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_...@hotmail.com
To: dtustud...@hotmail.com; us...@open-mpi.org
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: 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;
}
----------------------------------------------------------
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