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Subject: Re: [OMPI users] OMPI seg fault by a class with weird address.
From: Jack Bryan (dtustudy68_at_[hidden])
Date: 2011-03-15 11:42:29


I have tried export OMPI_MCA_memory_ptmalloc2_disable=1
It does not work. The same error.
thanks

From: samuel_at_[hidden]
To: users_at_[hidden]
Date: Tue, 15 Mar 2011 09:27:35 -0600
Subject: Re: [OMPI users] OMPI seg fault by a class with weird address.

I -think- setting OMPI_MCA_memory_ptmalloc2_disable to 1 will turn off OMPI's memory wrappers without having to rebuild. Someone please correct me if I'm wrong :-).
For example (bash-like shell):
export OMPI_MCA_memory_ptmalloc2_disable=1
Hope that helps,
 --Samuel K. GutierrezLos Alamos National Laboratory
 
On Mar 15, 2011, at 9:19 AM, Jack Bryan wrote:Thanks,
I do not have system administrator authorization. I am afraid that I cannot rebuild OpenMPI --without-memory-manager.
Are there other ways to get around it ?
For example, use other things to replace "ptmalloc" ?
Any help is really appreciated.
thanks

From: belaid_moa_at_[hidden]
To: dtustudy68_at_[hidden]; users_at_[hidden]
Subject: RE: [OMPI users] OMPI seg fault by a class with weird address.
Date: Tue, 15 Mar 2011 08:00:56 +0000

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:109109 ImportIndices();(gdb) cContinuing.
Breakpoint 2, ImportIndices () at src/index.cpp:120120 IdxNode = ReadFile("prepdata/idx_node.csv");(gdb) cContinuing.
Breakpoint 4, ReadFile (fileinput=0xd8663d "prepdata/idx_node.csv") at src/index.cpp:8686 Index TempIndex;(gdb) cContinuing.
Breakpoint 5, Index::Index (this=0x7fffffffcb80) at src/index.cpp:2020 Name(0) {}(gdb) cContinuing.
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:3232 ImportIndices();(gdb) cContinuing.
Breakpoint 2, ImportIndices () at src/index.cpp:115115 IdxNode = ReadFile("prepdata/idx_node.csv");(gdb) cContinuing.
Breakpoint 4, ReadFile (fileinput=0xd6bb9d "prepdata/idx_node.csv") at src/index.cpp:8686 Index TempIndex;(gdb) cContinuing.
Breakpoint 5, Index::Index (this=0x7fffffffd6d0) at src/index.cpp:2020 Name(0) {}(gdb) cContinuing.
Breakpoint 4, ReadFile (fileinput=0xd6bbb3 "prepdata/idx_ud.csv") at src/index.cpp:8686 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:2020 Name(0) {}
The Index has been called before this point and no problem:-------------------------------------------------------Breakpoint 9, Index::Index (this=0x117d800) at src/index.cpp:2020 Name(0) {}(gdb) cContinuing.
Breakpoint 9, Index::Index (this=0x117d860) at src/index.cpp:2020 Name(0) {}(gdb) cContinuing.----------------------------------------------------------------------------
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 classIndex::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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