compile nothing:
anton at ThinkPad-X230:~/work/MOAB/restart$ make
mpicxx -O0 -I/home/anton/FATHOM_DIR/moab/build/include restart.o -o restart -L/home/anton/FATHOM_DIR/zlib/zlib-1.2.8/gcc/lib -L/home/anton/FATHOM_DIR/hdf5/hdf5-1.8.11/gcc/lib -L/home/anton/FATHOM_DIR/zoltan/Zoltan_v3.6/gcc/lib -L/home/anton/FATHOM_DIR/parmetis/ParMETIS3_1 -L/home/anton/FATHOM_DIR/moab/build/lib -lMOAB -liMesh -lhdf5 -lzoltan -lparmetis -lmetis -lz
/home/anton/FATHOM_DIR/moab/build/lib/libMOAB.a(ReadCGNS.o): In function `moab::ReadCGNS::load_file(char const*, unsigned long const*, moab::FileOptions const&, moab::ReaderIface::SubsetList const*, moab::TagInfo* const*)':
ReadCGNS.cpp:(.text+0x741): undefined reference to `cg_open'
ReadCGNS.cpp:(.text+0x786): undefined reference to `cg_nbases'
ReadCGNS.cpp:(.text+0x864): undefined reference to `cg_nzones'
ReadCGNS.cpp:(.text+0x8da): undefined reference to `cg_zone_read'
ReadCGNS.cpp:(.text+0x8f5): undefined reference to `cg_nsections'
ReadCGNS.cpp:(.text+0xaa4): undefined reference to `cg_coord_read'
ReadCGNS.cpp:(.text+0xae7): undefined reference to `cg_coord_read'
ReadCGNS.cpp:(.text+0xb2a): undefined reference to `cg_coord_read'
ReadCGNS.cpp:(.text+0xeca): undefined reference to `cg_section_read'
ReadCGNS.cpp:(.text+0xf71): undefined reference to `cg_ElementDataSize'
ReadCGNS.cpp:(.text+0x102d): undefined reference to `cg_elements_read'
ReadCGNS.cpp:(.text+0x122d): undefined reference to `cg_ElementDataSize'
ReadCGNS.cpp:(.text+0x12d2): undefined reference to `cg_elements_read'
ReadCGNS.cpp:(.text+0x14d0): undefined reference to `cg_npe'
ReadCGNS.cpp:(.text+0x1a46): undefined reference to `cg_npe'
ReadCGNS.cpp:(.text+0x1b38): undefined reference to `cg_close'
/home/anton/FATHOM_DIR/moab/build/lib/libMOAB.a(WriteCGNS.o): In function `moab::WriteCGNS::write_coord_cgns(std::vector<unsigned long, std::allocator<unsigned long> >&)':
WriteCGNS.cpp:(.text+0x998): undefined reference to `cg_coord_write'
WriteCGNS.cpp:(.text+0x9b5): undefined reference to `cg_error_exit'
WriteCGNS.cpp:(.text+0x9e5): undefined reference to `cg_coord_write'
WriteCGNS.cpp:(.text+0xa06): undefined reference to `cg_error_exit'
WriteCGNS.cpp:(.text+0xa35): undefined reference to `cg_coord_write'
WriteCGNS.cpp:(.text+0xa56): undefined reference to `cg_error_exit'
/home/anton/FATHOM_DIR/moab/build/lib/libMOAB.a(WriteCGNS.o): In function `moab::WriteCGNS::write_file(char const*, bool, moab::FileOptions const&, unsigned long const*, int, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, moab::TagInfo* const*, int, int)':
WriteCGNS.cpp:(.text+0x2136): undefined reference to `cg_open'
WriteCGNS.cpp:(.text+0x2165): undefined reference to `cg_base_write'
WriteCGNS.cpp:(.text+0x21bd): undefined reference to `cg_zone_write'
WriteCGNS.cpp:(.text+0x223b): undefined reference to `cg_error_exit'
WriteCGNS.cpp:(.text+0x2259): undefined reference to `cg_error_exit'
WriteCGNS.cpp:(.text+0x2560): undefined reference to `cg_section_write'
WriteCGNS.cpp:(.text+0x257b): undefined reference to `cg_error_exit'
WriteCGNS.cpp:(.text+0x258d): undefined reference to `cg_close'
WriteCGNS.cpp:(.text+0x25a9): undefined reference to `cg_error_exit'
WriteCGNS.cpp:(.text+0x2742): undefined reference to `cg_section_write'
WriteCGNS.cpp:(.text+0x2763): undefined reference to `cg_error_exit'
WriteCGNS.cpp:(.text+0x2888): undefined reference to `cg_section_write'
WriteCGNS.cpp:(.text+0x28a3): undefined reference to `cg_error_exit'
collect2: ld returned 1 exit status
make: *** [restart] Error 1
________________________________________
From: Grindeanu, Iulian R. [iulian at mcs.anl.gov]
Sent: Wednesday, September 03, 2014 8:05 PM
To: Kanaev A.A.
Subject: RE: [MOAB-dev] building MOAB with CGNS support
can you run it manually?
just go to test/io
./cgns_test
Something else is wrong; I can't believe it is because of netcdf. The parallel tests that fail, why do they fail? Is it because you build without netcdf?
I can't figure it out :(
maybe it is a weird hdf5/zlib/slib dependency
________________________________________
From: Kanaev A.A. [kanaev at ibrae.ac.ru]
Sent: Wednesday, September 03, 2014 10:22 AM
To: Grindeanu, Iulian R.
Subject: RE: [MOAB-dev] building MOAB with CGNS support
cgns_test passed:
Making check in src
make[1]: Entering directory `/home/anton/FATHOM_DIR/moab_src/src'
make check-recursive
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/src'
Making check in parallel
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/src/parallel'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/src/parallel'
Making check in io
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/src/io'
Making check in mhdf
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/src/io/mhdf'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/src/io/mhdf'
Making check in .
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/src/io'
make[4]: Nothing to be done for `check-am'.
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/src/io'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/src/io'
Making check in LocalDiscretization
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/src/LocalDiscretization'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/src/LocalDiscretization'
Making check in .
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/src'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/src'
Making check in oldinc
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/src/oldinc'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/src/oldinc'
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/src'
make[1]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/src'
Making check in MeshFiles
make[1]: Entering directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles'
Making check in unittest
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest'
Making check in dagmc
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest/dagmc'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest/dagmc'
Making check in h5file
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest/h5file'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest/h5file'
Making check in io
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest/io'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest/io'
Making check in iGeom
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest/iGeom'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest/iGeom'
Making check in mbcslam
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest/mbcslam'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest/mbcslam'
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest'
make[3]: Nothing to be done for `check-am'.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest'
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles/unittest'
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles'
make[2]: Nothing to be done for `check-am'.
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles'
make[1]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/MeshFiles'
Making check in itaps
make[1]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps'
Making check in imesh
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps/imesh'
make check-am
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps/imesh'
make testc_cbind MOAB_iMesh_unit_tests MOAB_iMesh_extensions_tests ScdMeshF90 ScdMeshF77 FindAdjacencyF90 MOAB_iMeshP_unit_tests partest
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps/imesh'
make[4]: `testc_cbind' is up to date.
make[4]: `MOAB_iMesh_unit_tests' is up to date.
make[4]: `MOAB_iMesh_extensions_tests' is up to date.
make[4]: `ScdMeshF90' is up to date.
make[4]: `ScdMeshF77' is up to date.
make[4]: `FindAdjacencyF90' is up to date.
make[4]: `MOAB_iMeshP_unit_tests' is up to date.
make[4]: `partest' is up to date.
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps/imesh'
make check-TESTS
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps/imesh'
make[5]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps/imesh'
PASS: testc_cbind
PASS: MOAB_iMesh_unit_tests
PASS: MOAB_iMesh_extensions_tests
PASS: ScdMeshF90
PASS: ScdMeshF77
PASS: FindAdjacencyF90
PASS: MOAB_iMeshP_unit_tests
PASS: partest
==================
All 8 tests passed
==================
make[5]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps/imesh'
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps/imesh'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps/imesh'
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps/imesh'
Making check in igeom
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps/igeom'
make check-am
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps/igeom'
make testgeom testSmoothGeom testSmooth2
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps/igeom'
make[4]: `testgeom' is up to date.
make[4]: `testSmoothGeom' is up to date.
make[4]: `testSmooth2' is up to date.
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps/igeom'
make check-TESTS
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps/igeom'
make[5]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps/igeom'
PASS: testgeom
PASS: testSmoothGeom
PASS: testSmooth2
==================
All 3 tests passed
==================
make[5]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps/igeom'
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps/igeom'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps/igeom'
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps/igeom'
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/itaps'
make[2]: Nothing to be done for `check-am'.
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps'
make[1]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/itaps'
Making check in tools
make[1]: Entering directory `/home/anton/FATHOM_DIR/moab_src/tools'
Making check in .
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/tools'
make[2]: Nothing to be done for `check-am'.
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/tools'
Making check in mbzoltan
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/tools/mbzoltan'
make[2]: Nothing to be done for `check'.
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/tools/mbzoltan'
make[1]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/tools'
Making check in test
make[1]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test'
Making check in .
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test'
make range_test moab_test homxform_test scdseq_test scd_test_partn test_adj seq_man_test geom_util_test xform_test obb_test adaptive_kd_tree_tests bsp_tree_test file_options_test kd_tree_test var_len_test var_len_test_no_template tag_test mesh_set_test mbcn_test bsp_tree_poly_test reorder_test test_prog_opt coords_connect_iterate elem_eval_test spatial_locator_test test_boundbox adj_moab_test mbfacet_test gttool_test cropvol_test mergemesh_test mbground_test lloyd_smoother_test kd_tree_tool kd_tree_time
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test'
make[3]: `range_test' is up to date.
make[3]: `moab_test' is up to date.
make[3]: `homxform_test' is up to date.
make[3]: `scdseq_test' is up to date.
make[3]: `scd_test_partn' is up to date.
make[3]: `test_adj' is up to date.
make[3]: `seq_man_test' is up to date.
make[3]: `geom_util_test' is up to date.
make[3]: `xform_test' is up to date.
make[3]: `obb_test' is up to date.
make[3]: `adaptive_kd_tree_tests' is up to date.
make[3]: `bsp_tree_test' is up to date.
make[3]: `file_options_test' is up to date.
make[3]: `kd_tree_test' is up to date.
make[3]: `var_len_test' is up to date.
make[3]: `var_len_test_no_template' is up to date.
make[3]: `tag_test' is up to date.
make[3]: `mesh_set_test' is up to date.
make[3]: `mbcn_test' is up to date.
make[3]: `bsp_tree_poly_test' is up to date.
make[3]: `reorder_test' is up to date.
make[3]: `test_prog_opt' is up to date.
make[3]: `coords_connect_iterate' is up to date.
make[3]: `elem_eval_test' is up to date.
make[3]: `spatial_locator_test' is up to date.
make[3]: `test_boundbox' is up to date.
make[3]: `adj_moab_test' is up to date.
make[3]: `mbfacet_test' is up to date.
make[3]: `gttool_test' is up to date.
make[3]: `cropvol_test' is up to date.
make[3]: `mergemesh_test' is up to date.
make[3]: `mbground_test' is up to date.
make[3]: `lloyd_smoother_test' is up to date.
make[3]: `kd_tree_tool' is up to date.
make[3]: `kd_tree_time' is up to date.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test'
make check-TESTS
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test'
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test'
PASS: range_test
PASS: moab_test
PASS: homxform_test
PASS: scdseq_test
PASS: scd_test_partn
PASS: test_adj
PASS: seq_man_test
PASS: geom_util_test
PASS: xform_test
PASS: obb_test
PASS: adaptive_kd_tree_tests
PASS: bsp_tree_test
PASS: file_options_test
PASS: kd_tree_test
PASS: var_len_test
PASS: var_len_test_no_template
PASS: tag_test
PASS: mesh_set_test
PASS: mbcn_test
PASS: bsp_tree_poly_test
PASS: reorder_test
PASS: test_prog_opt
PASS: coords_connect_iterate
PASS: elem_eval_test
PASS: spatial_locator_test
PASS: test_boundbox
PASS: adj_moab_test
PASS: mbfacet_test
PASS: gttool_test
PASS: cropvol_test
PASS: mergemesh_test
PASS: mbground_test
PASS: lloyd_smoother_test
===================
All 33 tests passed
===================
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test'
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test'
Making check in io
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/io'
make readutil_test tqdcfr vtk_test cub_file_test gmsh_test nastran_test ideas_test stl_test smf_test cgns_test
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/io'
make[3]: `readutil_test' is up to date.
make[3]: `tqdcfr' is up to date.
make[3]: `vtk_test' is up to date.
make[3]: `cub_file_test' is up to date.
make[3]: `gmsh_test' is up to date.
make[3]: `nastran_test' is up to date.
make[3]: `ideas_test' is up to date.
make[3]: `stl_test' is up to date.
make[3]: `smf_test' is up to date.
make[3]: `cgns_test' is up to date.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/io'
make check-TESTS
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/io'
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/io'
PASS: readutil_test
PASS: tqdcfr
PASS: vtk_test
PASS: cub_file_test
PASS: gmsh_test
PASS: nastran_test
PASS: ideas_test
PASS: stl_test
PASS: smf_test
PASS: cgns_test
===================
All 10 tests passed
===================
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/io'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/io'
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/io'
Making check in dual
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/dual'
make dual_test
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/dual'
make[3]: `dual_test' is up to date.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/dual'
make check-TESTS
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/dual'
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/dual'
PASS: dual_test
=============
1 test passed
=============
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/dual'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/dual'
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/dual'
Making check in obb
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/obb'
make obb_test obb_time obb_tree_tool
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/obb'
make[3]: `obb_test' is up to date.
make[3]: `obb_time' is up to date.
make[3]: `obb_tree_tool' is up to date.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/obb'
make check-TESTS
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/obb'
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/obb'
PASS: obb_test
=============
1 test passed
=============
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/obb'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/obb'
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/obb'
Making check in perf
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/perf'
Making check in point_location
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/perf/point_location'
make point_location tree_searching_perf sploc_searching_perf
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/perf/point_location'
make[4]: `point_location' is up to date.
make[4]: `tree_searching_perf' is up to date.
make[4]: `sploc_searching_perf' is up to date.
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/perf/point_location'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/perf/point_location'
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/perf'
make perf seqperf adj_time perftool adj_mem_time tstt_perf_binding
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/perf'
make[4]: `perf' is up to date.
make[4]: `seqperf' is up to date.
make[4]: `adj_time' is up to date.
make[4]: `perftool' is up to date.
make[4]: `adj_mem_time' is up to date.
make[4]: `tstt_perf_binding' is up to date.
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/perf'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/perf'
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/perf'
Making check in h5file
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/h5file'
make h5test h5legacy h5varlen h5sets_test h5regression h5partial h5portable dump_sets
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/h5file'
make[3]: `h5test' is up to date.
make[3]: `h5legacy' is up to date.
make[3]: `h5varlen' is up to date.
make[3]: `h5sets_test' is up to date.
make[3]: `h5regression' is up to date.
make[3]: `h5partial' is up to date.
make[3]: `h5portable' is up to date.
make[3]: `dump_sets' is up to date.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/h5file'
make check-TESTS
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/h5file'
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/h5file'
PASS: h5test
PASS: h5legacy
PASS: h5varlen
PASS: h5sets_test
PASS: h5regression
PASS: h5partial
PASS: h5portable
==================
All 7 tests passed
==================
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/h5file'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/h5file'
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/h5file'
Making check in parallel
make[2]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/parallel'
make pcomm_unit scdtest pcomm_serial par_spatial_locator_test parallel_hdf5_test mhdf_parallel parallel_write_test parallel_unit_tests uber_parallel_test parallel_adj mbparallelcomm_test partcheck structured3 parmerge
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/parallel'
make[3]: `pcomm_unit' is up to date.
make[3]: `scdtest' is up to date.
make[3]: `pcomm_serial' is up to date.
make[3]: `par_spatial_locator_test' is up to date.
make[3]: `parallel_hdf5_test' is up to date.
make[3]: `mhdf_parallel' is up to date.
make[3]: `parallel_write_test' is up to date.
make[3]: `parallel_unit_tests' is up to date.
make[3]: `uber_parallel_test' is up to date.
make[3]: `parallel_adj' is up to date.
make[3]: `mbparallelcomm_test' is up to date.
make[3]: `partcheck' is up to date.
make[3]: `structured3' is up to date.
make[3]: `parmerge' is up to date.
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/parallel'
make check-TESTS
make[3]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/parallel'
make[4]: Entering directory `/home/anton/FATHOM_DIR/moab_src/test/parallel'
PASS: pcomm_unit
FAIL: scdtest
PASS: pcomm_serial
PASS: par_spatial_locator_test
FAIL: parallel_hdf5_test
PASS: mhdf_parallel
PASS: parallel_write_test
FAIL: parallel_unit_tests
PASS: uber_parallel_test
PASS: parallel_adj
================================
3 of 10 tests failed
See test/parallel/test-suite.log
================================
make[4]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/parallel'
make[3]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/parallel'
make[2]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test/parallel'
make[1]: Leaving directory `/home/anton/FATHOM_DIR/moab_src/test'
________________________________________
From: Grindeanu, Iulian R. [iulian at mcs.anl.gov]
Sent: Wednesday, September 03, 2014 6:42 PM
To: Kanaev A.A.
Subject: RE: [MOAB-dev] building MOAB with CGNS support
Did make check pass?
________________________________________
From: Kanaev A.A. [kanaev at ibrae.ac.ru]
Sent: Wednesday, September 03, 2014 8:58 AM
To: Grindeanu, Iulian R.
Subject: RE: [MOAB-dev] building MOAB with CGNS support
Here they are!
________________________________________
From: Grindeanu, Iulian R. [iulian at mcs.anl.gov]
Sent: Wednesday, September 03, 2014 5:09 PM
To: Kanaev A.A.
Cc: MOAB dev
Subject: RE: [MOAB-dev] building MOAB with CGNS support
Can you send config.log and your configure.log?
________________________________________
From: Kanaev A.A. [kanaev at ibrae.ac.ru]
Sent: Wednesday, September 03, 2014 7:51 AM
To: Grindeanu, Iulian R.
Subject: RE: [MOAB-dev] building MOAB with CGNS support
export FATHOM_DIR=/home/anton/FATHOM_DIR
export MPI2_PREFIX=/usr/lib/mpich2
export SZIP_VERSION_NUMBER=2.1
export SZIP_VERSION=szip-${SZIP_VERSION_NUMBER}
export SZIP_PREFIX=${FATHOM_DIR}/szip/${SZIP_VERSION}/gcc
export ZLIB_VERSION=zlib-1.2.8
export ZLIB_PREFIX=${FATHOM_DIR}/zlib/${ZLIB_VERSION}/gcc
export HDF5_VERSION=hdf5-1.8.11
export HDF5_PREFIX=${FATHOM_DIR}/hdf5/${HDF5_VERSION}/gcc
export zoltan_VERSION_NUMBER=3.6
export zoltan_PREFIX=${FATHOM_DIR}/zoltan/Zoltan_v${zoltan_VERSION_NUMBER}/gcc
export parmetis_PREFIX=${FATHOM_DIR}/parmetis/ParMETIS3_1
export CC=mpicc
export CXX=mpicxx
export F77=mpif77
export FC=mpif90
export F90=mpif90
./configure --prefix=${FATHOM_DIR}/moab/build --with-mpi=${MPI2_PREFIX} --without-netcdf --with-hdf5=${HDF5_PREFIX} --with-zlib=${ZLIB_PREFIX} --with-szlib=${SZIP_PREFIX} --with-zoltan=${zoltan_PREFIX} --with-parmetis=${parmetis_PREFIX} --with-cgns=/usr/local/lib --enable-igeom --enable-docs --with-doxygen=/home/anton/doxygen/bin --enable-static 2>&1 | tee configure.log
CGNS was configured with the same HDF5 lib
________________________________________
From: Grindeanu, Iulian R. [iulian at mcs.anl.gov]
Sent: Wednesday, September 03, 2014 4:41 PM
To: Kanaev A.A.
Cc: moab-dev at mcs.anl.gov
Subject: RE: [MOAB-dev] building MOAB with CGNS support
how did you configure moab?
you should not mix ccmio and cgns
so if you configure with cgns, do not configure with ccmio
this is your file converted to h5m
I don't see any cavity :)
Iulian
________________________________________
From: Kanaev A.A. [kanaev at ibrae.ac.ru]
Sent: Tuesday, September 02, 2014 4:58 PM
To: Grindeanu, Iulian R.
Cc: moab-dev at mcs.anl.gov
Subject: RE: [MOAB-dev] building MOAB with CGNS support
3.1.4 works right
next problem is when i do mbconvert Cavity.cgns Cavity.h5m i got an error message:
number of nodes = 5202
number of elems = 2500
number of parts = 3
Read "Cavity.cgns"
Writer with name MOAB for file Cavity.h5m using extension h5m was unsuccessful
Using default writer WriteHDF5Parallel for file Cavity.h5m
Failed to write "Cavity.h5m".
Error code: MB_FAILURE (16)
Error message: Invalid Quad4 element connectivity. Write Aborted
Cavity.cgns is attached, the file was created by Salome's export mesh to CGNS file
________________________________________
From: Grindeanu, Iulian R. [iulian at mcs.anl.gov]
Sent: Tuesday, September 02, 2014 5:05 AM
To: Vijay S. Mahadevan; Kanaev A.A.
Cc: moab-dev at mcs.anl.gov
Subject: RE: [MOAB-dev] building MOAB with CGNS support
I did not test version 3.2.1.
3.1.4 should be fine
how did you build cgns?
cgns should be built with the same version of hdf5 that you use for moab, to avoid conflicts (especially if you build shared)
Iulian
________________________________________
From: moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on behalf of Vijay S. Mahadevan [vijay.m at gmail.com]
Sent: Monday, September 01, 2014 5:09 PM
To: Kanaev A.A.
Cc: moab-dev at mcs.anl.gov
Subject: Re: [MOAB-dev] building MOAB with CGNS support
Anton, send us your config.log. If your configuration for CGNS was
valid, mbconvert should list the format.
Vijay
On Mon, Sep 1, 2014 at 4:36 PM, Kanaev A.A. <kanaev at ibrae.ac.ru> wrote:
> Hello Vijay,
> After building with --with-cgns=/usr/local/lib mbconvert - l shows same list of formats and there's no CGNS in it
> When i do mbconvert Mesh_1.cgns Mesh_1.h5m i got the message:
> HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0:
> #000: H5G.c line 463 in H5Gopen2(): unable to open group
> major: Symbol table
> minor: Can't open object
> #001: H5Gint.c line 320 in H5G__open_name(): group not found
> major: Symbol table
> minor: Object not found
> #002: H5Gloc.c line 430 in H5G_loc_find(): can't find object
> major: Symbol table
> minor: Object not found
> #003: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
> major: Symbol table
> minor: Object not found
> #004: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed
> major: Symbol table
> minor: Callback failed
> #005: H5Gloc.c line 385 in H5G_loc_find_cb(): object 'tstt' doesn't exist
> major: Symbol table
> minor: Object not found
> Failed to load "Mesh_1.cgns".
> Error code: MB_INDEX_OUT_OF_RANGE (1)
> Error message: Mesh_1.cgns: Trouble reading vertices
>
> Thanks,
> Anton
> ________________________________________
> From: Vijay S. Mahadevan [vijay.m at gmail.com]
> Sent: Tuesday, September 02, 2014 12:24 AM
> To: Kanaev A.A.
> Cc: moab-dev at mcs.anl.gov
> Subject: Re: [MOAB-dev] building MOAB with CGNS support
>
> Make sure the LD_LIBRARY_PATH contains the cgns installation library
> path (/usr/local/lib ?). To verify, you can run "ldd mbconvert" and
> see if any of the dynamic libraries are not resolved.
>
> Vijay
>
> On Mon, Sep 1, 2014 at 2:06 PM, Kanaev A.A. <kanaev at ibrae.ac.ru> wrote:
>> Hello MOAB-dev,
>>
>> Here's how i configure Makefile:
>> ...
>> ./configure --prefix=${FATHOM_DIR}/moab/build --with-mpi=${MPI2_PREFIX} --without-netcdf --with-hdf5=${HDF5_PREFIX} --with-zlib=${ZLIB_PREFIX} --with-szlib=${SZIP_PREFIX} --with-zoltan=${zoltan_PREFIX} --with-parmetis=${parmetis_PREFIX} --with-cgns=${FATHOM_DIR}/cgnslib_3.2.1/src --enable-igeom --enable-docs --with-doxygen=/home/anton/doxygen/bin --enable-static 2>&1 | tee configure.log
>>
>> configure goes ok:
>> ...
>> checking if CGNS support is enabled... yes
>> checking cgnslib.h usability... yes
>> checking cgnslib.h presence... yes
>> checking for cgnslib.h... yes
>> checking for cg_open in -lcgns... no
>> checking for cg_open in -lcgns... yes
>> ...
>>
>>
>> After build is done when i run mbconvert i got the following message:
>>
>> mbconvert: error while loading shared libraries: libcgns.so.3.2: cannot open shared object file: No such file or directory
>>
>> ${FATHOM_DIR}/cgnslib_3.2.1/src contains libcgns.so.3.2, it is also installed to /usr/local/lib
>>
>> What can be wrong?
>>
>> Thanks,
>> Anton
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