[C++-sig] Problem: boost_python 1.31 (release) causes huge memory allocation

Wirawan Purwanto wirawan at camelot.physics.wm.edu
Thu Jul 1 17:59:56 CEST 2004


Just a compliment, first: I am very new to boost::python library. I'm really 
impressed at the ease of use of that library. I have an existing code that I 
want to "manipulate" via python, and it only took me a few tests to get the 
simple interface up and running!

Now is the meat. :) To highlight where the questions are, I put "QUESTION:" at 
the beginning of the paragraph, below. Sorry if the detail is too long.

I am using Mandrake Linux 10 (kernel = 2.6.3-7mdk, gcc = 3.3.2-6mdk) and boost 
library version 1.31.0 (official release). I compiled the *whole* boost library 
using bjam, as directed in the website. The first attempt to "wrap" my code 
with boost::python went fine. Here's the wrapper initialization code:

     using namespace boost::python;

     TBH_PY_DEBUG(("Initializing HubbardGP module interface\n"));
         .def("OpenFiles", &HubbardGP::OpenFiles)
         .def("Solve", &HubbardGP::Solve)
         .def("ReportResults", &HubbardGP::ReportResults)
//        .add_property("ndim", &HubbardGP::ndim_pyget)
     TBH_PY_DEBUG(("Done initializing HubbardGP module interface\n"));

Please disregard "TBH_PY_DEBUG" there--it just calls C's printf function to 
print the string on the screen.

I built my shared object (HubbardGP.so) using make(1) for a stupid reason: I 
still don't understand completely bjam's quirks. I linked against the "release" 
version of libboost_python-gcc.so, in this way:

$ g++ -L/usr/local/lib -fPIC -Wall -ftemplate-depth-100 \
                -g -O0 -DDEBUG \
                -DBOOST_PYTHON_DYNAMIC_LIB \
                -DTBH_NDIM=1 -DTBH_USE_FFTW3 -D__section__=1 \
                -Isrc -Isrc/cp.inc \
                -I/usr/local/boost-1.31.0/include/boost-1_31 \
                -I/usr/include/python2.3 \
                -c src/test-lattice-params.cpp -o objs/HubbardGP.o

$ g++ -L/usr/local/lib -shared -Wall -static-libgcc \
                -llapack -lcblas -lf77blas -latlas -lfftw3 \
                -lg2c \
                -lboost_python-gcc \
                -L/usr/local/boost-1.31.0/lib \
                objs/HubbardGP.o -o HubbardGP.so

Do you see the difference? My code was compiled using DEBUG switch (and -O0), 
but then linked to the RELEASE variant of the boost::python lib.

QUESTION: is this an acceptable practice? I'm wondering if the DEBUG code must 
always be linked against the DEBUG boost::python lib and vice versa.

QUESTION: Without the .addproperty() stuff (that's commented in the snippet 
above), the code runs fine. But when I added the .addproperty() line, a 
calamity happens: when I was about to instantiate HubbardGP object, the 
computer froze. When I checked using top(1), the python program tries to 
allocate a huge chunk of memory, which did NOT happen before the .addproperty() 
is added in my wrapper. I re-ran strace(1), and found that the program (either 
python or the boost_python lib, or remotely possibly my own code?) attempted to 
allocate ~590MB of memory. Here's the strace(1) output, when I forcibly LIMIT 
the amount of vmem available to the program to 250 MB only:

   write(1, "Initializing HubbardGP module in"..., 40Initializing HubbardGP
   module interface) = 40
   write(1, "Done initializing HubbardGP modu"..., 45Done initializing
   HubbardGP module interface) = 45
   close(3)                                = 0
   futex(0x804a998, FUTEX_WAKE, 1)         = 0
   write(1, "Creating an instance of HubbardG"..., 34Creating an instance
   of HubbardGP) = 34
> 0) = -1 ENOMEM (Cannot allocate memory)
   brk(0)                                  = 0x80d6000
   brk(0x2b888000)                         = 0x80d6000
> 0) = -1 ENOMEM (Cannot allocate memory)
   -1, 0) = 0x87cb5000
   munmap(0x87cb5000, 307200)              = 0
   munmap(0x87e00000, 741376)              = 0
   mprotect(0x87d00000, 135168, PROT_READ|PROT_WRITE) = 0
> 0) = -1 ENOMEM (Cannot allocate memory)
   futex(0x401edaf4, FUTEX_WAKE, 2147483647) = 0
   futex(0x402207d4, FUTEX_WAKE, 2147483647) = 0
   write(2, "Traceback (most recent call last"..., 35Traceback (most recent
   call last):) = 35
   open("test-lattice-params.py", O_RDONLY|O_LARGEFILE) = 3
   write(2, "  File \"test-lattice-params.py\","..., 46  File
   "test-lattice-params.py", line 4, in ?) = 46
   fstat64(3, {st_mode=S_IFREG|0644, st_size=267, ...}) = 0
   0) = 0xab5b2000
   read(3, "import HubbardGP\n\nprint \"Creatin"..., 4096) = 267
   write(2, "    ", 4    )                     = 4
   write(2, "H = HubbardGP.HubbardGP()\n", 26H = HubbardGP.HubbardGP()
   ) = 26
   close(3)                                = 0
   munmap(0xab5b2000, 4096)                = 0
   write(2, "MemoryError", 11MemoryError)             = 11
   write(2, "\n", 1
   )                       = 1

There are 3 points when it tries to allocate huge amount of memory.

Now, I'm too new to both python and boost::python. Could you help me with this? 
I don't believe that my code was the one doing the mess. I tend to think that 
somehow the compiled boost_python code was acting up here. But I can't debug 
the code easily, as it involves running python itself in the debugger. How do 
you debug such a problem? Using python debugger is also not possible, since I 
don't think it allows going down to the C++-level code.

As a workaround, I could only link my HubbardGP.so against the DEBUG variant 
(libboost_python-gcc-d.so). Then the code went fine, even with .add_property() 

I tried once to regenerate the problem using a much smaller testcase, but the 
problem (huge mmap2) didn't show up.

As a reference, here's my python test code:

import HubbardGP
print "Creating an instance of HubbardGP"
H = HubbardGP.HubbardGP()
print "Done, now opening files"
x = H.OpenFiles("/tmp/file1.txt", "/tmp/file2.txt", "/tmp/file3.txt")
print "x is %d" % x

I would appreciate if someone helps me out in this respect.
The full source code of the wrapped C++ object is available if you need to look 
into it. But it's way too large to post here.


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