Thanks,From http://valgrind.org/docs/manual/mc-manual.html#mc-manual.mpiwrap
I find that
"Currently the wrappers are only buildable with mpiccs which are based on GNU
GCC or Intel's C++ Compiler."
The cluster which I am working on is using GNU Open MPI mpic++. i am afraid
that the Valgrind wrapper can work here.
I do not have system administrator authorization.
Are there other mem-checkers (open source) that can do this ?
thanks
Jack
> Subject: Re: [OMPI users] OMPI seg fault by a class with weird address.
> From: jsquy...@cisco.com
> Date: Tue, 15 Mar 2011 06:19:53 -0400
> CC: dtustud...@hotmail.com
> To: us...@open-mpi.org
>
> You may also want to run your program through a memory-checking debugger such
> as valgrind to see if it turns up any other problems.
>
> AFIK, ptmalloc should be fine for use with STL vector allocation.
>
>
> On Mar 15, 2011, at 4:00 AM, Belaid MOA wrote:
>
> > Hi Jack,
> > I may need to see the whole code to decide but my quick look suggest that
> > ptmalloc is causing a problem with STL-vector allocation. ptmalloc is the
> > openMPI internal malloc library. Could you try to build openMPI without
> > memory management (using --without-memory-manager) and let us know the
> > outcome. ptmalloc is not needed if you are not using an RDMA interconnect.
> >
> > With best regards,
> > -Belaid.
> >
> > From: dtustud...@hotmail.com
> > To: belaid_...@hotmail.com; us...@open-mpi.org
> > Subject: RE: [OMPI users] OMPI seg fault by a class with weird address.
> > Date: Tue, 15 Mar 2011 00:30:19 -0600
> >
> > Hi,
> >
> > Because the code is very long, I just show the calling relationship of
> > functions.
> >
> > main()
> > {
> > scheduler();
> >
> > }
> > scheduler()
> > {
> > ImportIndices();
> > }
> >
> > ImportIndices()
> > {
> > Index IdxNode ;
> > IdxNode = ReadFile("fileName");
> > }
> >
> > Index ReadFile(const char* fileinput)
> > {
> > Index TempIndex;
> > .........
> >
> > }
> >
> > vector<int> Index::GetPosition() const { return Position; }
> > vector<int> Index::GetColumn() const { return Column; }
> > vector<int> Index::GetYear() const { return Year; }
> > vector<string> Index::GetName() const { return Name; }
> > int Index::GetPosition(const int idx) const { return Position[idx]; }
> > int Index::GetColumn(const int idx) const { return Column[idx]; }
> > int Index::GetYear(const int idx) const { return Year[idx]; }
> > string Index::GetName(const int idx) const { return Name[idx]; }
> > int Index::GetSize() const { return Position.size(); }
> >
> > The sequential code works well, and there is no scheduler().
> >
> > The parallel code output from gdb:
> > ----------------------------------------------
> > Breakpoint 1, myNeplanTaskScheduler(CNSGA2 *, int, int, int, ._85 *, char,
> > int, message_para_to_workers_VecT &, MPI_Datatype, int &, int &,
> > std::vector<std::vector<double, std::allocator<double> >,
> > std::allocator<std::vector<double, std::allocator<double> > > > &,
> > std::vector<std::vector<double, std::allocator<double> >,
> > std::allocator<std::vector<double, std::allocator<double> > > > &,
> > std::vector<double, std::allocator<double> > &, int,
> > std::vector<std::vector<double, std::allocator<double> >,
> > std::allocator<std::vector<double, std::allocator<double> > > > &,
> > MPI_Datatype, int, MPI_Datatype, int) (nsga2=0x118c490,
> > popSize=<value optimized out>, nodeSize=<value optimized out>,
> > myRank=<value optimized out>, myChildpop=0x1208d80, genCandTag=65 'A',
> > generationNum=1, myPopParaVec=std::vector of length 4, capacity 4 =
> > {...},
> > message_to_master_type=0x7fffffffd540, myT1Flag=@0x7fffffffd68c,
> > myT2Flag=@0x7fffffffd688,
> > resultTaskPackageT1=std::vector of length 4, capacity 4 = {...},
> > resultTaskPackageT2Pr=std::vector of length 4, capacity 4 = {...},
> > xdataV=std::vector of length 4, capacity 4 = {...}, objSize=7,
> > resultTaskPackageT12=std::vector of length 4, capacity 4 = {...},
> > xdata_to_workers_type=0x121c410, myGenerationNum=1,
> > Mpara_to_workers_type=0x121b9b0, nconNum=0)
> > at src/nsga2/myNetplanScheduler.cpp:109
> > 109 ImportIndices();
> > (gdb) c
> > Continuing.
> >
> > Breakpoint 2, ImportIndices () at src/index.cpp:120
> > 120 IdxNode = ReadFile("prepdata/idx_node.csv");
> > (gdb) c
> > Continuing.
> >
> > Breakpoint 4, ReadFile (fileinput=0xd8663d "prepdata/idx_node.csv")
> > at src/index.cpp:86
> > 86 Index TempIndex;
> > (gdb) c
> > Continuing.
> >
> > Breakpoint 5, Index::Index (this=0x7fffffffcb80) at src/index.cpp:20
> > 20 Name(0) {}
> > (gdb) c
> > Continuing.
> >
> > Program received signal SIGSEGV, Segmentation fault.
> > 0x00002aaaab3b0b81 in opal_memory_ptmalloc2_int_malloc ()
> > from /opt/openmpi-1.3.4-gnu/lib/libopen-pal.so.0
> >
> > ---------------------------------------
> > the backtrace output from the above parallel OpenMPI code:
> >
> > (gdb) bt
> > #0 0x00002aaaab3b0b81 in opal_memory_ptmalloc2_int_malloc ()
> > from /opt/openmpi-1.3.4-gnu/lib/libopen-pal.so.0
> > #1 0x00002aaaab3b2bd3 in opal_memory_ptmalloc2_malloc ()
> > from /opt/openmpi-1.3.4-gnu/lib/libopen-pal.so.0
> > #2 0x0000003f7c8bd1dd in operator new(unsigned long) ()
> > from /usr/lib64/libstdc++.so.6
> > #3 0x00000000004646a7 in __gnu_cxx::new_allocator<int>::allocate (
> > this=0x7fffffffcb80, __n=0)
> > at
> > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h:88
> > #4 0x00000000004646cf in std::_Vector_base<int, std::allocator<int>
> > >::_M_allocate (this=0x7fffffffcb80, __n=0)
> > at
> > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h:127
> > #5 0x0000000000464701 in std::_Vector_base<int, std::allocator<int>
> > >::_Vector_base (this=0x7fffffffcb80, __n=0, __a=...)
> > at
> > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h:113
> > #6 0x0000000000464d0b in std::vector<int, std::allocator<int> >::vector (
> > this=0x7fffffffcb80, __n=0, __value=@0x7fffffffc968, __a=...)
> > at
> > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h:216
> > #7 0x00000000004890d7 in Index::Index (this=0x7fffffffcb80)
> > ---Type <return> to continue, or q <return> to quit---
> > at src/index.cpp:20
> > #8 0x000000000048927a in ReadFile (fileinput=0xd8663d
> > "prepdata/idx_node.csv")
> > at src/index.cpp:86
> > #9 0x0000000000489533 in ImportIndices () at src/index.cpp:120
> > #10 0x0000000000445e0e in myNeplanTaskScheduler(CNSGA2 *, int, int, int,
> > ._85 *, char, int, message_para_to_workers_VecT &, MPI_Datatype, int &, int
> > &, std::vector<std::vector<double, std::allocator<double> >,
> > std::allocator<std::vector<double, std::allocator<double> > > > &,
> > std::vector<std::vector<double, std::allocator<double> >,
> > std::allocator<std::vector<double, std::allocator<double> > > > &,
> > std::vector<double, std::allocator<double> > &, int,
> > std::vector<std::vector<double, std::allocator<double> >,
> > std::allocator<std::vector<double, std::allocator<double> > > > &,
> > MPI_Datatype, int, MPI_Datatype, int) (nsga2=0x118c490,
> > popSize=<value optimized out>, nodeSize=<value optimized out>,
> > myRank=<value optimized out>, myChildpop=0x1208d80, genCandTag=65 'A',
> > generationNum=1, myPopParaVec=std::vector of length 4, capacity 4 =
> > {...},
> > message_to_master_type=0x7fffffffd540, myT1Flag=@0x7fffffffd68c,
> > myT2Flag=@0x7fffffffd688,
> > resultTaskPackageT1=std::vector of length 4, capacity 4 = {...},
> > resultTaskPackageT2Pr=std::vector of length 4, capacity 4 = {...},
> > xdataV=std::vector of length 4, capacity 4 = {...}, objSize=7,
> > resultTaskPackageT12=std::vector of length 4, capacity 4 = {...},
> > xdata_to_workers_type=0x121c410, myGenerationNum=1,
> > Mpara_to_workers_type=0x121b9b0, nconNum=0)
> > ---Type <return> to continue, or q <return> to quit---
> > at src/nsga2/myNetplanScheduler.cpp:109
> > #11 0x000000000044f44b in main (argc=1, argv=0x7fffffffd998)
> > at src/nsga2/main-parallel2.cpp:216
> > ----------------------------------------------------
> >
> > What is "opal_memory_ptmalloc2_int_malloc ()" ?
> >
> > The gdb output from sequential code:
> > -------------------------------------
> > Breakpoint 1, main (argc=<value optimized out>, argv=<value optimized out>)
> > at src/nsga2/main-seq.cpp:32
> > 32 ImportIndices();
> > (gdb) c
> > Continuing.
> >
> > Breakpoint 2, ImportIndices () at src/index.cpp:115
> > 115 IdxNode = ReadFile("prepdata/idx_node.csv");
> > (gdb) c
> > Continuing.
> >
> > Breakpoint 4, ReadFile (fileinput=0xd6bb9d "prepdata/idx_node.csv")
> > at src/index.cpp:86
> > 86 Index TempIndex;
> > (gdb) c
> > Continuing.
> >
> > Breakpoint 5, Index::Index (this=0x7fffffffd6d0) at src/index.cpp:20
> > 20 Name(0) {}
> > (gdb) c
> > Continuing.
> >
> > Breakpoint 4, ReadFile (fileinput=0xd6bbb3 "prepdata/idx_ud.csv")
> > at src/index.cpp:86
> > 86 Index TempIndex;
> > (gdb) bt
> > #0 ReadFile (fileinput=0xd6bbb3 "prepdata/idx_ud.csv") at src/index.cpp:86
> > #1 0x0000000000471cc9 in ImportIndices () at src/index.cpp:116
> > #2 0x000000000043bba6 in main (argc=<value optimized out>,
> > argv=<value optimized out>) at src/nsga2/main-seq.cpp:32
> >
> > --------------------------------------
> > thanks
> >
> >
> > From: belaid_...@hotmail.com
> > To: us...@open-mpi.org; dtustud...@hotmail.com
> > Subject: RE: [OMPI users] OMPI seg fault by a class with weird address.
> > Date: Tue, 15 Mar 2011 06:16:35 +0000
> >
> > Hi Jack,
> > 1- Where is your main function to see how you called your class?
> > 2- I do not see the implementation of GetPosition, GetName, etc.?
> >
> > With best regards,
> > -Belaid.
> >
> >
> > From: dtustud...@hotmail.com
> > To: us...@open-mpi.org
> > Date: Mon, 14 Mar 2011 19:04:12 -0600
> > Subject: [OMPI users] OMPI seg fault by a class with weird address.
> >
> > Hi,
> >
> > I got a run-time error of a Open MPI C++ program.
> >
> > The following output is from gdb:
> >
> > --------------------------------------------------------------------------
> > Program received signal SIGSEGV, Segmentation fault.
> > 0x00002aaaab3b0b81 in opal_memory_ptmalloc2_int_malloc ()
> > from /opt/openmpi-1.3.4-gnu/lib/libopen-pal.so.0
> >
> > At the point
> >
> > Breakpoint 9, Index::Index (this=0x7fffffffcb80) at src/index.cpp:20
> > 20 Name(0) {}
> >
> > The Index has been called before this point and no problem:
> > -------------------------------------------------------
> > Breakpoint 9, Index::Index (this=0x117d800) at src/index.cpp:20
> > 20 Name(0) {}
> > (gdb) c
> > Continuing.
> >
> > Breakpoint 9, Index::Index (this=0x117d860) at src/index.cpp:20
> > 20 Name(0) {}
> > (gdb) c
> > Continuing.
> > ----------------------------------------------------------------------------
> >
> > It seems that the 0x7fffffffcb80 address is a problem.
> >
> > But, I donot know the reason and how to remove the bug.
> >
> > Any help is really appreciated.
> >
> > thanks
> >
> > the following is the index definition.
> >
> > ---------------------------------------------------------
> > class Index {
> > public:
> > Index();
> > Index(const Index& rhs);
> > ~Index();
> > Index& operator=(const Index& rhs);
> >
> > vector<int> GetPosition() const;
> > vector<int> GetColumn() const;
> > vector<int> GetYear() const;
> > vector<string> GetName() const;
> > int GetPosition(const int idx) const;
> > int GetColumn(const int idx) const;
> > int GetYear(const int idx) const;
> > string GetName(const int idx) const;
> > int GetSize() const;
> >
> > void Add(const int idx, const int col, const string& name);
> > void Add(const int idx, const int col, const int year, const
> > string& name);
> > void Add(const int idx, const Step& col, const string& name);
> > void WriteFile(const char* fileinput) const;
> >
> > private:
> > vector<int> Position;
> > vector<int> Column;
> > vector<int> Year;
> > vector<string> Name;
> > };
> > // Contructors and destructor for the Index class
> > Index::Index() :
> > Position(0),
> > Column(0),
> > Year(0),
> > Name(0) {}
> >
> > Index::Index(const Index& rhs) :
> > Position(rhs.GetPosition()),
> > Column(rhs.GetColumn()),
> > Year(rhs.GetYear()),
> > Name(rhs.GetName()) {}
> >
> > Index::~Index() {}
> >
> > Index& Index::operator=(const Index& rhs) {
> > Position = rhs.GetPosition();
> > Column = rhs.GetColumn(),
> > Year = rhs.GetYear(),
> > Name = rhs.GetName();
> > return *this;
> > }
> > ----------------------------------------------------------
> >
> >
> >
> > _______________________________________________ users mailing list
> > us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users
> > _______________________________________________
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> jsquy...@cisco.com
> For corporate legal information go to:
> http://www.cisco.com/web/about/doing_business/legal/cri/
>
