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Subject: Re: [OMPI users] OMPI seg fault by a class with weird address.
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2011-03-15 06:19:53


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: dtustudy68_at_[hidden]
> To: belaid_moa_at_[hidden]; users_at_[hidden]
> 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_moa_at_[hidden]
> To: users_at_[hidden]; dtustudy68_at_[hidden]
> 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: dtustudy68_at_[hidden]
> To: users_at_[hidden]
> 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;
> }
> ----------------------------------------------------------
>
>
>
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-- 
Jeff Squyres
jsquyres_at_[hidden]
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