Do you use exactly the same HDF5 version as mentioned in the instruction? If not, try it. -- 在2010-04-16 09:53:06,"ye Huang" <gjy2005nj@xxxxxxxxx> 写道: Hi, To be more specify, The HDF libraries and include files can be found in the directory:/usr/lib, such as: /usr/lib/libhdf5.so, /usr/lib/libhdf5.a, /usr/include/hdf5.h gjy 在 2010年4月16日 上午9:31,ye Huang <gjy2005nj@xxxxxxxxx>写道: Hi Philip, Thanks your tip. However, errors still exit. As the following: g++ -fPIC -I/home/gjyadi/code/overture/overture/Overture.v23/bin/../include -I. -DUSE_MESA -I/usr/local/A++/install/include -I/usr/include -I/usr/include -DBL_USE_DOUBLE -DBL_Solaris -I/usr/lib/perl/5.10/CORE -g -o plotStuff plotStuffDriver.o plotStuff.o -Wl,-rpath,/home/gjyadi/code/overture/overture/Overture.v23/bin/../lib -L/home/gjyadi/code/overture/overture/Overture.v23/bin/../lib -lOverture -lOverture_static -Wl,-rpath,/usr/lib -L/usr/lib -lhdf5 -ljpeg -lz -Wl,-rpath,/usr/local/A++/install/lib -L/usr/local/A++/install/lib -lApp -lApp_static -lgfortran -Wl,-rpath,/usr/lib/perl/5.10/CORE -L/usr/lib/perl/5.10/CORE -lperl -ldl -lm -lpthread -lc -lcrypt -Wl,-rpath,/usr/lib64 -L/usr/lib64 -lGL -lGLU -Wl,-rpath,/usr/lib64 -L/usr/lib64 -lXm -L/usr/lib64 -lXpm -lXp -lXt -lXmu -lXi -lXext -lX11 -lm /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::turnOffWarnings()' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::put(aString const*, aString const&, int)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::get(int*, aString const&, int) const' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::put(doubleArray const&, aString const&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::setMode(GenericDataBase::InputOutputMode const&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::find(aString*, aString const&, int const&, int&) const' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::put(aString const&, aString const&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::get(aString*, aString const&, int) const' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::get(aString&, aString const&) const' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::turnOnWarnings()' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::locate(GenericDataBase&, aString const&, aString const&) const' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::mount(aString const&, aString const&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::~HDF_DataBase()' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::get(int&, aString const&) const' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::get(double*, aString const&, int) const' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::HDF_DataBase()' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::find(GenericDataBase*, aString*, aString const&, int const&, int&) const' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::isNull() const' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::operator=(HDF_DataBase const&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::unmount()' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::put(int const&, aString const&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::operator=(GenericDataBase const&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture.so: undefined reference to `HDF_DataBase::get(doubleArray&, aString const&, Index*) const' collect2: ld returned 1 exit status make[1]: *** [plotStuff] Error 1 --------------------------------------------------- It seems that Overture could not link the HDF libraries. I had installed HDF with synatic package manager. Both libhdf5-mpich-de and libhdf5-mpich-1.6.6-0 are installed. The operating system is Ubuntu 9.1. By the way, I also install other libraries(motif, mesa) with synatic package manager. The compiling enviroments are set with: export CC=gcc export XLIBS=/usr export OpenGL=/usr export MOTIF=/usr export HDF=/usr export APlusPlus=/usr/local/A++/install export Overture=~/code/overture/overture/Overture.v23 export LD_LIBRARY_PATH=${MOTIF}/lib:{XLIBS}/lib:{HDF}/lib:{OpenGL}/lib:$Overture/lib:{APlusPlus}/lib export CXXFLAGS=-DBL_AUTO_INSTANTIATE Before using make to install overture, I excute the following command: ./configure useHDF5 Could you please help me to figure out the error? Thanks! gjy 2010/4/15 Philip Blakely <pmb39@xxxxxxxxx> Hi, You need to "export CXXFLAGS=-DBL_AUTO_INSTANTIATE" before running configure. If this doesn't work, then see //www.freelists.org/archive/overture for the list archive, and search for BL_AUTO_INSTANTIATE as this problem has come up before on the list. Philip On 04/15/2010 11:28 AM, ye Huang wrote: Hi Phillip, It works. However, errors still exits. Please help me to figure out. overture/overture/Overture.v23/bin/../lib -lOverture -lOverture_static -Wl,-rpath,/usr/lib -L/usr/lib -lhdf5 -ljpeg -lz -Wl,-rpath,/usr/local/A++/install/lib -L/usr/local/A++/install/lib -lApp -lApp_static -lgfortran -Wl,-rpath,/usr/lib/perl/5.10/CORE -L/usr/lib/perl/5.10/CORE -lperl -ldl -lm -lpthread -lc -lcrypt -Wl,-rpath,/usr/lib64 -L/usr/lib64 -lGL -lGLU -Wl,-rpath,/usr/lib64 -L/usr/lib64 -lXm -L/usr/lib64 -lXpm -lXp -lXt -lXmu -lXi -lXext -lX11 -lm /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture_static.a(BoxList.o): In function `BoxList': /home/gjyadi/code/overture/overture/Overture.v23/boxlib/BoxList.C:44: undefined reference to `List<Box>::List(List<Box> const&)' /home/gjyadi/code/overture/overture/Overture.v23/boxlib/BoxList.C:44: undefined reference to `List<Box>::List(List<Box> const&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture_static.a(BoxList.o): In function `BoxList::operator=(BoxList const&)': /home/gjyadi/code/overture/overture/Overture.v23/boxlib/BoxList.C:50: undefined reference to `List<Box>::operator=(List<Box> const&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture_static.a(BoxList.o): In function `BoxList::intersect(Box const&)': /home/gjyadi/code/overture/overture/Overture.v23/boxlib/BoxList.C:127: undefined reference to `List<Box>::remove(ListIterator<Box>&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture_static.a(BoxList.o): In function `complementIn(Box const&, BoxList const&)': /home/gjyadi/code/overture/overture/Overture.v23/boxlib/BoxList.C:153: undefined reference to `List<Box>::catenate(List<Box>&)' /home/gjyadi/code/overture/overture/Overture.v23/boxlib/BoxList.C:154: undefined reference to `List<Box>::remove(ListIterator<Box>&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture_static.a(BoxList.o): In function `BoxList::complementIn(Box const&, BoxList const&)': /home/gjyadi/code/overture/overture/Overture.v23/boxlib/BoxList.C:176: undefined reference to `List<Box>::catenate(List<Box>&)' /home/gjyadi/code/overture/overture/Overture.v23/boxlib/BoxList.C:177: undefined reference to `List<Box>::remove(ListIterator<Box>&)' /home/gjyadi/code/overture/overture/Overture.v23/bin/../lib/libOverture_static.a(BoxList.o): In function `BoxList::simplify()': /home/gjyadi/code/overture/overture/Overture.v23/boxlib/BoxList.C:341: undefined reference to `List<Box>::remove(ListIterator<Box>&)' Sorry for bothering you. Thanks! 2010/4/15 Philip Blakely <pmb39@xxxxxxxxx <mailto:pmb39@xxxxxxxxx>> Hi, I think this is an error in bin/Makefile. There should be a line in there that starts: OV_PERL_LIBRARIES = $(OV_RPATH) $(OV_PERL_LIB) (there's two identical lines in my version for some reason, it may be the same in yours) This should be: OV_PERL_LIBRARIES = $(OV_RPATH)$(OV_PERL_LIB) (i.e. there's a space removed) and the rest of the line is the same. This should solve your problem. Philip On 04/15/2010 08:31 AM, ye Huang wrote: Hi Philip, Following your guidance, I could compile most the souce codes. Thanks! However, I got some other errors during the compilation: make[1]: Leaving directory `/home/gjyadi/code/overture/overture/Overture.v23/lib' make[1]: Entering directory `/home/gjyadi/code/overture/overture/Overture.v23/bin' gcc -fPIC -I/home/gjyadi/code/overture/overture/Overture.v23/bin/../include -I. -DUSE_MESA -I/usr/local/A++/install/include -I/usr/include -I/usr/include -DBL_USE_DOUBLE -DBL_Solaris -I/usr/lib/perl/5.10/CORE -g -o plotStuff plotStuffDriver.o plotStuff.o -Wl,-rpath,/home/gjyadi/code/overture/overture/Overture.v23/bin/../lib -L/home/gjyadi/code/overture/overture/Overture.v23/bin/../lib -lOverture -lOverture_static -Wl,-rpath,/usr/lib -L/usr/lib -lhdf5 -ljpeg -lz -Wl,-rpath,/usr/local/A++/install/lib -L/usr/local/A++/install/lib -lApp -lApp_static -lgfortran -Wl,-rpath, /usr/lib/perl/5.10/CORE -L/usr/lib/perl/5.10/CORE -lperl -ldl -lm -lpthread -lc -lcrypt -Wl,-rpath,/usr/lib64 -L/usr/lib64 -lGL -lGLU -Wl,-rpath,/usr/lib64 -L/usr/lib64 -lXm -L/usr/lib64 -lXpm -lXp -lXt -lXmu -lXi -lXext -lX11 -lm /usr/bin/ld: /usr/lib/perl/5.10/CORE: No such file: File format not recognized collect2: ld returned 1 exit status make[1]: *** [plotStuff] Error 1 Could you help me to figure out? The /usr/lib/perl/5.10/CORE is a directory What the ld command needs? Thanks! gjy 2010/4/14 Philip Blakely <pmb39@xxxxxxxxx <mailto:pmb39@xxxxxxxxx> <mailto:pmb39@xxxxxxxxx <mailto:pmb39@xxxxxxxxx>>> Hello, I think you need to define the Overture environment variable: export Overture=~/code/overture/overture/Overture.v23 or setenv Overture=~/code/overture/overture/Overture.v23 depending on whether you're using the bash shell or csh shell, and probably some other environment variables, HDF, APlusPlus, and so on. See https://computation.llnl.gov/casc/Overture/henshaw/install/node10.html for details. Philip On 04/14/2010 11:31 AM, ye Huang wrote: Hello Everybody, Could you please help me to figure the following errors: gjyadi@yangsiqi-desktop:~/code/overture/overture/Overture.v23$ sudo make ----------------------------------------------------------------------- type <make help> for help. Run the configure script before running make ----------------------------------------------------------------------- rm -rf A++; rm -f OpenGL; rm -f HDF; ln -s A++; ln -s OpenGL; ln -s HDF make[1]: Entering directory `/home/gjyadi/code/overture/overture/Overture.v23/DataBase' perl ../config/makeDepend -f depend -Y -- -I/include -I. -DUSE_MESA -I/include -I/include -I/include -DBL_USE_DOUBLE -DBL_Solaris -I/usr/lib/perl/5.10/CORE -- GenericDataBase.C HDF_DataBase.C DataBaseBuffer.C ListOfHDF_DataBaseRCData.C run makedepend ... ...done touch depend_date g++ -fPIC -I/include -I. -DUSE_MESA -I/include -I/include -I/include -DBL_USE_DOUBLE -DBL_Solaris -I/usr/lib/perl/5.10/CORE -g -I/include -c GenericDataBase.C HDF_DataBase.C DataBaseBuffer.C ListOfHDF_DataBaseRCData.C GenericDataBase.C:1:29: error: GenericDataBase.h: No such file or directory GenericDataBase.C:3: error: ‘GenericDataBase’ does not name a type GenericDataBase.C:5: error: ‘GenericDataBase’ has not been declared GenericDataBase.C:8: error: ISO C++ forbids declaration of ‘aString’ with no type GenericDataBase.C:8: error: expected ‘,’ or ‘...’ before ‘&’ token GenericDataBase.C: In function ‘int gdbError(int)’: GenericDataBase.C:10: error: ‘cout’ was not declared in this scope GenericDataBase.C:10: error: ‘func’ was not declared in this scope GenericDataBase.C: At global scope: GenericDataBase.C:17: error: ‘GenericDataBase’ has not been declared GenericDataBase.C:18: error: ISO C++ forbids declaration of ‘GenericDataBase’ with no type GenericDataBase.C: In function ‘int GenericDataBase()’: GenericDataBase.C:27: error: ‘className’ was not declared in this scope GenericDataBase.C:28: error: ‘OvertureVersion’ was not declared in this scope GenericDataBase.C:28: error: ‘OVERTURE_VERSION’ was not declared in this scope GenericDataBase.C:30: error: ‘mode’ was not declared in this scope GenericDataBase.C:30: error: ‘normalMode’ was not declared in this scope GenericDataBase.C:31: error: ‘issueWarnings’ was not declared in this scope GenericDataBase.C:32: error: ‘referenceCountingList’ was not declared in this scope GenericDataBase.C:32: error: ‘NULL’ was not declared in this scope GenericDataBase.C:34: error: ‘Communication_Manager’ has not been declared GenericDataBase.C:35: error: ‘min’ was not declared in this scope .................. .................. HDF_DataBase.C:32: error: ‘FALSE’ was not declared in this scope HDF_DataBase.C: At global scope: HDF_DataBase.C:36: error: ‘HDF_DataBase’ is not a class or namespace HDF_DataBase.C:37: error: ISO C++ forbids declaration of ‘HDF_DataBase’ with no type HDF_DataBase.C:37: error: expected ‘,’ or ‘...’ before ‘&’ token HDF_DataBase.C:37: error: ISO C++ forbids declaration of ‘HDF_DataBase’ with no type HDF_DataBase.C: In function ‘int HDF_DataBase(int)’: HDF_DataBase.C:47: error: ‘rcData’ was not declared in this scope HDF_DataBase.C:47: error: ‘NULL’ was not declared in this scope HDF_DataBase.C:48: error: invalid use of ‘this’ in non-member function HDF_DataBase.C:48: error: ‘db’ was not declared in this scope HDF_DataBase.C: At global scope: HDF_DataBase.C:52: error: ‘HDF_DataBase’ is not a class or namespace HDF_DataBase.C:53: error: ISO C++ forbids declaration of ‘GenericDataBase’ with no type HDF_DataBase.C:53: error: expected ‘,’ or ‘...’ before ‘&’ token HDF_DataBase.C:53: error: ISO C++ forbids declaration of ‘HDF_DataBase’ with no type HDF_DataBase.C: In function ‘int HDF_DataBase(int)’: HDF_DataBase.C:52: error: redefinition of ‘int HDF_DataBase(int)’ HDF_DataBase.C:36: error: ‘int HDF_DataBase(int)’ previously defined here HDF_DataBase.C:63: error: ‘db’ was not declared in this scope HDF_DataBase.C:65: error: ‘rcData’ was not declared in this scope HDF_DataBase.C:65: error: ‘NULL’ was not declared in this scope HDF_DataBase.C:66: error: invalid use of ‘this’ in non-member function HDF_DataBase.C:66: error: ISO C++ forbids declaration of ‘type name’ with no type HDF_DataBase.C:66: error: ISO C++ forbids declaration of ‘type name’ with no type HDF_DataBase.C:66: error: expected primary-expression before ‘const’ HDF_DataBase.C:66: error: expected ‘)’ before ‘const’ HDF_DataBase.C:70: error: ‘cout’ was not declared in this scope HDF_DataBase.C: At global scope: HDF_DataBase.C:75: error: expected constructor, destructor, or type conversion before ‘*’ token HDF_DataBase.C:83: error: expected constructor, destructor, or type conversion before ‘&’ token HDF_DataBase.C:116: error: expected constructor, destructor, or type conversion before ‘&’ token DataBaseBuffer.C:2:28: error: OvertureDefine.h: No such file or directory DataBaseBuffer.C:4:28: error: DataBaseBuffer.h: No such file or directory DataBaseBuffer.C:5:29: error: ParallelUtility.h: No such file or directory DataBaseBuffer.C:8: error: ‘aString’ does not name a type DataBaseBuffer.C:11: error: expected initializer before ‘&’ token DataBaseBuffer.C:14: error: ‘DataBaseBuffer’ has not been declared DataBaseBuffer.C:15: error: ISO C++ forbids declaration of ‘DataBaseBuffer’ with no type DataBaseBuffer.C: In function ‘int DataBaseBuffer()’: DataBaseBuffer.C:20: error: only constructors take base initializers DataBaseBuffer.C:22: error: ‘streamIs’ was not declared in this scope DataBaseBuffer.C:22: error: ‘notOpen’ was not declared in this scope DataBaseBuffer.C:23: error: ‘OvertureVersion’ was not declared in this scope DataBaseBuffer.C:23: error: ‘OVERTURE_VERSION’ was not declared in this scope DataBaseBuffer.C: At global scope: DataBaseBuffer.C:26: error: expected constructor, destructor, or type conversion before ‘::’ token DataBaseBuffer.C:32: error: ‘DataBaseBuffer’ is not a class or namespace DataBaseBuffer.C:33: error: non-member function ‘bool isOpen()’ cannot have cv-qualifier DataBaseBuffer.C: In function ‘bool isOpen()’: DataBaseBuffer.C:36: error: ‘streamIs’ was not declared in this scope DataBaseBuffer.C:36: error: ‘notOpen’ was not declared in this scope DataBaseBuffer.C: At global scope: DataBaseBuffer.C:39: error: ‘DataBaseBuffer’ is not a class or namespace DataBaseBuffer.C:40: error: variable or field ‘openBuffer’ declared void DataBaseBuffer.C:40: error: ‘GenericDataBase’ was not declared in this scope DataBaseBuffer.C:40: error: ‘db’ was not declared in this scope DataBaseBuffer.C:40: error: expected primary-expression before ‘const’ ListOfHDF_DataBaseRCData.C:5:26: error: HDF_DataBase.h: No such file or directory ListOfHDF_DataBaseRCData.C:6:38: error: ListOfHDF_DataBaseRCData.h: No such file or directory ListOfHDF_DataBaseRCData.C:12: error: ‘ListOfHDF_DataBaseRCData’ has not been declared ListOfHDF_DataBaseRCData.C:12: error: ISO C++ forbids declaration of ‘ListOfHDF_DataBaseRCData’ with no type ListOfHDF_DataBaseRCData.C: In function ‘int ListOfHDF_DataBaseRCData()’: ListOfHDF_DataBaseRCData.C:21: error: ‘listLength’ was not declared in this scope ListOfHDF_DataBaseRCData.C:22: error: ‘aList’ was not declared in this scope ListOfHDF_DataBaseRCData.C:23: error: ‘memAlloc’ was not declared in this scope ListOfHDF_DataBaseRCData.C: At global scope: ListOfHDF_DataBaseRCData.C:28: error: ‘ListOfHDF_DataBaseRCData’ is not a class or namespace ListOfHDF_DataBaseRCData.C:28: error: ISO C++ forbids declaration of ‘ListOfHDF_DataBaseRCData’ with no type ListOfHDF_DataBaseRCData.C:28: error: expected ‘,’ or ‘...’ before ‘&’ token ListOfHDF_DataBaseRCData.C:28: error: ISO C++ forbids declaration of ‘ListOfHDF_DataBaseRCData’ with no type ListOfHDF_DataBaseRCData.C: In function ‘int ListOfHDF_DataBaseRCData(int)’: ListOfHDF_DataBaseRCData.C:37: error: ‘listLength’ was not declared in this scope ListOfHDF_DataBaseRCData.C:37: error: ‘X’ was not declared in this scope ListOfHDF_DataBaseRCData.C:40: error: ‘aList’ was not declared in this scope ListOfHDF_DataBaseRCData.C:41: error: ‘memAlloc’ was not declared in this scope ListOfHDF_DataBaseRCData.C:42: error: return-statement with no value, in function returning ‘int’ ListOfHDF_DataBaseRCData.C:45: error: ‘aList’ was not declared in this scope ListOfHDF_DataBaseRCData.C:45: error: ‘HDF_DataBaseRCData’ was not declared in this scope ListOfHDF_DataBaseRCData.C:45: error: expected type-specifier before ‘HDF_DataBaseRCData’ ListOfHDF_DataBaseRCData.C:45: error: expected ‘)’ before ‘HDF_DataBaseRCData’ ListOfHDF_DataBaseRCData.C:45: error: expected ‘;’ before ‘HDF_DataBaseRCData’ ListOfHDF_DataBaseRCData.C:46: error: ‘memAlloc’ was not declared in this scope ListOfHDF_DataBaseRCData.C: At global scope: ListOfHDF_DataBaseRCData.C:54: error: expected constructor, destructor, or type conversion before ‘::’ token ListOfHDF_DataBaseRCData.C:66: error: expected constructor, destructor, or type conversion before ‘&’ token make[1]: *** [DataBase_date] Error 1 make[1]: Leaving directory `/home/gjyadi/code/overture/overture/Overture.v23/DataBase' make: *** [all] Error 2 gjyadi@yangsiqi-desktop:~/code/overture/overture/Overture.v23$ Best Wishes gjy -- 祝好! Jiaye Gan -- 祝好! Jiaye Gan