Re: Too long computational time
Hi Olena, Welcome to the relax mailing lists! The list you have posted to is that for relax software development, but you are probably after the list for relax users. Would you be able to create a new message to the relax-users mailing list instead (https://mail.gna.org/listinfo/relax-users/), copying and pasting the original text? The relax users mailing list has many more subscribers and I think a few signed up to the list have virtual machine experiences that would help you. It is also a better place to discuss using relax as there are currently around 80 NMR spectroscopists signed up who may be able to answer some of your questions. Cheers, Edward On 21 July 2014 10:58, Olena olena.dobrovol...@unibo.it wrote: Hello, I am a new user of Relax. I started the calculation of Relax on June 12 on the virtual machine Ubuntu installed on Windows. The Relax control window does not report any Errors or Warnings, and the last output folder 'Prolate' with the 6th round is dated by July 3. It has been more than a month of the calculation already, while in the manual it says no more than two weeks. I typed 'top i' in the Terminal, and the program is still running. Can anyone help? I do not see it producing more output since July 3. Would appreciate any advice. Olena ___ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel ___ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
Re: r24623 - /branches/disp_spin_speed/lib/dispersion/lm63.py
Hi Troels! It looks like you're back :) I hope you had a great holiday! Just so you know, it'll be my turn in a week and a half. Did you see my message at http://article.gmane.org/gmane.science.nmr.relax.devel/6491 ? I think that if we include both sets of changes, it would really increase the impact of the release. It would be a good reason to have your super fast code together with an increase the minor version number. For the change here, I have one suggestion. You need to know about the trick of using a \ character at the end of the line. In Python, this actually means that the line continues despite the newline character. To avoid this in such equations, I always add a space after the \ so that the end of the line is \ . Without this, the equation will be distorted in the API documentation (http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63-module.html), with the next R2eff line being joined to the end of this one. Cheers, Edward On 22 July 2014 16:51, tlin...@nmr-relax.com wrote: Author: tlinnet Date: Tue Jul 22 16:51:33 2014 New Revision: 24623 URL: http://svn.gna.org/viewcvs/relax?rev=24623view=rev Log: Code validation of lib/dispersion/lm63.py. Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis. Modified: branches/disp_spin_speed/lib/dispersion/lm63.py Modified: branches/disp_spin_speed/lib/dispersion/lm63.py URL: http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/lm63.py?rev=24623r1=24622r2=24623view=diff == --- branches/disp_spin_speed/lib/dispersion/lm63.py (original) +++ branches/disp_spin_speed/lib/dispersion/lm63.py Tue Jul 22 16:51:33 2014 @@ -43,7 +43,7 @@ The equation used is:: - phi_ex / 4 * nu_cpmg / kex \ \ + phi_ex / 4 * nu_cpmg / kex \ \ R2eff = R20 + -- * | 1 - --- * tanh | --- | | , kex \ kex \ 4 * nu_cpmg / / @@ -67,6 +67,7 @@ # Python module imports. from numpy import isfinite, min, sum, tanh from numpy.ma import fix_invalid, masked_where + def r2eff_LM63(r20=None, phi_ex=None, kex=None, cpmg_frqs=None, back_calc=None): Calculate the R2eff values for the LM63 model. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-comm...@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits ___ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
Re: r24622 - /branches/disp_spin_speed/lib/dispersion/lm63_3site.py
Hi Troels, For this change, the spacing in i = 2 is not necessary in the equation and it makes it wider than the sum symbol which should not be the case. In such docstring equations, the code validation script gives lots of false positives that you can ignore. Cheers, Edward On 22 July 2014 16:51, tlin...@nmr-relax.com wrote: Author: tlinnet Date: Tue Jul 22 16:51:32 2014 New Revision: 24622 URL: http://svn.gna.org/viewcvs/relax?rev=24622view=rev Log: Code validation of lib/dispersion/lm63_3site.py. Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis. Modified: branches/disp_spin_speed/lib/dispersion/lm63_3site.py Modified: branches/disp_spin_speed/lib/dispersion/lm63_3site.py URL: http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/lm63_3site.py?rev=24622r1=24621r2=24622view=diff == --- branches/disp_spin_speed/lib/dispersion/lm63_3site.py (original) +++ branches/disp_spin_speed/lib/dispersion/lm63_3site.py Tue Jul 22 16:51:32 2014 @@ -44,10 +44,10 @@ The equation used is:: _3_ - \phi_ex_i / 4 * nu_cpmg / ki \ \ + \phi_ex_i / 4 * nu_cpmg / ki \ \ R2eff = R20 + * | 1 - --- * tanh | --- | | . /__ ki \ ki \ 4 * nu_cpmg / / - i=2 + i = 2 For deconvoluting the parameters, see the relax user manual or the reference: @@ -94,10 +94,13 @@ # Once off parameter conversions. # The phi_ex_B / kB parameter value. rex_B = phi_ex_B / kB + # The phi_ex_C / kC parameter value. rex_C = phi_ex_C / kC + # Approximate chemical exchange rate constant between sites A and B (the exchange rate in rad/s) divided by 4. quart_kB = kB / 4.0 + # Approximate chemical exchange rate constant between sites A and C (the exchange rate in rad/s) divided by 4. quart_kC = kC / 4.0 ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-comm...@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits ___ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
Re: r24628 - /branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py
Hi Troels, For this change, it might be better to revert it. This changes the original Maple script from Nikolai Skrynnikov which I simply copied and pasted unmodified. It's not very important, but it might be useful to preserve the original form. Cheers, Edward On 22 July 2014 16:51, tlin...@nmr-relax.com wrote: Author: tlinnet Date: Tue Jul 22 16:51:42 2014 New Revision: 24628 URL: http://svn.gna.org/viewcvs/relax?rev=24628view=rev Log: Code validation of lib/dispersion/ns_cpmg_2site_expanded.py. Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis. Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py URL: http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py?rev=24628r1=24627r2=24628view=diff == --- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py (original) +++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py Tue Jul 22 16:51:42 2014 @@ -74,9 +74,9 @@ #tcp:=0.040/N; Ksym:=sqrt(Ka*Kb); -#dX:=(Ka-Kb+I*dw)/2; # Ra=Rb +#dX:=(Ka-Kb+I*dw)/2;# Ra=Rb dX:=((Ra-Rb)+(Ka-Kb)+I*dw)/2; - + L:=([[-dX, Ksym], [Ksym, dX]]); # in the end everything is multiplied by exp(-0.5*(Ra+Rb+Ka+Kb)*(Tc+2*tpalmer)) @@ -117,7 +117,7 @@ cGG:=evalm(GG2*Pspalmer*GG1); #s0:=array([Kb, Ka]); -s0:=array([sqrt(Kb),sqrt(Ka)]);# accounts for exchange symmetrization +s0:=array([sqrt(Kb),sqrt(Ka)]); # accounts for exchange symmetrization st:=evalm(cGG*s0); #obs:=(1/(Ka+Kb))*st[1]; obs:=(sqrt(Kb)/(Ka+Kb))*st[1]; # accounts for exchange symmetrization ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-comm...@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits ___ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
Re: r24636 - /branches/disp_spin_speed/lib/dispersion/two_point.py
This change will also be problematic having \ at the end of the line. Regards, Edward On 22 July 2014 16:51, tlin...@nmr-relax.com wrote: Author: tlinnet Date: Tue Jul 22 16:51:57 2014 New Revision: 24636 URL: http://svn.gna.org/viewcvs/relax?rev=24636view=rev Log: Code validation of lib/dispersion/two_point.py. Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis. Modified: branches/disp_spin_speed/lib/dispersion/two_point.py Modified: branches/disp_spin_speed/lib/dispersion/two_point.py URL: http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/two_point.py?rev=24636r1=24635r2=24636view=diff == --- branches/disp_spin_speed/lib/dispersion/two_point.py(original) +++ branches/disp_spin_speed/lib/dispersion/two_point.pyTue Jul 22 16:51:57 2014 @@ -32,7 +32,7 @@ The formula is:: - -1 / I1 \ + -1 / I1 \ R2eff = --- * ln | -- | , relax_T \ I0 / ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-comm...@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits ___ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
Re: r24336 - /branches/disp_spin_speed/target_functions/relax_disp.py
2014-06-27 17:28 GMT+02:00 Edward d'Auvergne edw...@nmr-relax.com: Also the documentation in the get_back_calc() method of the target function needs a little polish - it is not a float that is returned. So, the running list: - Some modules have = operators outside of functions that need spaces around them. Done - Trailing whitespace, most of it is in the trunk, but there are some new ones. Just run: grep $ lib/dispersion/* | grep -v Done - There are some empty lines straight after a 'for' loop in many places. Done - Your copyright in the tsmfk01.py file needs to be extended to 2014. Done - There are some FIXME comments in the lib.dispersion package. They are not critical, and are in module which is not used yet. - In some places, comment lines require empty lines before them (in target_functions.relax_disp and lib.dispersion). Where? Can you give example? - Not very important, but the target function calc_ns_mmq_3site_chi2() can have the Once off parameter conversions shifted into the lib.dispersion module to simplify this. Done - The newline spacing between target function methods needs some fixes. Done? - The 'chi2_sum' initialisation in func_ns_mmq_2site() should go. Done - The get_back_calc() method of the target function needs a little polish - it is not a float that is returned. Done Best Troels Cheers, Edward On 27 June 2014 17:26, Edward d'Auvergne edw...@nmr-relax.com wrote: To add to the list of trivialities to fix: - The 'chi2_sum' initialisation in func_ns_mmq_2site() should go. Cheers, Edward On 27 June 2014 17:23, Edward d'Auvergne edw...@nmr-relax.com wrote: Let me see. You've covered most of the running list, there's just one or two things left. I'll add a few more trivial things as well. - Some modules have = operators outside of functions that need spaces around them. - Trailing whitespace, most of it is in the trunk, but there are some new ones. Just run: grep $ lib/dispersion/* | grep -v - There are some empty lines straight after a 'for' loop in many places. - Your copyright in the tsmfk01.py file needs to be extended to 2014. - There are some FIXME comments in the lib.dispersion package. - In some places, comment lines require empty lines before them (in target_functions.relax_disp and lib.dispersion). - Not very important, but the target function calc_ns_mmq_3site_chi2() can have the Once off parameter conversions shifted into the lib.dispersion module to simplify this. - The newline spacing between target function methods needs some fixes. I'll keep looking. I'm guessing you will not be tackling the numeric models to speed them up to match 'NS CPMG 2-site expanded' model via the ultimate solution of brute-force expansion (http://www.mail-archive.com/relax-users@gna.org/msg01641.html) any time soon. This will have a similar effect as the ultimate speed up at http://www.mail-archive.com/relax-devel%40gna.org/msg05691.html which you have so successfully achieved in this branch. Can you remember if there were any other changes required? I will create a new timings file just before tagging the relax release. Cheers, Edward On 27 June 2014 16:53, Troels Emtekær Linnet tlin...@nmr-relax.com wrote: This sounds good. What is needed to be done, to merge disp_spin_speed in trunk now? Best Troels 2014-06-27 15:53 GMT+02:00 Edward d'Auvergne edw...@nmr-relax.com: Hmmm: $ grep -c out=\|einsum lib/dispersion/* lib/dispersion/b14.py:0 lib/dispersion/cr72.py:2 lib/dispersion/dpl94.py:0 lib/dispersion/__init__.py:0 lib/dispersion/it99.py:0 lib/dispersion/lm63_3site.py:0 lib/dispersion/lm63.py:0 lib/dispersion/m61b.py:0 lib/dispersion/m61.py:0 lib/dispersion/matrix_exponential.py:5 lib/dispersion/matrix_power.py:0 lib/dispersion/mmq_cr72.py:0 lib/dispersion/mp05.py:0 lib/dispersion/ns_cpmg_2site_3d.py:6 lib/dispersion/ns_cpmg_2site_expanded.py:0 lib/dispersion/ns_cpmg_2site_star.py:3 lib/dispersion/ns_matrices.py:0 lib/dispersion/ns_mmq_2site.py:12 lib/dispersion/ns_mmq_3site.py:12 lib/dispersion/ns_r1rho_2site.py:3 lib/dispersion/ns_r1rho_3site.py:3 lib/dispersion/tap03.py:0 lib/dispersion/tp02.py:0 lib/dispersion/tsmfk01.py:0 lib/dispersion/two_point.py:0 What do you think of the idea of making this a hard dependency: Index: dep_check.py === --- dep_check.py(revision 24343) +++ dep_check.py(working copy) @@ -37,6 +37,9 @@ # numpy. try: import numpy +if float(numpy.version.version[:3]) 1.6: +sys.stderr.write(Version %s of the 'numpy' dependency is not supported, numpy = 1.6 is required.\n % numpy.version.version) +sys.exit() except ImportError: sys.stderr.write(The dependency 'numpy' has not been installed.\n) sys.exit() This might be the easiest way, just forcing users to upgrade. I've used the out
Re: r24336 - /branches/disp_spin_speed/target_functions/relax_disp.py
Hi Ed. I wont change anymore. This development line is way overdue. Best Troels 2014-06-27 18:03 GMT+02:00 Edward d'Auvergne edw...@nmr-relax.com: Here is one more point. For the DPL94 model, the denominator is kex**2 + spin_lock_fields**2. This can only be zero when kex is zero, and then there should be no exchange. Therefore we can add a kex == 0 check at the start to return R1_R2 and then delete the mask_denom_zero logic. This should slightly speed things up by removing one 'if' statement. Also, kex**2 is not a repetitive operation. Cheers, Edward On 27 June 2014 17:33, Edward d'Auvergne edw...@nmr-relax.com wrote: There are also a number of double spacing issues. You can find these by running: $ ./devel_scripts/code_validator lib/dispersion/b14.py $ ./devel_scripts/code_validator lib/dispersion/cr72.py Etc. Some things can be ignored, like the capitals in the function name and double spacing or trailing spacing for equations in docstrings. This script will identify most formatting problems remaining. Cheers, Edward On 27 June 2014 17:28, Edward d'Auvergne edw...@nmr-relax.com wrote: Also the documentation in the get_back_calc() method of the target function needs a little polish - it is not a float that is returned. So, the running list: - Some modules have = operators outside of functions that need spaces around them. - Trailing whitespace, most of it is in the trunk, but there are some new ones. Just run: grep $ lib/dispersion/* | grep -v - There are some empty lines straight after a 'for' loop in many places. - Your copyright in the tsmfk01.py file needs to be extended to 2014. - There are some FIXME comments in the lib.dispersion package. - In some places, comment lines require empty lines before them (in target_functions.relax_disp and lib.dispersion). - Not very important, but the target function calc_ns_mmq_3site_chi2() can have the Once off parameter conversions shifted into the lib.dispersion module to simplify this. - The newline spacing between target function methods needs some fixes. - The 'chi2_sum' initialisation in func_ns_mmq_2site() should go. - The get_back_calc() method of the target function needs a little polish - it is not a float that is returned. Cheers, Edward On 27 June 2014 17:26, Edward d'Auvergne edw...@nmr-relax.com wrote: To add to the list of trivialities to fix: - The 'chi2_sum' initialisation in func_ns_mmq_2site() should go. Cheers, Edward On 27 June 2014 17:23, Edward d'Auvergne edw...@nmr-relax.com wrote: Let me see. You've covered most of the running list, there's just one or two things left. I'll add a few more trivial things as well. - Some modules have = operators outside of functions that need spaces around them. - Trailing whitespace, most of it is in the trunk, but there are some new ones. Just run: grep $ lib/dispersion/* | grep -v - There are some empty lines straight after a 'for' loop in many places. - Your copyright in the tsmfk01.py file needs to be extended to 2014. - There are some FIXME comments in the lib.dispersion package. - In some places, comment lines require empty lines before them (in target_functions.relax_disp and lib.dispersion). - Not very important, but the target function calc_ns_mmq_3site_chi2() can have the Once off parameter conversions shifted into the lib.dispersion module to simplify this. - The newline spacing between target function methods needs some fixes. I'll keep looking. I'm guessing you will not be tackling the numeric models to speed them up to match 'NS CPMG 2-site expanded' model via the ultimate solution of brute-force expansion (http://www.mail-archive.com/relax-users@gna.org/msg01641.html) any time soon. This will have a similar effect as the ultimate speed up at http://www.mail-archive.com/relax-devel%40gna.org/msg05691.html which you have so successfully achieved in this branch. Can you remember if there were any other changes required? I will create a new timings file just before tagging the relax release. Cheers, Edward On 27 June 2014 16:53, Troels Emtekær Linnet tlin...@nmr-relax.com wrote: This sounds good. What is needed to be done, to merge disp_spin_speed in trunk now? Best Troels 2014-06-27 15:53 GMT+02:00 Edward d'Auvergne edw...@nmr-relax.com: Hmmm: $ grep -c out=\|einsum lib/dispersion/* lib/dispersion/b14.py:0 lib/dispersion/cr72.py:2 lib/dispersion/dpl94.py:0 lib/dispersion/__init__.py:0 lib/dispersion/it99.py:0 lib/dispersion/lm63_3site.py:0 lib/dispersion/lm63.py:0 lib/dispersion/m61b.py:0 lib/dispersion/m61.py:0 lib/dispersion/matrix_exponential.py:5 lib/dispersion/matrix_power.py:0 lib/dispersion/mmq_cr72.py:0 lib/dispersion/mp05.py:0 lib/dispersion/ns_cpmg_2site_3d.py:6 lib/dispersion/ns_cpmg_2site_expanded.py:0 lib/dispersion/ns_cpmg_2site_star.py:3 lib/dispersion/ns_matrices.py:0
Re: r24336 - /branches/disp_spin_speed/target_functions/relax_disp.py
Hi, It all looks good, but you just have a few fixes for the last few commits with the broken equations in docstrings due to spacing changes. You can find these with: $ grep $ lib/dispersion/* $ grep i = 2 lib/dispersion/* I have some more responses below: - There are some empty lines straight after a 'for' loop in many places. Done There are a few more, just search for the text for ei in range(self.NE in the target function. - There are some FIXME comments in the lib.dispersion package. They are not critical, and are in module which is not used yet. Ok. - In some places, comment lines require empty lines before them (in target_functions.relax_disp and lib.dispersion). Where? Can you give example? You also fixed some of the empty lines before comments formatting, but there are still some in target_function/relax_disp.py. For example see # Structure of r20a and r20b. The full and outer dimensions structures.. There are a few in the __init__() method. - The newline spacing between target function methods needs some fixes. Done? It looks done :) Cheers, Edward ___ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
[task #7807] Speed-up of dispersion models for Clustered analysis
Follow-up Comment #486, task #7807 (project relax): This development branch is now complete, and I ask for merge to trunk. ___ Reply to this item at: http://gna.org/task/?7807 ___ Message sent via/by Gna! http://gna.org/ ___ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
