March 2014 - cgma-dev - mailman3.cels.anl.gov

Re: [cgma-dev] [MOAB-dev] [Meshkit-dev] How to build cgma+moab+lasso+meshkit+mesquite together succesfully on Ubuntu 12.04 LTS 64 Bit?
by Jiangtao Hu 20 Mar '14

20 Mar '14

cgma For cgma 13.1, I use OCC 6.6.0 and the compile process is OK, but the make check process appear some tests failed. If I use OCE replace OCC, the compile process also is OK, but make check process appear some compile errors. Can I use OCE to replace OCC?Which OCE version is better? $ autoreconf -fi $ ./configure --prefix=/home/why/software/itaps --enable-shared --with-occ=/home/why/software/OCC/660/Linux $ make $ make check $ make install As Rajeev said, we didn't test OCE on Linux. Your approach of using OCC6.6.0 on cgma13.1 build for Linux system should work if you apply the geom/OCC/occ_patches_6.6.0 on your OCC6.6.0 build. Good luck! Jane Asst. Researcher Dept. of Engineering Physics UW @ Madison "And we know that for those who love God, that is, for those who are called according to his purpose, all things are working together for good." (Romans 8:28) On Thursday, March 20, 2014 9:11 AM, Rajeev Jain <jain(a)mcs.anl.gov> wrote: Hi Huayi, Yes, we have successfully built on Ubuntu 12.04LTS. We use OCE for OSX and OCC for Linux, you may be able to use OCE for Linux, but we haven't tested this. Regarding, the Zoltan error: try using /usr/lib in MOAB prefix, the directory should have libparmetis.a file. I've CC'd moab-dev and cgm-dev, they may give more input. My configure line for mesquite is: --with-imesh=/Users/rajeevjain/pll/install/moab/ --with-igeom=/Users/rajeevjain/pll/install/cgmtrunk/ --with-irel=/Users/rajeevjain/pll/install/lasso/ IMESH_DEFS=/Users/rajeevjain/pll/install/moab/lib/iMesh-Defs.inc IGEOM_DEFS=/Users/rajeevjain/pll/install/CGM-2k14/lib/iGeom-Defs.inc IREL_DEFS=/Users/rajeevjain/pll/install/lasso/lib/iRel-Defs.inc --prefix=/Users/rajeevjain/pll/install/mesquite-2.99 --with-mpi --enable-debug Rajeev ________________________________ From: "魏华祎(Wei, Huayi)" <huayiwei1984(a)gmail.com> To: "meshkit-dev(a)mcs.anl.gov" <meshkit-dev(a)mcs.anl.gov> Sent: Subject: [Meshkit-dev] How to build cgma+moab+lasso+meshkit+mesquite together succesfully on Ubuntu 12.04 LTS 64 Bit? Hi, there, I want to implement some mesh generation and optimization algorithms based on MeshKit. But I find it very hard to build cgma+moab+lasso+meshkit+mesquite together successfully. My os is Ubuntu 12.04 LTS 64 bit. I first install most of the dependents from Ubuntu source: $ sudo apt-get install openmpi-bin libopenmpi-dev openmpi-common openmpi-checkpoint $ sudo apt-get install libparmetis-dev libparmetis3.1 $ sudo apt-get install libscotch-5.1 libscotch-dev $ sudo apt-get install libptscotch-5.1 libptscotch-dev $ sudo apt-get install netcdf-bin python-netcdf libnetcdf6 libnetcdf-dev $ sudo apt-get install h5utils hdf5-tools libhdf5-openmpi-1.8.4 libhdf5-openmpi-dev Zoltan I can compile and install Zoltan 3.8 without any error: $ ../configure --prefix=/home/why/software/zoltan --enable-mpi --with-mpi=/usr/lib/openmpi --with-libs=-lsuperlu --with-parmetis --with-parmetis-incdir=/usr/include/parmetis --with-parmetis-libdir=/usr/lib --with-scotch --with-scotch-libdir=/usr/lib --with-scotch-incdir=/usr/include/sc otch $ make install cgma For cgma 13.1, I use OCC 6.6.0 and the compile process is OK, but the make check process appear some tests failed. If I use OCE replace OCC, the compile process also is OK, but make check process appear some compile errors. Can I use OCE to replace OCC?Which OCE version is better? $ autoreconf -fi $ ./configure --prefix=/home/why/software/itaps --enable-shared --with-occ=/home/why/software/OCC/660/Linux $ make $ make check $ make install moab For moab 4.6, I configure it like this: $ autoreconf -fi $ ./configure --prefix=/home/why/software/itaps \ --enable-docs \ --with-mpi \ --with-netcdf \ --with-hdf5 \ --with-zoltan=/home/why/software/zoltan \ --with-parmetis=/usr \ --with-vtk=/home/why/software/vtk \ --with-vtk-lib-suffix=-6.0 But it appear such an error, is the version 3.8 of zoltan suitable? checking for zoltan_cpp.h... yes checking for Zoltan_LB_Partition in -lzoltan... no checking for Zoltan_LB_Partition in -lzoltan... no configure: error: zoltan library not found or not usable. Perhaps you need to specify --with-parmetis=[DIR]? lasso For lasso, $ ./configure --prefix=/home/why/software/itaps --with-mpi --with-igeom=/home/why/software/itaps --with-imesh=/home/why/software/itaps $ make $ make check $ make install mesquite For mesquite 2.3, I can compile it successfully like this: $ autoreconf -fi $ ./configure --prefix=/home/why/software/mesquite/230/ --with-mpi $ make $ make install Here do I need to add the ―with-igeom, ―with-imesh, ―irel, or ―imeshp option? MeshKit $ ./configure --prefix=/home/why/software/itaps --with-mpi --with-igeom=/home/why/software/itaps --with-imesh=/home/why/software/itaps--with-irel=/home/why/software/itaps --with-fbigeom=/home/why/software/itaps --with-tetgen=/home/why/software/tetgen/tetgen1.5.0 --with-triangle=/home/why/software/triangle --with-netgen=/usr --with-mesquite=/home/why/software/mesquite/230 Does anyone have installed MeshKit on Ubuntu 12.04 LTS? Please give me some suggestion and help me to install MeshKit correctly, thanks very much. Best Huayi

1 0

Re: [cgma-dev] [Meshkit-dev] How to build cgma+moab+lasso+meshkit+mesquite together succesfully on Ubuntu 12.04 LTS 64 Bit?
by Rajeev Jain 20 Mar '14

20 Mar '14

Hi Huayi, Yes, we have successfully built on Ubuntu 12.04LTS. We use OCE for OSX and OCC for Linux, you may be able to use OCE for Linux, but we haven't tested this. Regarding, the Zoltan error: try using /usr/lib in MOAB prefix, the directory should have libparmetis.a file. I've CC'd moab-dev and cgm-dev, they may give more input. My configure line for mesquite is: --with-imesh=/Users/rajeevjain/pll/install/moab/ --with-igeom=/Users/rajeevjain/pll/install/cgmtrunk/ --with-irel=/Users/rajeevjain/pll/install/lasso/ IMESH_DEFS=/Users/rajeevjain/pll/install/moab/lib/iMesh-Defs.inc IGEOM_DEFS=/Users/rajeevjain/pll/install/CGM-2k14/lib/iGeom-Defs.inc IREL_DEFS=/Users/rajeevjain/pll/install/lasso/lib/iRel-Defs.inc --prefix=/Users/rajeevjain/pll/install/mesquite-2.99 --with-mpi --enable-debug Rajeev ________________________________ From: "魏华祎(Wei, Huayi)" <huayiwei1984(a)gmail.com> To: "meshkit-dev(a)mcs.anl.gov" <meshkit-dev(a)mcs.anl.gov> Sent: Subject: [Meshkit-dev] How to build cgma+moab+lasso+meshkit+mesquite together succesfully on Ubuntu 12.04 LTS 64 Bit? Hi, there, I want to implement some mesh generation and optimization algorithms based on MeshKit. But I find it very hard to build cgma+moab+lasso+meshkit+mesquite together successfully. My os is Ubuntu 12.04 LTS 64 bit. I first install most of the dependents from Ubuntu source: $ sudo apt-get install openmpi-bin libopenmpi-dev openmpi-common openmpi-checkpoint $ sudo apt-get install libparmetis-dev libparmetis3.1 $ sudo apt-get install libscotch-5.1 libscotch-dev $ sudo apt-get install libptscotch-5.1 libptscotch-dev $ sudo apt-get install netcdf-bin python-netcdf libnetcdf6 libnetcdf-dev $ sudo apt-get install h5utils hdf5-tools libhdf5-openmpi-1.8.4 libhdf5-openmpi-dev Zoltan I can compile and install Zoltan 3.8 without any error: $ ../configure --prefix=/home/why/software/zoltan --enable-mpi --with-mpi=/usr/lib/openmpi --with-libs=-lsuperlu --with-parmetis --with-parmetis-incdir=/usr/include/parmetis --with-parmetis-libdir=/usr/lib --with-scotch --with-scotch-libdir=/usr/lib --with-scotch-incdir=/usr/include/sc otch $ make install cgma For cgma 13.1, I use OCC 6.6.0 and the compile process is OK, but the make check process appear some tests failed. If I use OCE replace OCC, the compile process also is OK, but make check process appear some compile errors. Can I use OCE to replace OCC?Which OCE version is better? $ autoreconf -fi $ ./configure --prefix=/home/why/software/itaps --enable-shared --with-occ=/home/why/software/OCC/660/Linux $ make $ make check $ make install moab For moab 4.6, I configure it like this: $ autoreconf -fi $ ./configure --prefix=/home/why/software/itaps \ --enable-docs \ --with-mpi \ --with-netcdf \ --with-hdf5 \ --with-zoltan=/home/why/software/zoltan \ --with-parmetis=/usr \ --with-vtk=/home/why/software/vtk \ --with-vtk-lib-suffix=-6.0 But it appear such an error, is the version 3.8 of zoltan suitable? checking for zoltan_cpp.h... yes checking for Zoltan_LB_Partition in -lzoltan... no checking for Zoltan_LB_Partition in -lzoltan... no configure: error: zoltan library not found or not usable. Perhaps you need to specify --with-parmetis=[DIR]? lasso For lasso, $ ./configure --prefix=/home/why/software/itaps --with-mpi --with-igeom=/home/why/software/itaps --with-imesh=/home/why/software/itaps $ make $ make check $ make install mesquite For mesquite 2.3, I can compile it successfully like this: $ autoreconf -fi $ ./configure --prefix=/home/why/software/mesquite/230/ --with-mpi $ make $ make install Here do I need to add the ―with-igeom, ―with-imesh, ―irel, or ―imeshp option? MeshKit $ ./configure --prefix=/home/why/software/itaps --with-mpi --with-igeom=/home/why/software/itaps --with-imesh=/home/why/software/itaps--with-irel=/home/why/software/itaps --with-fbigeom=/home/why/software/itaps --with-tetgen=/home/why/software/tetgen/tetgen1.5.0 --with-triangle=/home/why/software/triangle --with-netgen=/usr --with-mesquite=/home/why/software/mesquite/230 Does anyone have installed MeshKit on Ubuntu 12.04 LTS? Please give me some suggestion and help me to install MeshKit correctly, thanks very much. Best Huayi

1 0

Can I use OCE to replace OCC?
by "魏华祎(Wei, Huayi)" 19 Mar '14

19 Mar '14

Hi, there, I tried to use OCE to replace OCC and can compile cgma (13.1) without any error. But the make check fails. So does cgma is with OCE? Or which OCE version is better? best Huayi

1 0

Re: [cgma-dev] CGM make check not working for me...
by Grindeanu, Iulian R. 13 Mar '14

13 Mar '14

I would do a make distclean, set the LD_LIBRARY_PATH, autoreconf , etc are your .libs folder clean? Iulian ________________________________________ From: cgma-dev-bounces(a)mcs.anl.gov [cgma-dev-bounces(a)mcs.anl.gov] on behalf of Tim Tautges (ANL) [tautges(a)mcs.anl.gov] Sent: Thursday, March 13, 2014 4:04 PM To: CGMA Development Subject: [cgma-dev] CGM make check not working for me... ... I'm seeing the following error: make[3]: Entering directory `/code/CGMcubit2/itaps' make chaman test_edge_orient testgeom make[4]: Entering directory `/code/CGMcubit2/itaps' /bin/bash ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -g -R/cubit/cubit13.1/bin -L/cubit/cubit13.1/bin -o chaman chaman.o libiGeom.la ../libcgm.la -lm libtool: link: g++ -Wall -pipe -pedantic -g -o .libs/chaman chaman.o -L/cubit/cubit13.1/bin ./.libs/libiGeom.so ../.libs/libcgm.so -lm -Wl,-rpath -Wl,/home/tautges/code/CGMcubit2/lib -Wl,-rpath -Wl,/cubit/cubit13.1/bin ./.libs/libiGeom.so: undefined reference to `CubitSimpleAttrib::operator=(CubitSimpleAttrib const&)' ./.libs/libiGeom.so: undefined reference to `CubitSimpleAttrib::character_type() const' ./.libs/libiGeom.so: undefined reference to `CubitSimpleAttrib::CubitSimpleAttrib(CubitSimpleAttrib const&)' ./.libs/libiGeom.so: undefined reference to `CubitAttribManager::register_attrib_type(int, char const*, char const*, CubitAttrib* (*)(RefEntity*, CubitSimpleAttrib const&), bool, bool, bool, bool, bool, bool)' ./.libs/libiGeom.so: undefined reference to `RefEntityFactory::instance()' ./.libs/libiGeom.so: undefined reference to `CubitSimpleAttrib::CubitSimpleAttrib(std::vector<CubitString, std::allocator<CubitString> > const*, std::vector<double, std::allocator<double> > const*, std::vector<int, std::allocator<int> > const*)' ./.libs/libiGeom.so: undefined reference to `CGMApp::startup(std::vector<CubitString, std::allocator<CubitString> > const&)' I'm seeing that same error trying to build a MeshKit-based app, so I don't think it's anything specific to those particular executables in itaps. My configure line is: $ ./configure --with-cubit=/cubit/cubit13.1 --disable-optimize --enable-debug --prefix=/home/tautges/code/CGMcubit2 --enable-shared --enable-igeom Oddly, I tried the same thing with cubit14.1, and got a different set of unresolved refs, but otherwise the same result: make[3]: Entering directory `/code/CGMcubit2/itaps' make chaman test_edge_orient testgeom make[4]: Entering directory `/code/CGMcubit2/itaps' g++ -DHAVE_CONFIG_H -I. -I.. -I../geom/parallel -I../geom -DLITTLE_ENDIAN=BYTE_ORDER -DTEMPLATE_DEFS_INCLUDED -DHAVE_ACIS -DSRCDIR=. -I../util -I../geom -I../init -Wall -pipe -pedantic -g -MT chaman.o -MD -MP -MF .deps/chaman.Tpo -c -o chaman.o chaman.cc mv -f .deps/chaman.Tpo .deps/chaman.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -g -R/cubit/cubit14.1/bin -L/cubit/cubit14.1/bin -o chaman chaman.o libiGeom.la ../libcgm.la -lm libtool: link: g++ -Wall -pipe -pedantic -g -o .libs/chaman chaman.o -L/cubit/cubit14.1/bin ./.libs/libiGeom.so ../.libs/libcgm.so -lm -Wl,-rpath -Wl,/home/tautges/code/CGMcubit2/lib -Wl,-rpath -Wl,/cubit/cubit14.1/bin ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::translate(Body*, CubitVector const&, bool, bool)' ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::rotate(BasicTopologyEntity*, CubitVector const&, double, bool, bool)' ./.libs/libiGeom.so: undefined reference to `CubitMessage::print_error(char const*, ...)' ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::translate(BasicTopologyEntity*, CubitVector const&, bool, bool)' ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::reflect(DLIList<Body*>, CubitVector const&, CubitVector const&, bool)' ./.libs/libiGeom.so: undefined reference to `CubitString::operator==(char const*) const' ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::reflect(BasicTopologyEntity*, CubitVector const&, CubitVector const&, bool, bool)' ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::rotate(Body*, CubitVector const&, double, bool, bool)' collect2: error: ld returned 1 exit status make[4]: *** [chaman] Error 1 make[4]: Leaving directory `/code/CGMcubit2/itaps' Any clues? -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges(a)mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

1 0

CGM make check not working for me...
by Tim Tautges (ANL) 13 Mar '14

13 Mar '14

... I'm seeing the following error: make[3]: Entering directory `/code/CGMcubit2/itaps' make chaman test_edge_orient testgeom make[4]: Entering directory `/code/CGMcubit2/itaps' /bin/bash ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -g -R/cubit/cubit13.1/bin -L/cubit/cubit13.1/bin -o chaman chaman.o libiGeom.la ../libcgm.la -lm libtool: link: g++ -Wall -pipe -pedantic -g -o .libs/chaman chaman.o -L/cubit/cubit13.1/bin ./.libs/libiGeom.so ../.libs/libcgm.so -lm -Wl,-rpath -Wl,/home/tautges/code/CGMcubit2/lib -Wl,-rpath -Wl,/cubit/cubit13.1/bin ./.libs/libiGeom.so: undefined reference to `CubitSimpleAttrib::operator=(CubitSimpleAttrib const&)' ./.libs/libiGeom.so: undefined reference to `CubitSimpleAttrib::character_type() const' ./.libs/libiGeom.so: undefined reference to `CubitSimpleAttrib::CubitSimpleAttrib(CubitSimpleAttrib const&)' ./.libs/libiGeom.so: undefined reference to `CubitAttribManager::register_attrib_type(int, char const*, char const*, CubitAttrib* (*)(RefEntity*, CubitSimpleAttrib const&), bool, bool, bool, bool, bool, bool)' ./.libs/libiGeom.so: undefined reference to `RefEntityFactory::instance()' ./.libs/libiGeom.so: undefined reference to `CubitSimpleAttrib::CubitSimpleAttrib(std::vector<CubitString, std::allocator<CubitString> > const*, std::vector<double, std::allocator<double> > const*, std::vector<int, std::allocator<int> > const*)' ./.libs/libiGeom.so: undefined reference to `CGMApp::startup(std::vector<CubitString, std::allocator<CubitString> > const&)' I'm seeing that same error trying to build a MeshKit-based app, so I don't think it's anything specific to those particular executables in itaps. My configure line is: $ ./configure --with-cubit=/cubit/cubit13.1 --disable-optimize --enable-debug --prefix=/home/tautges/code/CGMcubit2 --enable-shared --enable-igeom Oddly, I tried the same thing with cubit14.1, and got a different set of unresolved refs, but otherwise the same result: make[3]: Entering directory `/code/CGMcubit2/itaps' make chaman test_edge_orient testgeom make[4]: Entering directory `/code/CGMcubit2/itaps' g++ -DHAVE_CONFIG_H -I. -I.. -I../geom/parallel -I../geom -DLITTLE_ENDIAN=BYTE_ORDER -DTEMPLATE_DEFS_INCLUDED -DHAVE_ACIS -DSRCDIR=. -I../util -I../geom -I../init -Wall -pipe -pedantic -g -MT chaman.o -MD -MP -MF .deps/chaman.Tpo -c -o chaman.o chaman.cc mv -f .deps/chaman.Tpo .deps/chaman.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -g -R/cubit/cubit14.1/bin -L/cubit/cubit14.1/bin -o chaman chaman.o libiGeom.la ../libcgm.la -lm libtool: link: g++ -Wall -pipe -pedantic -g -o .libs/chaman chaman.o -L/cubit/cubit14.1/bin ./.libs/libiGeom.so ../.libs/libcgm.so -lm -Wl,-rpath -Wl,/home/tautges/code/CGMcubit2/lib -Wl,-rpath -Wl,/cubit/cubit14.1/bin ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::translate(Body*, CubitVector const&, bool, bool)' ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::rotate(BasicTopologyEntity*, CubitVector const&, double, bool, bool)' ./.libs/libiGeom.so: undefined reference to `CubitMessage::print_error(char const*, ...)' ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::translate(BasicTopologyEntity*, CubitVector const&, bool, bool)' ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::reflect(DLIList<Body*>, CubitVector const&, CubitVector const&, bool)' ./.libs/libiGeom.so: undefined reference to `CubitString::operator==(char const*) const' ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::reflect(BasicTopologyEntity*, CubitVector const&, CubitVector const&, bool, bool)' ./.libs/libiGeom.so: undefined reference to `GeometryQueryTool::rotate(Body*, CubitVector const&, double, bool, bool)' collect2: error: ld returned 1 exit status make[4]: *** [chaman] Error 1 make[4]: Leaving directory `/code/CGMcubit2/itaps' Any clues? -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges(a)mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

1 0

Jenkins build is back to normal : cgm32bit #350
by jenkins-ci＠mcs.anl.gov 13 Mar '14

13 Mar '14

See <https://jenkins-ci.mcs.anl.gov/job/cgm32bit/350/>

1 0

Re: [cgma-dev] buildbot failure in cgm-shared: failed svn
by Grindeanu, Iulian R. 13 Mar '14

13 Mar '14

My problem, I changed the buildbot configuration file, but I forgot to restart. Please ignore all these nightly error builds Iulian ________________________________ From: cgma-dev-bounces(a)mcs.anl.gov [cgma-dev-bounces(a)mcs.anl.gov] on behalf of cgma-dev(a)mcs.anl.gov [cgma-dev(a)mcs.anl.gov] Sent: Thursday, March 13, 2014 1:18 AM To: cgma-dev(a)mcs.anl.gov Subject: [cgma-dev] buildbot failure in cgm-shared: failed svn Fathom<http://gnep.mcs.anl.gov:8010/>: cgm-shared<http://gnep.mcs.anl.gov:8010/builders/cgm-shared> build #1466<http://gnep.mcs.anl.gov:8010/builders/cgm-shared/builds/1466> Results: failed svn Buildslave: gnep Revision: None Reason: The Nightly scheduler named 'cgm-shared-nightly' triggered this build Log Excerpt Restored 'itaps/SIDL/gserver/iGeom_Factory_Impl.hh' Restored 'itaps/iGeom_FCDefs.h' Restored 'geom/parallel/CGMmpi_config.h' Restored 'geom/parallel/stamp-h2' Restored 'geom/stamp-h3'

1 0

buildbot failure in cgm-shared: failed svn
by cgma-dev＠mcs.anl.gov 13 Mar '14

13 Mar '14

1 0

buildbot failure in cgm-cub-parstatru: failed svn
by cgma-dev＠mcs.anl.gov 13 Mar '14

13 Mar '14

1 0

buildbot failure in cgm-occ-sta: failed svn
by cgma-dev＠mcs.anl.gov 13 Mar '14

13 Mar '14

1 0