Re: r7704 - /1.3/test_suite/system_tests/palmer.py -- October 15, 2008 - 03:46

Hi Ed,

This reminds me of a test I've done last year...

I tested the two compiled versions of ModelFree-4.20 (either compiled
with gcc or Portland) and got interesting results.

=============================================
Using the test given with ModelFree-4.20, here are some benchmarks :

compiler    1        2        3        4
========    =====    =====    =====    =====
gcc         21:11    17:45    15:36    15:40
Portland    11:27     9:00     7:45     7:50
=============================================

It seems that the Portland compiled version is ~ 2 x faster than the one
compiled with gcc, at least on the 4 x86 Gentoo Linux computers tested...

Should we print a line advising the users to use, if they can, the
fastest version (Portland compiled)..? Or maybe we could at least advise
the user to test both versions on their architecture...

Regards,


Séb  :)




edward@xxxxxxxxxxxxx wrote:
> Author: bugman
> Date: Wed Oct 15 00:43:39 2008
> New Revision: 7704
>
> URL: http://svn.gna.org/viewcvs/relax?rev=7704&view=rev
> Log:
> Modified the Modelfree4 system tests to work with the Portland C compiler 
> Linux version.
>
> The modelfree4 Linux binary compiled with Gnu gcc gives different results, 
> sometimes quite large, to
> the Linux binary compiled with the Portland C compiler.  The tests now 
> catch this.  There may be
> problems with the Mac OS X Modelfree4 binary still.
>
>
> Modified:
>     1.3/test_suite/system_tests/palmer.py
>
> Modified: 1.3/test_suite/system_tests/palmer.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/palmer.py?rev=7704&r1=7703&r2=7704&view=diff
> ==============================================================================
> --- 1.3/test_suite/system_tests/palmer.py (original)
> +++ 1.3/test_suite/system_tests/palmer.py Wed Oct 15 00:43:39 2008
> @@ -70,14 +70,126 @@
>          # Execute the script.
>          self.relax.interpreter.run(script_file=sys.path[-1] + 
> '/test_suite/system_tests/scripts/palmer.py')
>  
> +        # Determine if the Gnu gcc or Portland C compiler version is being 
> used.
> +        spin = return_spin(':0', pipe='m2')
> +        if spin.te == 1.951*1e-12:
> +            compiler = 'gcc'    # Gnu gcc modelfree4 version.
> +        else:
> +            compiler = 'pgf'    # Portland C compiler modelfree4 version.
> +
>          # Checks for model m1, m2, and m3 mfout file reading.
>          models = ['m1', 'm2', 'm3']
>          params = [['S2'], ['S2', 'te'], ['S2', 'Rex']]
>          spin_names = [':-2&:Gly', ':-1&:Gly', ':0&:Gly']
> -        s2 = [[0.869, 0.732, 0.802], [0.869, 0.730, 0.755], [0.715, 0.643, 
> 0.734]]
> -        te = [[None, None, None], [0.0, 1.951, 1319.171], [None, None, 
> None]]
> -        rex = [[None, None, None], [None, None, None], [4.308, 4.278, 
> 1.017]]
> +        if compiler == 'gcc':
> +            s2 = [[0.869, 0.732, 0.802], [0.869, 0.730, 0.755], [0.715, 
> 0.643, 0.734]]
> +            te = [[None, None, None], [0.0, 1.951, 1319.171], [None, None, 
> None]]    # Gnu gcc modelfree4 version.
> +            rex = [[None, None, None], [None, None, None], [4.308, 4.278, 
> 1.017]]
> +        else:
> +            s2 = [[0.869, 0.732, 0.802], [0.869, 0.730, 0.755], [0.715, 
> 0.643, 0.732]]
> +            te = [[None, None, None], [0.0, 1.952, 1319.172], [None, None, 
> None]]    # Portland C compiler modelfree4 version.
> +            rex = [[None, None, None], [None, None, None], [4.308, 4.278, 
> 1.050]]
>          chi2 = [[36.6223, 20.3954, 5.2766], [36.6223, 20.3299, 0.0], 
> [1.9763, 0.6307, 5.2766]]
> +        for model_index in xrange(3):
> +            print "Model " + `models[model_index]`
> +            for spin_index in xrange(3):
> +                print "Spin " + `spin_names[spin_index]`
> +
> +                # Get the spin.
> +                spin = return_spin(spin_names[spin_index], 
> pipe=models[model_index])
> +
> +                # Conversions.
> +                if te[model_index][spin_index]:
> +                    te[model_index][spin_index] = 
> te[model_index][spin_index] * 1e-12
> +                if rex[model_index][spin_index]:
> +                    rex[model_index][spin_index] = 
> rex[model_index][spin_index] / (2.0 * pi * spin.frq[0])**2
> +
> +                # Checks.
> +                self.assertEqual(spin.model, models[model_index])
> +                self.assertEqual(spin.params, params[model_index])
> +                self.assertEqual(spin.s2, s2[model_index][spin_index])
> +                self.assertEqual(spin.s2f, None)
> +                self.assertEqual(spin.s2s, None)
> +                if te[model_index][spin_index] == None:
> +                    self.assertEqual(spin.te, te[model_index][spin_index])
> +                else:
> +                    self.assertAlmostEqual(spin.te, 
> te[model_index][spin_index])
> +                self.assertEqual(spin.tf, None)
> +                self.assertEqual(spin.ts, None)
> +                self.assertEqual(spin.rex, rex[model_index][spin_index])
> +                self.assertEqual(spin.chi2, chi2[model_index][spin_index])
> +
> +        # Checks for the final mfout file reading.
> +        models = ['m3', 'm3', 'm2']
> +        params = [['S2', 'Rex'], ['S2', 'Rex'], ['S2', 'te']]
> +        s2 = [0.844, 0.760, 0.592]
> +        te = [None, None, 1809.287]
> +        rex = [0.0, 0.394, None]
> +        chi2 = [1.7964, 0.7391, 0.0000]
> +        for spin_index in xrange(3):
> +            # Get the spin.
> +            spin = return_spin(spin_names[spin_index], pipe='aic')
> +
> +            # Conversions.
> +            if te[spin_index]:
> +                te[spin_index] = te[spin_index] * 1e-12
> +            if rex[spin_index]:
> +                rex[spin_index] = rex[spin_index] / (2.0 * pi * 
> spin.frq[0])**2
> +
> +            # Checks.
> +            self.assertEqual(spin.model, models[spin_index])
> +            self.assertEqual(spin.params, params[spin_index])
> +            self.assertEqual(spin.s2, s2[spin_index])
> +            self.assertEqual(spin.s2f, None)
> +            self.assertEqual(spin.s2s, None)
> +            self.assertEqual(spin.te, te[spin_index])
> +            self.assertEqual(spin.tf, None)
> +            self.assertEqual(spin.ts, None)
> +            self.assertEqual(spin.rex, rex[spin_index])
> +            self.assertEqual(spin.chi2, chi2[spin_index])
> +
> +        # Final global values.
> +        final_pipe = pipes.get_pipe('aic')
> +        self.assertEqual(final_pipe.chi2, 2.5355)
> +        self.assertEqual(final_pipe.diff_tensor.tm, 12.050)
> +
> +
> +    def test_palmer_omp(self):
> +        """Test a complete model-free analysis using 'Modelfree4' with the 
> OMP relaxation data, a PDB file, and a spheroid tensor."""
> +
> +        # Test for the presence of the Modelfree4 binary (skip the test if 
> not present).
> +        try:
> +            test_binary('modelfree4')
> +        except:
> +            return
> +
> +        # Execute the script.
> +        self.relax.interpreter.run(script_file=sys.path[-1] + 
> '/test_suite/system_tests/scripts/palmer_omp.py')
> +
> +        # Catch a the old, buggy modelfree4 versions and complain loudly!
> +        spin = return_spin(':9', pipe='m2')
> +        if spin.s2 == 0.855:
> +            raise RelaxError, "You are using an old, buggy Modelfree4 
> version!  You must upgrade to version 4.20 or later."
> +
> +        # Determine if the Gnu gcc or Portland C compiler version is being 
> used.
> +        if spin.te == 20.043*1e-12:
> +            compiler = 'gcc'    # Gnu gcc modelfree4 version.
> +        else:
> +            compiler = 'pgf'    # Portland C compiler modelfree4 version.
> +
> +        # Model m1, m2, and m3 mfout file data.
> +        models = ['m1', 'm2', 'm3']
> +        params = [['S2'], ['S2', 'te'], ['S2', 'Rex']]
> +        spin_names = [':9', ':10', ':11']
> +        s2 = [[0.822, 0.799, 0.823], [0.788, 0.777, 0.812], [0.822, 0.799, 
> 0.823]]
> +        if compiler == 'gcc':
> +            te = [[None, None, None], [61.506, 36.084, 20.043], [None, 
> None, None]]
> +        else:
> +            te = [[None, None, None], [61.506, 36.087, 20.039], [None, 
> None, None]]
> +        rex = [[None, None, None], [None, None, None], [0.0, 0.0, 0.0]]
> +        chi2 = [[143.6773, 105.1767, 61.6684], [40.9055, 57.1562, 
> 48.4927], [143.6773, 105.1767, 61.6684]]
> +
> +        # Checks for model m1, m2, and m3 mfout file reading.
>          for model_index in xrange(3):
>              print "Model " + `models[model_index]`
>              for spin_index in xrange(3):
> @@ -104,13 +216,19 @@
>                  self.assertEqual(spin.rex, rex[model_index][spin_index])
>                  self.assertEqual(spin.chi2, chi2[model_index][spin_index])
>  
> +        # Final mfout file data.
> +        models = ['m2', 'm2', 'm2']
> +        params = [['S2', 'te'], ['S2', 'te'], ['S2', 'te']]
> +        if compiler == 'gcc':
> +            s2 = [0.782, 0.760, 0.785]
> +            te = [60.009, 29.134, 12.590]
> +            chi2 = [24.0495, 8.1168, 0.5332]
> +        else:
> +            s2 = [0.755, 0.761, 0.787]
> +            te = [52.197, 29.361, 12.677]
> +            chi2 = [7.254, 8.0437, 0.5327]
> +
>          # Checks for the final mfout file reading.
> -        models = ['m3', 'm3', 'm2']
> -        params = [['S2', 'Rex'], ['S2', 'Rex'], ['S2', 'te']]
> -        s2 = [0.844, 0.760, 0.592]
> -        te = [None, None, 1809.287]
> -        rex = [0.0, 0.394, None]
> -        chi2 = [1.7964, 0.7391, 0.0000]
>          for spin_index in xrange(3):
>              # Get the spin.
>              spin = return_spin(spin_names[spin_index], pipe='aic')
> @@ -118,8 +236,6 @@
>              # Conversions.
>              if te[spin_index]:
>                  te[spin_index] = te[spin_index] * 1e-12
> -            if rex[spin_index]:
> -                rex[spin_index] = rex[spin_index] / (2.0 * pi * 
> spin.frq[0])**2
>  
>              # Checks.
>              self.assertEqual(spin.model, models[spin_index])
> @@ -127,90 +243,7 @@
>              self.assertEqual(spin.s2, s2[spin_index])
>              self.assertEqual(spin.s2f, None)
>              self.assertEqual(spin.s2s, None)
> -            self.assertEqual(spin.te, te[spin_index])
> -            self.assertEqual(spin.tf, None)
> -            self.assertEqual(spin.ts, None)
> -            self.assertEqual(spin.rex, rex[spin_index])
> -            self.assertEqual(spin.chi2, chi2[spin_index])
> -
> -        # Final global values.
> -        final_pipe = pipes.get_pipe('aic')
> -        self.assertEqual(final_pipe.chi2, 2.5355)
> -        self.assertEqual(final_pipe.diff_tensor.tm, 12.050)
> -
> -
> -    def test_palmer_omp(self):
> -        """Test a complete model-free analysis using 'Modelfree4' with the 
> OMP relaxation data, a PDB file, and a spheroid tensor."""
> -
> -        # Test for the presence of the Modelfree4 binary (skip the test if 
> not present).
> -        try:
> -            test_binary('modelfree4')
> -        except:
> -            return
> -
> -        # Execute the script.
> -        self.relax.interpreter.run(script_file=sys.path[-1] + 
> '/test_suite/system_tests/scripts/palmer_omp.py')
> -
> -        # Catch a the old, buggy modelfree4 versions and complain loudly!
> -        spin = return_spin(':9', pipe='m2')
> -        if spin.s2 == 0.855:
> -            raise RelaxError, "You are using an old, buggy Modelfree4 
> version!  You must upgrade to version 4.20 or later."
> -
> -        # Checks for model m1, m2, and m3 mfout file reading.
> -        models = ['m1', 'm2', 'm3']
> -        params = [['S2'], ['S2', 'te'], ['S2', 'Rex']]
> -        spin_names = [':9', ':10', ':11']
> -        s2 = [[0.822, 0.799, 0.823], [0.788, 0.777, 0.812], [0.822, 0.799, 
> 0.823]]
> -        te = [[None, None, None], [61.506, 36.084, 20.043], [None, None, 
> None]]
> -        rex = [[None, None, None], [None, None, None], [0.0, 0.0, 0.0]]
> -        chi2 = [[143.6773, 105.1767, 61.6684], [40.9055, 57.1562, 
> 48.4927], [143.6773, 105.1767, 61.6684]]
> -        for model_index in xrange(3):
> -            print "Model " + `models[model_index]`
> -            for spin_index in xrange(3):
> -                print "Spin " + `spin_names[spin_index]`
> -
> -                # Get the spin.
> -                spin = return_spin(spin_names[spin_index], 
> pipe=models[model_index])
> -
> -                # Conversions.
> -                if te[model_index][spin_index]:
> -                    te[model_index][spin_index] = 
> te[model_index][spin_index] * 1e-12
> -                if rex[model_index][spin_index]:
> -                    rex[model_index][spin_index] = 
> rex[model_index][spin_index] / (2.0 * pi * spin.frq[0])**2
> -
> -                # Checks.
> -                self.assertEqual(spin.model, models[model_index])
> -                self.assertEqual(spin.params, params[model_index])
> -                self.assertEqual(spin.s2, s2[model_index][spin_index])
> -                self.assertEqual(spin.s2f, None)
> -                self.assertEqual(spin.s2s, None)
> -                self.assertEqual(spin.te, te[model_index][spin_index])
> -                self.assertEqual(spin.tf, None)
> -                self.assertEqual(spin.ts, None)
> -                self.assertEqual(spin.rex, rex[model_index][spin_index])
> -                self.assertEqual(spin.chi2, chi2[model_index][spin_index])
> -
> -        # Checks for the final mfout file reading.
> -        models = ['m2', 'm2', 'm2']
> -        params = [['S2', 'te'], ['S2', 'te'], ['S2', 'te']]
> -        s2 = [0.782, 0.760, 0.785]
> -        te = [60.009, 29.134, 12.590]
> -        chi2 = [24.0495, 8.1168, 0.5332]
> -        for spin_index in xrange(3):
> -            # Get the spin.
> -            spin = return_spin(spin_names[spin_index], pipe='aic')
> -
> -            # Conversions.
> -            if te[spin_index]:
> -                te[spin_index] = te[spin_index] * 1e-12
> -
> -            # Checks.
> -            self.assertEqual(spin.model, models[spin_index])
> -            self.assertEqual(spin.params, params[spin_index])
> -            self.assertEqual(spin.s2, s2[spin_index])
> -            self.assertEqual(spin.s2f, None)
> -            self.assertEqual(spin.s2s, None)
> -            self.assertEqual(spin.te, te[spin_index])
> +            self.assertAlmostEqual(spin.te, te[spin_index])
>              self.assertEqual(spin.tf, None)
>              self.assertEqual(spin.ts, None)
>              self.assertEqual(spin.rex, None)
> @@ -218,8 +251,15 @@
>  
>          # Final global values.
>          final_pipe = pipes.get_pipe('aic')
> -        self.assertEqual(final_pipe.chi2, 32.6995)
> -        self.assertEqual(final_pipe.diff_tensor.tm, 8.964)
> -        self.assertEqual(final_pipe.diff_tensor.Dratio, 1.324)
> -        self.assertEqual(final_pipe.diff_tensor.theta, (-52.070 / 360.0) * 
> 2.0 * pi + pi)
> -        self.assertEqual(final_pipe.diff_tensor.phi, (2.377 / 360.0) * 2.0 
> * pi)
> +        if compiler == 'gcc':
> +            self.assertEqual(final_pipe.chi2, 32.6995)
> +            self.assertEqual(final_pipe.diff_tensor.tm, 8.964)
> +            self.assertEqual(final_pipe.diff_tensor.Dratio, 1.324)
> +            self.assertEqual(final_pipe.diff_tensor.theta, (-52.070 / 
> 360.0) * 2.0 * pi + pi)
> +            self.assertEqual(final_pipe.diff_tensor.phi, (2.377 / 360.0) * 
> 2.0 * pi)
> +        else:
> +            self.assertEqual(final_pipe.chi2, 15.8304)
> +            self.assertEqual(final_pipe.diff_tensor.tm, 8.443)
> +            self.assertEqual(final_pipe.diff_tensor.Dratio, 1.053)
> +            self.assertEqual(final_pipe.diff_tensor.theta, (68.864 / 
> 360.0) * 2.0 * pi)
> +            self.assertEqual(final_pipe.diff_tensor.phi, (73.913 / 360.0) 
> * 2.0 * pi)
>
>
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