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May 15, 2007, 09:40 |
Hi everyone,
I am trying to
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New Member
Alex Londono
Join Date: Mar 2009
Location: Medellin, Antioquia, Colombia
Posts: 9
Rep Power: 17 |
Hi everyone,
I am trying to include a new postprocessing utility named GradU, what I need is to write all the tensor values for every simulation time, it should be easy, because there is in OF 1.3 an utility magGradU, so I took this code and changed just minor things. The problem is that when I try to compile this utility, a compilation problem appers. The main code is this one (GradU.C): ------------------------------- #include "fvCFD.H" // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // Main program: int main(int argc, char *argv[]) { # include "addTimeOptions.H" # include "setRootCase.H" # include "createTime.H" // Get times list instantList Times = runTime.times(); // set startTime and endTime depending on -time and -latestTime options # include "checkTimeOptions.H" runTime.setTime(Times[startTime], startTime); # include "createMesh.H" for (label i=startTime; i<endTime; i++) { runTime.setTime(Times[i], i); Info<< "Time = " << runTime.timeName() << endl; IOobject Uheader ( "U", runTime.timeName(), mesh, IOobject::MUST_READ ); // Check U exists if (Uheader.headerOk()) { mesh.readUpdate(); Info<< " Reading U" << endl; volVectorField U(Uheader, mesh); Info<< " Calculating GradU" << endl; volScalarField GradU ( IOobject ( "GradU", runTime.timeName(), mesh, IOobject::NO_READ ), mag(fvc::grad(U)) ); GradU.write(); } else { Info<< " No U" << endl; } } return(0); } // ************************************************** *********************** // But when I type wmake I obtain: -------------------------------------------------------------------------------- -- SOURCE_DIR=. SOURCE=GradU.C ; g++ -m32 -Dlinux -DDP -Wall -W -Wno-unused-parameter -Wold-style-cast -O3 -DNoRepository -ftemplate-depth-30 -I/home/alondono/OpenFOAM/OpenFOAM-1.3/src/finiteVolume/lnInclude -I/home/alondono/OpenFOAM/OpenFOAM-1.3/src/OpenFOAM/lnInclude -IlnInclude -I. -fPIC -pthread -c $SOURCE -o Make/linuxGcc4DPOpt/GradU.o /home/alondono/OpenFOAM/OpenFOAM-1.3/wmake/bashScripts/mkObjectDir /home/alondono/OpenFOAM/OpenFOAM-1.3/applications/bin/linuxGcc4DPOpt/GradU g++ -m32 -Dlinux -DDP -Wall -W -Wno-unused-parameter -Wold-style-cast -O3 -DNoRepository -ftemplate-depth-30 -I/home/alondono/OpenFOAM/OpenFOAM-1.3/src/finiteVolume/lnInclude -I/home/alondono/OpenFOAM/OpenFOAM-1.3/src/OpenFOAM/lnInclude -IlnInclude -I. -fPIC -pthread Make/linuxGcc4DPOpt/GradU.o -L/home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt \ -lfiniteVolume -lfoamUtil -lOpenFOAM -liberty -o /home/alondono/OpenFOAM/OpenFOAM-1.3/applications/bin/linuxGcc4DPOpt/GradU /usr/bin/ld: warning: libtriSurface.so, needed by /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libmeshTools.so, needed by /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libPstream.so, needed by /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libOpenFOAM.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libfoamUser.so, needed by /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libOpenFOAM.so, not found (try using -rpath or -rpath-link) /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::polyMeshAdder::addWithoutPatches(Foam::poly Mesh&, Foam::polyMesh const&, Foam::faceCoupleInfo const&)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::IPstream::IPstream(int, int, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::operator>>(Foam::Istream&, Foam::wallPoint&)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `typeinfo for Foam::triSurface' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::wallPoint::greatPoint' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libOpenFOAM.so: referencia a `vtable for Foam:Pstream' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::triSurface::~triSurface()' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::IPstream::read(int, char*, int)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::cellDistFuncs::correctBoundaryFaceCells(Foa m::HashSet<int,> > const&, Foam::Field<double>&, Foam::Map<int>&) const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::operator<<(Foam:stream&, Foam::wallPoint const&)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libOpenFOAM.so: referencia a `Foam::Pstream::exit(int)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::polyMeshAdder::polyMeshAdder()' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::triSurface::operator=(Foam::triSurface const&)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::cellDistFuncs::cellDistFuncs(Foam::polyMesh const&)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::cellDistFuncs::correctBoundaryPointCells(Fo am::HashSet<int,> > const&, Foam::Field<double>&, Foam::Map<int>&) const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::orientedSurface::orientedSurface(Foam::triS urface const&, Foam::Vector<double> const&, bool)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::cellDistFuncs::getPatchIDs(Foam::word const&) const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::cellDistFuncs::smallestDist(Foam::Vector<do uble> const&, Foam::polyPatch const&, int, Foam::List<int> const&, int&) const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::triSurface::triSurface(Foam::List<foam::lab elledtri> const&, Foam::Field<foam::vector<double> > const&)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::patchWave::~patchWave()' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::mapAddedPolyMesh::oldCellMap() const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::cellDistFuncs::cellDistFuncs(Foam::polyMesh const&)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::cellDistFuncs::getPointNeighbours(Foam::Pri mitivePatch<foam::face,> > const&> const&, int, Foam::List<int>&) const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::triSurface::triSurface()' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::triSurface::movePoints(Foam::Field<foam::ve ctor<double> > const&)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::cellDistFuncs::sumPatchSize(Foam::HashSet<i nt,> > const&) const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::triSurface::~triSurface()' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::mapAddedPolyMesh::addedFaceMap() const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libOpenFOAM.so: referencia a `Foam::Pstream::addValidParOptions(Foam::HashTable <foam::string,>&)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::mapAddedPolyMesh::oldFaceMap() const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::cellDistFuncs::maxPatchSize(Foam::HashSet<i nt,> > const&) const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::patchWave::patchWave(Foam::polyMesh const&, Foam::HashSet<int,> > const&, bool)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::reduce(double&, Foam::sumOp<double> const&)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libOpenFOAM.so: referencia a `Foam::Pstream::init(int&, char**&)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libOpenFOAM.so: referencia a `Foam::Pstream::abort()' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::mapAddedPolyMesh::addedCellMap() const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam::triSurface::subsetMesh(Foam::List<bool> const&, Foam::List<int>&, Foam::List<int>&) const' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam:Pstream::write(int, char const*, int, bool)' sin definir /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libfiniteVolume.so: referencia a `Foam:Pstream::~OPstream()' sin definir collect2: ld returned 1 exit status make: *** [/home/alondono/OpenFOAM/OpenFOAM-1.3/applications/bin/linuxGcc4DPOpt/GradU] Error 1 -------------------------------------------------------------------------------- ------------------- So in conclusion Error 1 and it can not create the executable file. I also changed the Make and FoamX files and I executed as root but this problem still exist. What should I do, it's necessary to modify another file for compiling a new utility?? Thanks in advance, Alex L. |
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May 15, 2007, 09:42 |
Sorry,
The main code is thi
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#2 |
New Member
Alex Londono
Join Date: Mar 2009
Location: Medellin, Antioquia, Colombia
Posts: 9
Rep Power: 17 |
Sorry,
The main code is this one: \*---------------------------------------------------------------------------*/ #include "fvCFD.H" // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // Main program: int main(int argc, char *argv[]) { # include "addTimeOptions.H" # include "setRootCase.H" # include "createTime.H" // Get times list instantList Times = runTime.times(); // set startTime and endTime depending on -time and -latestTime options # include "checkTimeOptions.H" runTime.setTime(Times[startTime], startTime); # include "createMesh.H" for (label i=startTime; i<endTime; i++) { runTime.setTime(Times[i], i); Info<< "Time = " << runTime.timeName() << endl; IOobject Uheader ( "U", runTime.timeName(), mesh, IOobject::MUST_READ ); // Check U exists if (Uheader.headerOk()) { mesh.readUpdate(); Info<< " Reading U" << endl; volVectorField U(Uheader, mesh); Info<< " Calculating GradU" << endl; volTensorField GradU ( IOobject ( "GradU", runTime.timeName(), mesh, IOobject::NO_READ ), mag(fvc::grad(U)) ); GradU.write(); } else { Info<< " No U" << endl; } } return(0); } // ************************************************** *********************** // |
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May 16, 2007, 18:02 |
Hi Alex!
The good news: the
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#3 |
Assistant Moderator
Bernhard Gschaider
Join Date: Mar 2009
Posts: 4,225
Rep Power: 51 |
Hi Alex!
The good news: the error messages say that the .C file was compiled to a .o file (so there is no problem with your program), but (the bad news) it was not possible to link it (and I have no idea why). Could you post the Make/options, Make/files-files?
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May 17, 2007, 22:29 |
Hi Bernhard,
These are the
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#4 |
New Member
Alex Londono
Join Date: Mar 2009
Location: Medellin, Antioquia, Colombia
Posts: 9
Rep Power: 17 |
Hi Bernhard,
These are the files, Make/Options EXE_INC = \ -I$(LIB_SRC)/finiteVolume/lnInclude EXE_LIBS = \ -lfiniteVolume \ -lfoamUtil Make/files GradU.C EXE = $(FOAM_APPBIN)/GradU And if it's useful, this is the FoamX/GradU.cfg file // GradU tool definition description "grad(U) calculation"; GradUDict { type dictionary; description "GradU control dictionary"; dictionaryPath "system"; entries { arguments { type rootCaseTimeArguments; } } } // ************************************************** *********************** // Thanks for your help. Regards, Alex L. |
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May 21, 2007, 08:52 |
Hi Alex!
Either I'm missing
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#5 |
Assistant Moderator
Bernhard Gschaider
Join Date: Mar 2009
Posts: 4,225
Rep Power: 51 |
Hi Alex!
Either I'm missing something very obious about your case or something is very strange on your machine. BTW: What kind of Linux are you using (version)? Are the libraries that are "missing" (your intial posting) during linking, actually there? For instance /home/alondono/OpenFOAM/OpenFOAM-1.3/lib/linuxGcc4DPOpt/libtriSurface.so Are they readable for you? What does the file-command think of them? Bernhard
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May 21, 2007, 20:43 |
Hi Bernhard,
I think I have
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#6 |
New Member
Alex Londono
Join Date: Mar 2009
Location: Medellin, Antioquia, Colombia
Posts: 9
Rep Power: 17 |
Hi Bernhard,
I think I have found the problem, and it appears to be what you asked me about: the linux version. Using Ubuntu this utility does not compile and the problem seems to be that a library (.so file) is missing. Using OpenSUSE 10.1 this utility works properly and creates the EXE file, and besides it prints the GradU tensor as I expected. Thanks for your help. With kind regards, |
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April 11, 2008, 09:09 |
onyx-bridge 313% gdb ../../../
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#7 |
Senior Member
Daniel WEI (老魏)
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onyx-bridge 313% gdb ../../../wmake/rules/sgi*/wmkdep
GNU gdb 6.6 Copyright (C) 2006 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "mips-sgi-irix6.5"... (gdb) r dynamicFvMesh.C Starting program: /disk4/usr/people/student3/OpenFOAM/OpenFOAM-1.4.1/wmake/rules/sgiN32Gcc/wmkdep dynamicFvMesh.C Making dependency list for source file dynamicFvMesh.C $(OBJECTS_DIR)/dynamicFvMesh.o: dynamicFvMesh.dep 1111dynamicFvMesh.dep: dynamicFvMesh.C 1111dynamicFvMesh.dep: dynamicFvMesh.H could not open file fvMesh.H for source file dynamicFvMesh.C could not open file autoPtr.H for source file dynamicFvMesh.C could not open file runTimeSelectionTables.H for source file dynamicFvMesh.C Program received signal SIGSEGV, Segmentation fault. fread () at /xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/stdio/fread.c:37 37 /xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/stdio/fread.c: No such file or directory. in /xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/stdio/fread.c (gdb) bt #0 fread () at /xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/stdio/fread.c:37 #1 0x10002b74 in yylex () #2 0x10003250 in main () (gdb) q The program is running. Exit anyway? (y or n) y onyx-bridge 314% uname -a IRIX64 onyx-bridge 6.5 01080747 IP35 onyx-bridge 315% ulimit -a time(seconds) unlimited file(blocks) unlimited data(kbytes) unlimited stack(kbytes) 65536 memory(kbytes) 29096416 coredump(blocks) unlimited nofiles(descriptors) 200 vmemory(kbytes) unlimited concurrency(threads) 1024 onyx-bridge 316% Hi Bernhard, Concerning the beginning of this thread, I have a question. I try to compile OpenFOAM on Irix6.5, yet I met core dump everytime when wmkdep is called. So, it is quite fatal that after compilation icoFoam failed with SegV. For instance, when I wmake libso dynamicFVMesh, after it is finished, I get a bad dynamicFVMesh.so and with a core file under src/dynamicFVMesh directory. Here is the information when I try to debug it. ----------------------------- onyx-bridge 313% gdb ../../../wmake/rules/sgi*/wmkdep GNU gdb 6.6 Copyright (C) 2006 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "mips-sgi-irix6.5"... (gdb) r dynamicFvMesh.C Starting program: /disk4/usr/people/student3/OpenFOAM/OpenFOAM-1.4.1/wmake/rules/sgiN32Gcc/wmkdep dynamicFvMesh.C Making dependency list for source file dynamicFvMesh.C $(OBJECTS_DIR)/dynamicFvMesh.o: dynamicFvMesh.dep 1111dynamicFvMesh.dep: dynamicFvMesh.C 1111dynamicFvMesh.dep: dynamicFvMesh.H could not open file fvMesh.H for source file dynamicFvMesh.C could not open file autoPtr.H for source file dynamicFvMesh.C could not open file runTimeSelectionTables.H for source file dynamicFvMesh.C Program received signal SIGSEGV, Segmentation fault. fread () at /xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/stdio/fread.c:37 37 /xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/stdio/fread.c: No such file or directory. in /xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/stdio/fread.c (gdb) bt #0 fread () at /xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/stdio/fread.c:37 #1 0x10002b74 in yylex () #2 0x10003250 in main () (gdb) q The program is running. Exit anyway? (y or n) y onyx-bridge 314% uname -a IRIX64 onyx-bridge 6.5 01080747 IP35 onyx-bridge 315% ulimit -a time(seconds) unlimited file(blocks) unlimited data(kbytes) unlimited stack(kbytes) 65536 memory(kbytes) 29096416 coredump(blocks) unlimited nofiles(descriptors) 200 vmemory(kbytes) unlimited concurrency(threads) 1024 onyx-bridge 316% So, what does this line mean? #0 fread () at /xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/stdio/fread.c:37 Please help, thanks! Daniel
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April 11, 2008, 09:17 |
I am very sorry for the wrong
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Senior Member
Daniel WEI (老魏)
Join Date: Mar 2009
Location: Beijing, China
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I am very sorry for the wrong post!
What I want to say is the error message: ------------------------------------------- ....not found (try using -rpath or -rpath-link) ------------------------------------------- is most likely because gnu-ld is not successfully installed. For I am working on porting OpenFOAM to IRIX but no avail now, and I met the same problem as you were, Alex. I am trying to figure it out.
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~ Daniel WEI ------------- Boeing Research & Technology - China Beijing, China |
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