Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator
The paper looks good. Do some more work and publish many Sent from my iPhone On 17-Jan-2013, at 8:18 PM, "James Starlight" wrote: Dear Gromacs Developers! Using sd1 integrator I've obtain good performance with the core-5 + GTX 670 ( 13ns\per day) for the system of 60k atoms. That results on 30% better than with the sd integrator. Buit on my another work-station which differs only by slower GPU ( GT 640). I've obtained some gpu\cpu mis-match. Force evaluation time GPU/CPU: 6.835 ms/2.026 ms = 3.373( # on the first station with GTX 670 I ve obtained GPU/CPU: ratio close to 1. At both cases I'm using the same simulation parameters with 0,8 cutoffs (it's also important that in the second case I've calculated another system consisted of 33k atoms by means of umbrella sampling pulling)). Could you tell me how I could increase performance on my second station ( to reduce gpucpu ratio) ? I've attached log for that simulation here http://www.sendspace.com/file/x0e3z8 James 2013/1/17 Szilárd Páll : > Hi, > > Just to note for the users who might read this: the report is valid, some > non-thread-parallel code is the reason and we hope to have a fix for 4.6.0. > > For updates, follow the issue #1211. > > Cheers, > > -- > Szilárd > > > On Wed, Jan 16, 2013 at 4:45 PM, Berk Hess wrote: > >> >> The issue I'm referring to is about a factor of 2 in update and >> constraints, but here it's much more. >> I just found out that the SD update is not OpenMP threaded (and I even >> noted in the code why this is). >> I reopened the issue and will find a solution. >> >> Cheers. >> >> Berk >> >> >>> Date: Wed, 16 Jan 2013 16:20:32 +0100 >>> Subject: Re: [gmx-users] >60% slowdown with GPU / verlet and sd >> integrator >>> From: mark.j.abra...@gmail.com >>> To: gmx-users@gromacs.org >>> >>> We should probably note this effect on the wiki somewhere? >>> >>> Mark >>> >>> On Wed, Jan 16, 2013 at 3:44 PM, Berk Hess wrote: >>> Hi, Unfortunately this is not a bug, but a feature! We made the non-bondeds so fast on the GPU that integration and constraints take more time. The sd1 integrator is almost as fast as the md integrator, but slightly less accurate. In most cases that's a good solution. I closed the redmine issue: http://redmine.gromacs.org/issues/1121 Cheers, Berk > Date: Wed, 16 Jan 2013 17:26:18 +0300 > Subject: Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator > From: jmsstarli...@gmail.com > To: gmx-users@gromacs.org > > Hi all! > > I've also done some calculations with the SD integraator used as the > thermostat ( without t_coupl ) with the system of 65k atoms I >> obtained > 10ns\day performance on gtc 670 and 4th core i5. > I haventrun any simulations with MD integrator yet so It should test >> it. > > James > > 2013/1/15 Szilárd Páll : >> Hi Floris, >> >> Great feedback, this needs to be looked into. Could you please >> file a bug >> report, preferably with a tpr (and/or all inputs) as well as log >> files. >> >> Thanks, >> >> -- >> Szilárd >> >> >> On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens < floris_buel...@yahoo.com>wrote: >> >>> Hi, >>> >>> >>> I'm seeing MD simulation running a lot slower with the sd >> integrator than >>> with md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found >> no >>> documented indication that this should be the case. >>> Timings and logs pasted in below - wall time seems to be >> accumulating up >>> in Update and Rest, adding up to >60% of total. The effect is >> still there >>> without GPU, ca. 40% slowdown when switching from group to Verlet with the >>> SD integrator >>> System: Xeon E5-1620, 1x GTX 680, gromacs >>> 4.6-beta3-dev-20130107-e66851a-unknown, GCC 4.4.6 and 4.7.0 >>> >>> I didn't file a bug report yet as I don't have much variety of >> testing >>> conditions available right now, I hope someone else has a moment >> to try to >>> reproduce? >>> >>> Timings: >>> >>> cpu (ns/day) >>> sd / verlet: 6 >>> sd / group: 10 >>> md / verlet: 9.2 >>> md / group: 11.4 >>> >>> gpu (ns/day) >>> sd / verlet: 11 >>> md / verlet: 29.8 >>> >>> >>> >>> **MD integrator, GPU / verlet >>> >>> M E G A - F L O P S A C C O U N T I N G >>> >>> NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet >> kernels >>> RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table >>> W3=SPC/TIP3p W4=TIP4p (single or pairs) >>> V&F=Potential and force V=Potential only F=Force only >>> >>> Computing: M-Number M-Flops % Flops >>>
RE: [gmx-users] Test mail
ok Date: Sat, 17 Dec 2011 16:33:25 +0530 From: priya.thiyagaraja...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Test mail Greetings, THis is a mail to test my gromacs mailing list connection -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] lost ngmx
Hello gmx-users I have compiled gromacs on Debian/Linux wiht the option --with-x but the ngmx binary has not been generated. I don´t have gnome or kde installed, but I have installed xserver-xorg and I can export VMD with ssh. Do I need to install gnome or kde? if the answer is yes, Do I need to compile gromacs again? or Is there a way to just compile ngmx? Thanks in advance -- Víctor E. Bahamonde Padilla Laboratorio Fisicoquimica Molecular Departamento de Química Facultad de Ciencias Universidad de Chile Phone: 562-978-7443 vedua...@ug.uchile.cl -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem running grompp - error message here
Hello, when I run grompp I get the following error message always. Whoever has a correct fix to get rid of this error message and get the actual result, Please suggest. Thanking you Dr. Victor A. Doss processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 2 bonded neighbours for SOL 82 Excluding 2 bonded neighbours for SOL 9514 NOTE: System has non-zero total charge: 8.00e+00 processing coordinates... double-checking input for internal consistency... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/grompp.c, line: 1134 Fatal error: There were 3 error(s) processing your input --- "Can't You Make This Thing Go Faster ?" (Black Crowes) d...@dv-laptop:~/g _ Twice the fun—Share photos while you chat with Windows Live Messenger. http://www.microsoft.com/india/windows/windowslive/messenger.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in running grompp
Hello, when I run grompp I get the following error message always. Whoever has a correct fix to get rid of this error message and get the actual result, Please suggest. Thanking you Dr. Victor A. Doss _ The new Windows Live Messenger. You don’t want to miss this. http://www.microsoft.com/india/windows/windowslive/messenger.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] residual negative charge?
Hello everybody, I'm trying to use gromacs to model an aza-type macrocycle (17 atoms around the ring). The structure does not include any aminoacids or sugars so, I'm building the itp file by hand. I started with a base topology from the PRODRG server and then added all the missing hydrogens (I want to use OPLS/AA). The problem is that, after assigning all the atom types as best as I could, I end up with a residual charge = -0.034. The macrocycle itself should be neutral. Does this mean I need to develop new parameters? Is there any way to fix this without reparametrizing? Thanx Victor M. Rosas García Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] polarizable water?
Hello everybody, Currently, I have a SPC water box with some Ca(2+) and CO3(2-) ions swimming around (I defined the itp file for carbonate, got the charges from ab initio calcs, the whole system is electroneutral). How do I define the water to be polarizable? Regards Victor M. Rosas García, PhD Coordinador del Posgrado en Ciencias Facultad de Ciencias Quimicas, UANL e-mail: [EMAIL PROTECTED] Tel: (81) 8329-4010 ext. 6253 Fax: (81) 8376-5375 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] box of water with ions
Hello everybody, I'm trying to build a water box with some calcium carbonate in it but, for the life of me, I cannot get it right. I can build a box of water with CaCl without any problems. I have a grompp.mdp file and then: genbox -box 2 2 2 -cs spc216 -o h2o.gro pdb2gmx -f h2o.gro -q h2o.pdb -n index.ndx grompp -f grompp.mdp -c h2o.gro -n index.ndx -p topol.top -o topol.tpr mdrun -v genion -s topol.tpr -o out.gro -pname Ca -pq 2 -np 5 -nname Cl -nq -1 -nn 10 and then pdb2gmx... mdrun... No problem there. I am aware that genion cannot introduce polyatomic ions so, to generate a box of water with CaCO3 I tried to introduce the anion first with genbox and then the Ca with genion (I have CO2(-2) as a pdb file): genbox -box 2 2 2 -cs spc216 -ci co3.pdb -nmol 10 pdb2gmx -f out.gro -q out.pdb -n index.ndx and I got the following error message: [snip, snip] --- Program pdb2gmx, VERSION 3.3 Source code file: resall.c, line: 438 Fatal error: Residue 'DRG' not found in residue topology database --- So, I tried x2top: x2top -f out.gro -o topol.top and then I got [snip, snip] --- Program x2top, VERSION 3.3 Source code file: futil.c, line: 537 Fatal error: Library file ffG43a1.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) --- so, neither pdb2gmx nor x2top worked. I submitted CO3(-2) to the prodrg server and I have all the files, but it gave me SIX *.TOP files so, I don't really know which one to use. None of them seem (to me) to fit the format of the gromacs topology files I saw in the gromacs documentation. Needless to say, I am FAR from being an experienced gromacs user, although I do have experience in computational chemistry, just not molecular dynamics. Any recommendations? Victor M. Rosas García, PhD Coordinador del Posgrado en Ciencias Facultad de Ciencias Quimicas, UANL e-mail: [EMAIL PROTECTED] Tel: (81) 8329-4010 ext. 6253 Fax: (81) 8376-5375 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
