Mailman 3 November 2007 - SciPy-User

Another memory quirk
by Anand Patil 03 Nov '07

03 Nov '07

Hi all, Not sure if this is related to my last post but the script below leaks memory like mad... PLEASE DON'T RUN IT, I don't want to be responsible for crashing your computer! Is there any safe way to store a ravelled view of an array in a subclass like this? I'm using the ravelled view inside a very tight loop & would rather not spend time calling ravel() if possible. Many thanks in advance, Anand from numpy import * from PyMC import * class MyArray(ndarray): pass for i in xrange(1000): A=zeros((1000,1000),dtype=float) A = A.view(MyArray) # If I uncomment this and run it, a huge memory leak ensues. # A._ravelled = A.ravel()

2 1

[Fwd: Re: Memory quirk]
by Travis E. Oliphant 03 Nov '07

03 Nov '07

1 0

Bug in scipy.sparse
by Olivier Verdier 02 Nov '07

02 Nov '07

The first thing I'm surprised about with scipy.sparse is that it uses the matrix type instead of the array type. This is very unfortunate, in my opinion. The bug is that a sparse matrix won't work correctly with `dot` and `array`: spmat = speye(3,3) vec = array([1,0,0]) dot(spmat, vec) returns: array([ (0, 0) 1.0 (1, 1) 1.0 (2, 2) 1.0, (0, 0) 0.0 (1, 1) 0.0 (2, 2) 0.0, (0, 0) 0.0 (1, 1) 0.0 (2, 2) 0.0], dtype=object) Ouch!! The right result may however be obtained with spmat * vec. This is a pity because any code that works with arrays or matrices in general and uses `dot` to do the matrix vector multiplication will be *broken* with sparse matrices. How reliable is scipy.sparse? Is there any plan to make it more compatible with the array type? Behave like the array type? How can I help? == Olivier

4 3

Installing TimeSeries
by Bradford Cross 01 Nov '07

01 Nov '07

Install works OK for MAskedArray but fails for TimeSeries with following output: bcross@ubuntu:~/maskedarray$ sudo python setup.py install Password: running install running build running config_fc running build_py running install_lib running install_data running install_egg_info Removing /usr/lib/python2.5/site-packages/maskedarray-0.0.0.egg-info Writing /usr/lib/python2.5/site-packages/maskedarray-0.0.0.egg-info bcross@ubuntu:~/maskedarray$ cd bcross@ubuntu:~$ cd timeseries/ bcross@ubuntu:~/timeseries$ sudo python setup.py install Warning: Assuming default configuration (./lib/{setup_lib,setup}.py was not found) Appending timeseries.lib configuration to timeseries Ignoring attempt to set 'name' (from 'timeseries' to 'timeseries.lib') Warning: Assuming default configuration (./tests/{setup_tests,setup}.py was not found) Appending timeseries.tests configuration to timeseries Ignoring attempt to set 'name' (from 'timeseries' to 'timeseries.tests') running install running build running config_fc running build_src building extension "timeseries.cseries" sources running build_py running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'timeseries.cseries' extension compiling C sources C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall -Wstrict-prototypes -fPIC compile options: '-I/usr/lib/python2.5/site-packages/numpy/core/include/numpy -I./include -I/usr/lib/python2.5/site-packages/numpy/core/include -I/usr/include/python2.5 -c' gcc: ./src/cseries.c In file included from ./src/cseries.c:1: ./include/c_lib.h:4:20: error: Python.h: No such file or directory ./include/c_lib.h:5:26: error: structmember.h: No such file or directory In file included from /usr/lib/python2.5/site-packages/numpy/core/include/numpy/arrayobject.h:14, from ./include/c_lib.h:6, from ./src/cseries.c:1: /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:91:2: error: #error Must use Python with unicode enabled. In file included from /usr/lib/python2.5/site-packages/numpy/core/include/numpy/arrayobject.h:14, from ./include/c_lib.h:6, from ./src/cseries.c:1: /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:918: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:919: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'npy_uintp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1009: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1010: error: expected ')' before '*' token /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1012: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1012: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1013: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1023: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1023: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1025: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1025: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1026: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1028: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1031: error: expected ')' before '*' token /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1034: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1036: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1037: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1037: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1039: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1044: error: expected specifier-qualifier-list before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1057: error: expected specifier-qualifier-list before 'PyArray_GetItemFunc' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1159: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1191: error: expected specifier-qualifier-list before 'PyObject' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1201: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1227: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1234: error: expected declaration specifiers or '...' before 'PyObject' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1367: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1505: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1562: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1762: error: expected specifier-qualifier-list before 'npy_intp' In file included from /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1777, from /usr/lib/python2.5/site-packages/numpy/core/include/numpy/arrayobject.h:14, from ./include/c_lib.h:6, from ./src/cseries.c:1: /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:397: error: 'NULL' undeclared here (not in a function) /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h: In function '_import_array': /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:945: error: 'PyObject' undeclared (first use in this function) /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:945: error: (Each undeclared identifier is reported only once /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:945: error: for each function it appears in.) /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:945: error: 'numpy' undeclared (first use in this function) /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:945: warning: implicit declaration of function 'PyImport_ImportModule' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:946: error: 'c_api' undeclared (first use in this function) /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:948: warning: implicit declaration of function 'PyObject_GetAttrString' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:949: warning: implicit declaration of function 'Py_DECREF' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:950: warning: implicit declaration of function 'PyCObject_Check' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:951: warning: implicit declaration of function 'PyCObject_AsVoidPtr' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:958: warning: implicit declaration of function 'PyErr_Format' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:958: error: 'PyExc_RuntimeError' undeclared (first use in this function) In file included from ./src/cseries.c:1: ./include/c_lib.h: At top level: ./include/c_lib.h:19: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_lib.h:20: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_lib.h:21: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_lib.h:22: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_lib.h:23: error: expected ')' before '*' token ./include/c_lib.h:24: error: expected ')' before '*' token ./include/c_lib.h:26: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_lib.h:28: error: expected ')' before '*' token In file included from ./src/cseries.c:2: ./include/c_dates.h:103: error: expected ')' before '*' token ./include/c_dates.h:109: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:110: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:113: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:114: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:115: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:116: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:118: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:119: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:121: error: expected ')' before '*' token In file included from ./src/cseries.c:3: ./include/c_tseries.h:6: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_tseries.h:8: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_tseries.h:9: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_tseries.h:10: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_tseries.h:11: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_tseries.h:13: error: expected ')' before '*' token ./src/cseries.c:5: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'cseries_methods' ./src/cseries.c:55: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'initcseries' In file included from ./src/cseries.c:1: ./include/c_lib.h:4:20: error: Python.h: No such file or directory ./include/c_lib.h:5:26: error: structmember.h: No such file or directory In file included from /usr/lib/python2.5/site-packages/numpy/core/include/numpy/arrayobject.h:14, from ./include/c_lib.h:6, from ./src/cseries.c:1: /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:91:2: error: #error Must use Python with unicode enabled. In file included from /usr/lib/python2.5/site-packages/numpy/core/include/numpy/arrayobject.h:14, from ./include/c_lib.h:6, from ./src/cseries.c:1: /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:918: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:919: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'npy_uintp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1009: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1010: error: expected ')' before '*' token /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1012: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1012: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1013: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1023: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1023: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1025: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1025: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1026: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1028: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1031: error: expected ')' before '*' token /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1034: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1036: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1037: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1037: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1039: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1044: error: expected specifier-qualifier-list before 'npy_intp' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1057: error: expected specifier-qualifier-list before 'PyArray_GetItemFunc' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1159: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1191: error: expected specifier-qualifier-list before 'PyObject' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1201: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1227: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1234: error: expected declaration specifiers or '...' before 'PyObject' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1367: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1505: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1562: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1762: error: expected specifier-qualifier-list before 'npy_intp' In file included from /usr/lib/python2.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:1777, from /usr/lib/python2.5/site-packages/numpy/core/include/numpy/arrayobject.h:14, from ./include/c_lib.h:6, from ./src/cseries.c:1: /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:397: error: 'NULL' undeclared here (not in a function) /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h: In function '_import_array': /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:945: error: 'PyObject' undeclared (first use in this function) /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:945: error: (Each undeclared identifier is reported only once /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:945: error: for each function it appears in.) /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:945: error: 'numpy' undeclared (first use in this function) /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:945: warning: implicit declaration of function 'PyImport_ImportModule' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:946: error: 'c_api' undeclared (first use in this function) /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:948: warning: implicit declaration of function 'PyObject_GetAttrString' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:949: warning: implicit declaration of function 'Py_DECREF' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:950: warning: implicit declaration of function 'PyCObject_Check' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:951: warning: implicit declaration of function 'PyCObject_AsVoidPtr' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:958: warning: implicit declaration of function 'PyErr_Format' /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:958: error: 'PyExc_RuntimeError' undeclared (first use in this function) In file included from ./src/cseries.c:1: ./include/c_lib.h: At top level: ./include/c_lib.h:19: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_lib.h:20: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_lib.h:21: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_lib.h:22: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_lib.h:23: error: expected ')' before '*' token ./include/c_lib.h:24: error: expected ')' before '*' token ./include/c_lib.h:26: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_lib.h:28: error: expected ')' before '*' token In file included from ./src/cseries.c:2: ./include/c_dates.h:103: error: expected ')' before '*' token ./include/c_dates.h:109: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:110: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:113: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:114: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:115: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:116: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:118: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:119: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_dates.h:121: error: expected ')' before '*' token In file included from ./src/cseries.c:3: ./include/c_tseries.h:6: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_tseries.h:8: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_tseries.h:9: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_tseries.h:10: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_tseries.h:11: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token ./include/c_tseries.h:13: error: expected ')' before '*' token ./src/cseries.c:5: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'cseries_methods' ./src/cseries.c:55: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'initcseries' error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.5/site-packages/numpy/core/include/numpy -I./include -I/usr/lib/python2.5/site-packages/numpy/core/include -I/usr/include/python2.5 -c ./src/cseries.c -o build/temp.linux-i686-2.5/src/cseries.o" failed with exit status 1

2 1

Bug in scipy.integrate.odeint ?
by LB 01 Nov '07

01 Nov '07

Hi, I find the behaviour of scipy.integrate.odeint very strange : >>> from numpy import * >>> from scipy import integrate >>> >>> def f(x, t): ... return cos(x) ... >>> >>> X0 = array([0.0]) >>> X0_ini = X0.copy() >>> t = linspace(0, 20., 200) >>> X = integrate.odeint(f, X0, t) >>> X0 == X0_ini array([False], dtype=bool) >>> X0 == X[-1] array([True], dtype=bool) Why do odeint modify X0 ? Is there any reason for this ? For me, it seems really like a bug and could easily lead to bugs if there's no mention of this in the doc string. -- LB

2 1

SciPY/NumPY - rhel4 installation issues....
by bruce 01 Nov '07

01 Nov '07

Hi. I'm trying to install numpy/scipy on a rhel system with python v2.4.3 I'm following the information from various sites. My goal is to be able to successfully get numpy/scipy up/running, with a few basic tests. I'm using the tar files for: drwxr-xr-x 6 root root 4096 Oct 31 19:30 . drwxr-xr-x 32 root root 4096 Oct 31 12:26 .. drwxr-xr-x 12 root root 4096 Oct 31 18:29 ATLAS -rw-r--r-- 1 root root 3192987 Oct 31 12:35 atlas3.8.0.tar.gz drwxr-x--- 8 13686 731 4096 Oct 31 18:11 lapack-3.1.1 -rw-r--r-- 1 root root 10407595 Feb 26 2007 lapack-3.1.1.tgz drwxrwxr-x 4 test test 4096 Oct 31 19:43 numpy-1.0.3.1 -rw-r--r-- 1 root root 1500255 Oct 31 12:49 numpy-1.0.3.1.tar.gz -rw-r--r-- 1 root root 54 Oct 31 12:27 readme.txt drwxrwxr-x 3 test test 4096 Sep 22 01:14 scipy-0.6.0 -rw-r--r-- 1 root root 6572954 Oct 31 12:52 scipy-0.6.0.tar.gz I believe I've successfully downloaded/built/installed the atlas/lapack apps. I'm using a RHEL4 system with a single 1.8GHz. processor. I did a: "python setup.py install" for numpy, and it appeared to finish. I then did a: "python setup.py install" for scipy, and got the following err: [root@mfgtest3 <Branch GodzillaTest1.1.2> scipy-0.6.0]# python setup.py install Traceback (most recent call last): File "setup.py", line 53, in ? setup_package() File "setup.py", line 28, in setup_package from numpy.distutils.core import setup File "/usr/lib/python2.4/site-packages/numpy/__init__.py", line 39, in ? import core File "/usr/lib/python2.4/site-packages/numpy/core/__init__.py", line 5, in ? import multiarray ImportError: /usr/lib/python2.4/site-packages/numpy/core/multiarray.so: undefined symbol: PyUnicodeUCS2_FromUnicode I can't find anything via google to indicate what's the cause... Any thoughts/comments would be seriously helpful!! Could this be an issue of incompatible versions between numpy/scipy?? thanks -sam

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Generating random variables in a joint normal distribution?
by Parvel Gu 01 Nov '07

01 Nov '07

Hi all, Since I am fresh to use SciPy for simulation, I am not sure about how to get a sequence of pairs of random variables in a joint normal distribution. I have read the info docs in the module scipy.stats. It seems that only the normal distribution rvs for single variable is provided. Thus one sequence of random variables could be get by calling stats.norm.rvs() for times (right?). But if I want pairs of random variables, for example, (p, s), which are expected to be in the joint normal distribution of some given coefficient ro, would there be any routine provided to do this just like stats.norm.rvs? If currently there is no such routine, would there be some workaround to achieve this by combining the existing routines? I am not very good at numerical probabilities... Any suggestions would be much appreciated:) Regards, Parvel

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