Follow-up Comment #56, task #7807 (project relax):
A 10x speed up on clustered analysis.
Checked on:
Hardware information:
Machine: x86_64
Processor: x86_64
Processor name: Intel(R) Core(TM) i5-3470 CPU @ 3.20GHz
Endianness: little
Total RAM size: 3705 Mb
Total swap size: 3839 Mb
Operating system information:
System: Linux
Release: 2.6.32-431.17.1.el6.x86_64
Version: #1 SMP Fri Apr 11 17:27:00 EDT 2014
GNU/Linux version: Red Hat Enterprise Linux Client 6.5 Santiago
Distribution: redhat 6.5 Santiago
Full platform string:
Linux-2.6.32-431.17.1.el6.x86_64-x86_64-with-redhat-6.5-Santiago
Timing for:
3 fields
('sfrq: ', 600000000.0, 'number of cpmg frq', 15, array([ 2., 6., 10., 14.,
18., 22., 26., 30., 34., 38., 42., 46., 50., 54., 58.]))
('sfrq: ', 800000000.0, 'number of cpmg frq', 20, array([ 2., 6., 10., 14.,
18., 22., 26., 30., 34., 38., 42., 46., 50., 54., 58., 62., 66., 70., 74.,
78.]))
('sfrq: ', 900000000.0, 'number of cpmg frq', 22, array([ 2., 6., 10., 14.,
18., 22., 26., 30., 34., 38., 42., 46., 50., 54., 58., 62., 66., 70., 74.,
78., 82., 86.]))
iterations of function call: 1000
Timed for simulating 1 or 100 clustered spins.
##############################################################################################
ncalls tottime percall cumtime percall filename:lineno(function)
############################
For disp_spin_speed r23759 #
############################
1 spin:
1 0.000 0.000 0.496 0.496 <string>:1(<module>)
1 0.001 0.001 0.496 0.496 profiling_cr72.py:419(single)
1000 0.001 0.000 0.486 0.000 profiling_cr72.py:405(calc)
1000 0.009 0.000 0.485 0.000
relax_disp.py:995(func_CR72_full)
1000 0.038 0.000 0.472 0.000
relax_disp.py:524(calc_CR72_chi2)
1003 0.097 0.000 0.374 0.000 cr72.py:101(r2eff_CR72)
4003 0.071 0.000 0.242 0.000 numeric.py:2056(allclose)
16046 0.081 0.000 0.081 0.000 {method 'reduce' of
'numpy.ufunc' objects}
8015 0.009 0.000 0.070 0.000 fromnumeric.py:1762(any)
100 spins:
1 0.000 0.000 2.084 2.084 <string>:1(<module>)
1 0.002 0.002 2.084 2.084 profiling_cr72.py:441(cluster)
1000 0.002 0.000 2.005 0.002 profiling_cr72.py:405(calc)
1000 0.034 0.000 2.003 0.002
relax_disp.py:995(func_CR72_full)
1000 0.141 0.000 1.960 0.002
relax_disp.py:524(calc_CR72_chi2)
1300 1.100 0.001 1.676 0.001 cr72.py:101(r2eff_CR72)
4300 0.245 0.000 0.507 0.000 numeric.py:2056(allclose)
3000 0.037 0.000 0.164 0.000 shape_base.py:761(tile)
17828 0.126 0.000 0.126 0.000 {method 'reduce' of
'numpy.ufunc' objects}
4000 0.110 0.000 0.110 0.000 {method 'repeat' of
'numpy.ndarray' objects}
8609 0.011 0.000 0.086 0.000 fromnumeric.py:1762(any)
############################
For trunk r23753 #
############################
1 spin:
1 0.000 0.000 0.347 0.347 <string>:1(<module>)
1 0.001 0.001 0.347 0.347 profiling_cr72.py:419(single)
1000 0.001 0.000 0.339 0.000 profiling_cr72.py:405(calc)
1000 0.008 0.000 0.338 0.000
relax_disp.py:908(func_CR72_full)
1000 0.032 0.000 0.326 0.000
relax_disp.py:456(calc_CR72_chi2)
3003 0.176 0.000 0.243 0.000 cr72.py:100(r2eff_CR72)
12036 0.060 0.000 0.060 0.000 {method 'reduce' of
'numpy.ufunc' objects}
3000 0.025 0.000 0.049 0.000 chi2.py:32(chi2)
6003 0.008 0.000 0.048 0.000 fromnumeric.py:1621(sum)
100 spins:
1 0.000 0.000 32.247 32.247 <string>:1(<module>)
1 0.002 0.002 32.247 32.247 profiling_cr72.py:441(cluster)
1000 0.002 0.000 32.196 0.032 profiling_cr72.py:405(calc)
1000 0.012 0.000 32.194 0.032
relax_disp.py:908(func_CR72_full)
1000 3.291 0.003 32.171 0.032
relax_disp.py:456(calc_CR72_chi2)
300300 17.361 0.000 23.819 0.000 cr72.py:100(r2eff_CR72)
1200927 5.767 0.000 5.767 0.000 {method 'reduce' of
'numpy.ufunc' objects}
300000 2.512 0.000 4.803 0.000 chi2.py:32(chi2)
600300 0.750 0.000 4.636 0.000 fromnumeric.py:1621(sum)
600300 0.590 0.000 3.410 0.000 _methods.py:23(_sum)
300300 0.290 0.000 2.174 0.000 fromnumeric.py:2048(amax)
300300 0.274 0.000 1.939 0.000 fromnumeric.py:2132(amin)
----------
Python information:
Architecture: 64bit ELF
Python version: 2.7.6
Python branch:
Python build: default, Apr 11 2014 13:46:04
Python compiler: GCC 4.1.2 20080704 (Red Hat 4.1.2-52)
Libc version: glibc 2.2.5
Python implementation: CPython
Python revision:
Python executable:
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/bin/python
Python flags: sys.flags(debug=0, py3k_warning=0,
division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0,
dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0,
tabcheck=0, verbose=0, unicode=0, bytes_warning=0, hash_randomization=0)
Python float info: sys.float_info(max=1.7976931348623157e+308,
max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16, radix=2,
rounds=1)
Python module path:
['/sbinlab2/tlinnet/software/NMR-relax/disp_spin_speed',
'/sbinlab2/software/CCP4-Linux_6.3.0/ccp4-6.3.0/share/python',
'/sbinlab2/tlinnet', '/sbinlab2/software/x64/haddock2.1',
'/sbinlab2/software/x64/lib64/python2.6/site-packages',
'/sbinlab2/software/x64/ccpnmr/ccpnmr2.3/python',
'/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python27.zip',
'/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7',
'/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/plat-linux2',
'/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/lib-tk',
'/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/lib-old',
'/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/lib-dynload',
'/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/lib/python2.7/site-packages',
'/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/lib/python2.7/site-packages/PIL',
'/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/site-packages']
Python packages and modules (most are optional):
Name Installed Version Path
minfx True 1.0.6
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/lib/python2.7/site-packages/minfx
bmrblib True 1.0.3
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/lib/python2.7/site-packages/bmrblib
numpy True 1.8.0
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/lib/python2.7/site-packages/numpy
scipy True 0.13.3
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/lib/python2.7/site-packages/scipy
wxPython True 2.8.10.1 (gtk2-unicode)
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/lib/python2.7/site-packages/wx
matplotlib True 1.3.1
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/lib/python2.7/site-packages/matplotlib
mpi4py True 1.2.2
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/lib/python2.7/site-packages/mpi4py
epydoc True 3.0.1
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/lib/python2.7/site-packages/epydoc
optparse True 1.5.3
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/optparse.pyc
readline True
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/lib/python2.7/site-packages/readline.pyc
profile True
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/profile.pyc
bz2 True
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/lib-dynload/bz2.so
gzip True
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/gzip.pyc
io True
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/io.pyc
xml True 0.8.4 (internal)
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/xml/__init__.pyc
xml.dom.minidom True
/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/xml/dom/minidom.pyc
relax information:
Version: repository checkout r23759
svn+ssh://svn.gna.org/svn/relax/branches/disp_spin_speed
Processor fabric: Uni-processor.
relax C modules:
Module Compiled File type
Path
target_functions.relax_fit True ELF 64-bit LSB shared object,
x86-64, version 1 (SYSV), dynamically linked, not stripped
/sbinlab2/tlinnet/software/NMR-relax/disp_spin_speed/target_functions/relax_fit.so
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[task #7807] Speed-up of dispersion models for Clustered analysis