slow access to objects within 'cell' variables
Łukasz Sowiński
lukasz.sowinski at post.pl
Thu Jan 8 09:50:40 CST 2009
Bug report for Octave 3.0.3 configured for i686-pc-linux-gnu
Description:
-----------
* Access to objects within cell type depends on their size and can be
really slow.
F.i. if
a{1} = zeros(1, 10);
b{1} = zeros(1, 10000000);
then
a{1}(1) = 1;
is much faster than
b{1}(1) = 1;
.
Repeat-By:
---------
* Please execute the following code:
n_write = 1000;
for n_alloc = n_write*[1 10 100 1000]
y{1} = zeros(1, n_alloc);
timer = -cputime;
for i=1:n_write
y{1}(:, i) = 1;
endfor
disp(timer + cputime);
endfor
Configuration (please do not edit this section):
-----------------------------------------------
uname output: Linux gentoo 2.6.27-gentoo-r5 #2 SMP PREEMPT Sat Dec
13 16:04:21 Local time zone must be set-- i686 Intel(R) Core(TM)2 CPU
T5500 @ 1.66GHz GenuineIntel GNU/Linux
configure opts: '--prefix=/usr' '--host=i686-pc-linux-gnu'
'--mandir=/usr/share/man' '--infodir=/usr/share/info'
'--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib'
'--localstatedir=/var/state/octave' '--enable-shared'
'--with-blas=-lblas ' '--with-lapack=-llapack -lblas '
'--without-hdf5' '--without-curl' '--with-zlib' '--without-fftw'
'--without-umfpack' '--without-colamd' '--without-ccolamd'
'--without-cholmod' '--without-cxsparse' '--enable-readline'
'--build=i686-pc-linux-gnu' 'build_alias=i686-pc-linux-gnu'
'host_alias=i686-pc-linux-gnu' 'CFLAGS=-O2 -march=prescott -pipe
-fomit-frame-pointer' 'LDFLAGS=' 'CXXFLAGS=-O2 -march=prescott -pipe
-fomit-frame-pointer'
Fortran compiler: i686-pc-linux-gnu-gfortran
FFLAGS: -O -mieee-fp
F2C: @F2C@
F2CFLAGS: @F2CFLAGS@
FLIBS: -L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2
-L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../../i686-pc-linux-gnu/lib
-L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../.. -lz -lgfortranbegin
-lgfortran -lm
CPPFLAGS:
INCFLAGS: -I. -I. -I./liboctave -I./src -I./libcruft/misc
C compiler: i686-pc-linux-gnu-gcc, version 4.1.2 (Gentoo 4.1.2 p1.0.2)
CFLAGS: -O2 -march=prescott -pipe -fomit-frame-pointer
CPICFLAG: -fPIC
C++ compiler: i686-pc-linux-gnu-g++, version 4.1.2
CXXFLAGS: -O2 -march=prescott -pipe -fomit-frame-pointer
CXXPICFLAG: -fPIC
LD_CXX: i686-pc-linux-gnu-g++
LDFLAGS:
LIBFLAGS: -L.
RLD_FLAG: -Wl,-rpath -Wl,/usr/lib/octave-3.0.3
BLAS_LIBS: -llapack -lblas -lblas
FFTW_LIBS:
LIBS: -lreadline -lncurses -ldl -lz -lm
LEXLIB:
LIBGLOB:
SED: /bin/sed
DEFS:
-DPACKAGE_NAME="" -DPACKAGE_TARNAME="" -DPACKAGE_VERSION=""
-DPACKAGE_STRING="" -DPACKAGE_BUGREPORT="" -DOCTAVE_SOURCE=1
-D_GNU_SOURCE=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
-DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSEPCHAR=':'
-DSEPCHAR_STR=":" -D__NO_MATH_INLINES=1 -DCXX_NEW_FRIEND_TEMPLATE_DECL=1
-DCXX_ISO_COMPLIANT_LIBRARY=1 -DCXX_ABI=gnu_v3 -DHAVE_LIBM=1
-DHAVE_QHULL=1 -DHAVE_PCRE=1 -DHAVE_REGEXEC=1 -DHAVE_REGEX=1
-DHAVE_ZLIB_H=1 -DHAVE_ZLIB=1 -DHAVE_GLPK_H=1 -DHAVE_GLPK=1
-DHAVE_IEEE754_DATA_FORMAT=1 -DF77_FUNC(name,NAME)=name ## _
-DF77_FUNC_(name,NAME)=name ## _ -DHAVE_BLAS=1 -DHAVE_GETHOSTNAME=1
-DHAVE_GETPWNAM=1 -DHAVE_DEV_T=1 -DHAVE_INO_T=1 -DHAVE_NLINK_T=1
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-DHAVE_CURSES_H=1 -DHAVE_DLFCN_H=1 -DHAVE_FCNTL_H=1 -DHAVE_FLOAT_H=1
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-DHAVE_MEMORY_H=1 -DHAVE_NCURSES_H=1 -DHAVE_POLL_H=1 -DHAVE_PWD_H=1
-DHAVE_STDINT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_IOCTL_H=1
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-DHAVE_TERMCAP_H=1 -DHAVE_UNISTD_H=1 -DHAVE_UTIME_H=1 -DHAVE_SSTREAM=1
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-DHAVE_FNMATCH=1 -DHAVE_GLOB=1 -DHAVE_ATEXIT=1 -DHAVE_BASENAME=1
-DHAVE_BCOPY=1 -DHAVE_BZERO=1 -DHAVE_CANONICALIZE_FILE_NAME=1
-DHAVE_CHMOD=1 -DHAVE_DUP2=1 -DHAVE_ENDGRENT=1 -DHAVE_ENDPWENT=1
-DHAVE_EXECVP=1 -DHAVE_FCNTL=1 -DHAVE_FORK=1 -DHAVE_GETCWD=1
-DHAVE_GETEGID=1 -DHAVE_GETEUID=1 -DHAVE_GETGID=1 -DHAVE_GETGRENT=1
-DHAVE_GETGRGID=1 -DHAVE_GETGRNAM=1 -DHAVE_GETPGRP=1 -DHAVE_GETPID=1
-DHAVE_GETPPID=1 -DHAVE_GETPWENT=1 -DHAVE_GETPWUID=1 -DHAVE_GETTIMEOFDAY=1
-DHAVE_GETUID=1 -DHAVE_GETWD=1 -DHAVE_KILL=1 -DHAVE_LGAMMA=1
-DHAVE_LINK=1 -DHAVE_LOCALTIME_R=1 -DHAVE_LSTAT=1 -DHAVE_MEMMOVE=1
-DHAVE_MKDIR=1 -DHAVE_MKFIFO=1 -DHAVE_MKSTEMP=1 -DHAVE_ON_EXIT=1
-DHAVE_PIPE=1 -DHAVE_POLL=1 -DHAVE_PUTENV=1 -DHAVE_RAISE=1
-DHAVE_READLINK=1 -DHAVE_REALPATH=1 -DHAVE_RENAME=1 -DHAVE_RINDEX=1
-DHAVE_RMDIR=1 -DHAVE_ROUND=1 -DHAVE_SELECT=1 -DHAVE_SETGRENT=1
-DHAVE_SETLOCALE=1 -DHAVE_SETPWENT=1 -DHAVE_SETVBUF=1 -DHAVE_SIGACTION=1
-DHAVE_SIGLONGJMP=1 -DHAVE_SIGPENDING=1 -DHAVE_SIGPROCMASK=1
-DHAVE_SIGSUSPEND=1 -DHAVE_SNPRINTF=1 -DHAVE_STAT=1 -DHAVE_STRCASECMP=1
-DHAVE_STRDUP=1 -DHAVE_STRERROR=1 -DHAVE_STRNCASECMP=1 -DHAVE_STRPTIME=1
-DHAVE_STRSIGNAL=1 -DHAVE_SYMLINK=1 -DHAVE_TEMPNAM=1 -DHAVE_TGAMMA=1
-DHAVE_UMASK=1 -DHAVE_UNAME=1 -DHAVE_UNLINK=1 -DHAVE_USLEEP=1
-DHAVE_UTIME=1 -DHAVE_VFPRINTF=1 -DHAVE_VSPRINTF=1 -DHAVE_VSNPRINTF=1
-DHAVE_WAITPID=1 -DHAVE_STRFTIME=1 -DHAVE_LIBDL=1 -DHAVE_DLOPEN=1
-DHAVE_DLSYM=1 -DHAVE_DLERROR=1 -DHAVE_DLCLOSE=1 -DHAVE_DLOPEN_API=1
-DENABLE_DYNAMIC_LINKING=1 -DHAVE_TIMEVAL=1 -DHAVE_FINITE=1
-DHAVE_ISNAN=1 -DHAVE_ISINF=1 -DHAVE_COPYSIGN=1 -DHAVE_DECL_SIGNBIT=1
-DHAVE_ACOSH=1 -DHAVE_ASINH=1 -DHAVE_ATANH=1 -DHAVE_ERF=1 -DHAVE_ERFC=1
-DHAVE_EXP2=1 -DHAVE_LOG2=1 -DHAVE_STRUCT_STAT_ST_BLKSIZE=1
-DHAVE_STRUCT_STAT_ST_BLOCKS=1 -DHAVE_STRUCT_STAT_ST_RDEV=1
-DHAVE_STRUCT_TM_TM_ZONE=1 -DHAVE_TM_ZONE=1 -DUSE_READLINE=1
-DEXCEPTION_IN_MATH=1 -DRETSIGTYPE=void -DHAVE_DECL_SYS_SIGLIST=1
-DHAVE_POSIX_SIGNALS=1 -DRETSIGTYPE_IS_VOID=1 -DHAVE_GETRUSAGE=1
-DHAVE_TIMES=1 -DYYTEXT_POINTER=1 -DGNUPLOT_BINARY="gnuplot"
User-preferences (please do not edit this section):
--------------------------------------------------
EDITOR = /bin/nano
EXEC_PATH =
/usr/libexec/octave/3.0.3/site/exec/i686-pc-linux-gnu:/usr/libexec/octave/api-v32/site/exec/i686-pc-linux-gnu:/usr/libexec/octave/site/exec/i686-pc-linux-gnu:/usr/libexec/octave/3.0.3/exec/i686-pc-linux-gnu:/usr/bin:/usr/bin:/usr/local/bin:/usr/bin:/bin:/opt/bin:/usr/i686-pc-linux-gnu/gcc-bin/4.1.2:/opt/blackdown-jdk-1.4.2.03/bin:/opt/blackdown-jdk-1.4.2.03/jre/bin:/usr/qt/3/bin:/usr/games/bin
IMAGE_PATH = .:/usr/share/octave/3.0.3/imagelib
PAGER = /usr/bin/less
PS1 = \s:\#>
PS2 = >
PS4 = +
beep_on_error = 0
completion_append_char =
crash_dumps_octave_core = 1
echo_executing_commands = 0
fixed_point_format = 0
gnuplot_binary = gnuplot
gnuplot_command_end =
gnuplot_command_plot = pl
gnuplot_command_replot = rep
gnuplot_command_splot = sp
gnuplot_command_title = t
gnuplot_command_using = u
gnuplot_command_with = w
history_file = /home/lukasz/.octave_hist
history_size = 1024
ignore_function_time_stamp = none
info_file = /usr/share/info/octave.info
info_program = info
makeinfo_program = makeinfo
max_recursion_depth = 256
output_max_field_width = 5
output_precision = 5
page_output_immediately = 0
page_screen_output = 0
print_answer_id_name = 1
print_empty_dimensions = 1
save_precision = 16
saving_history = 1
sighup_dumps_octave_core = 1
sigterm_dumps_octave_core = 1
silent_functions = 0
split_long_rows = 1
string_fill_char =
struct_levels_to_print = 2
suppress_verbose_help_message = 0
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