Re: [gmx-users] number of DD cells
Moeed wrote: Hello, I am attempting to increase the density using NPT. As I increase the pressure to compress the system after some steps simulation crashes. I thought maybe its becasue I am compressing too fast but even when I take a stepwise approach to compress gradually the same error comes up. The density at the point of crash is about 30 SI while I need 650 which is the actual density. Topology file is generated successfully and also I did EM before MD. Initial box size is 30 nm. As suggested in the link below I reduced the size to 20 nm (there are 2500 atoms in the system ) but the same error appears. http://lists.gromacs.org/pipermail/gmx-users/2009-April/041488.html I also tried less -np from 7 to 4 but no success. Can you please tell me what this exclamation mark mean which I get at times in parallel trials.(vol 0.99 !) Domain decomposition relies on dividing your system up into reliably-sized domains in order to communicate force, coordinate, energy, etc. information. If something happens to skew or annihilate these domains, the algorithm crashes. The exclamation marks indicate (in a general sense) that the DD algorithm has detected something dangerously wrong. If you're trying to make drastic changes to the size or dimensions of your system, DD is a bad choice and you'll likely have to use particle decomposition (mdrun -pd). snip fourierspacing = 0.3 You're setting yourself up for inaccurate PME calculations with this. Use 0.1 - 0.12 unless you've got some compelling reason to decrease your accuracy. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] number of DD cells
Hello Justin, Thanks. 1- I changed the setting below because of the note I used to get: NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing Also, earlier on I read one of your messages about the trade off between accuracy and speed for this setting and that no systematic study has been done how exactly accuracy is changing. I actually need to work with systems with 40 000 atoms or even more and electrostatics slows down my runs to a great extent. Can you please give an idea on to what extent the accuracy affects the result say for fourierspacing = 0.2 . I mean it affects second decimal or...? I need to go for a setting which speeds up calculations as much as possible while being reasonable. How would you deal with this? What value would you pick? Thank you, moeed fourierspacing = 0.3 You're setting yourself up for inaccurate PME calculations with this. Use 0.1 - 0.12 unless you've got some compelling reason to decrease your accuracy. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Moeed Shahamat Graduate Student (Materials Modeling Research Group) McGill University- Department of Chemical Engineering Montreal, Quebec H3A 2B2, Canada Web: http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php Web:http://mmrg.chemeng.mcgill.ca/ -- 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
Re: [gmx-users] number of DD cells
Moeed wrote: Hello Justin, Thanks. 1- I changed the setting below because of the note I used to get: NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing I'm guessing this pertains to your expanded system, before you've obtained an optimum density? If so, you're only going to be losing performance for some simulations, but not all. It also depends on just how bad the load imbalance is. If you can set it such that you can easily specify -npme to match the PP:PME ratio, then you shouldn't be hurt too badly. Also, earlier on I read one of your messages about the trade off between accuracy and speed for this setting and that no systematic study has been done how exactly accuracy is changing. I actually need to work with systems with 40 000 atoms or even more and electrostatics slows down my runs to a great extent. Can you please give an idea on to what extent the accuracy affects the result say for fourierspacing = 0.2 . I mean it affects second decimal or...? I need to go for a setting which You may want to look into g_tune_pme. It should provide this sort of information. There was also some discussion about this just a few weeks ago, but I don't have the time or desire to go rooting through the list archive at the moment. speeds up calculations as much as possible while being reasonable. How would you deal with this? What value would you pick? Ideally, one that is well-tested and that you can defend to a critical audience. If 0.12 is standard, and I have no desire to experiment with accuracy, I tend to stick with that :) -Justin Thank you, moeed fourierspacing = 0.3 You're setting yourself up for inaccurate PME calculations with this. Use 0.1 - 0.12 unless you've got some compelling reason to decrease your accuracy. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Moeed Shahamat Graduate Student (Materials Modeling Research Group) McGill University- Department of Chemical Engineering Montreal, Quebec H3A 2B2, Canada Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php Web:http://mmrg.chemeng.mcgill.ca/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] number of DD cells
Justin A. Lemkul wrote: Moeed wrote: Hello Justin, Thanks. 1- I changed the setting below because of the note I used to get: NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing I'm guessing this pertains to your expanded system, before you've obtained an optimum density? If so, you're only going to be losing performance for some simulations, but not all. It also depends on just how bad the load imbalance is. If you can set it such that you can easily specify -npme to match the PP:PME ratio, then you shouldn't be hurt too badly. Also, earlier on I read one of your messages about the trade off between accuracy and speed for this setting and that no systematic study has been done how exactly accuracy is changing. I actually need to work with systems with 40 000 atoms or even more and electrostatics slows down my runs to a great extent. Can you please give an idea on to what extent the accuracy affects the result say for fourierspacing = 0.2 . I mean it affects second decimal or...? I need to go for a setting which You may want to look into g_tune_pme. It should provide this sort of information. There was also some discussion about this just a few weeks ago, but I don't have the time or desire to go rooting through the list archive at the moment. Sorry, that should be g_pme_error. -Justin speeds up calculations as much as possible while being reasonable. How would you deal with this? What value would you pick? Ideally, one that is well-tested and that you can defend to a critical audience. If 0.12 is standard, and I have no desire to experiment with accuracy, I tend to stick with that :) -Justin Thank you, moeed fourierspacing = 0.3 You're setting yourself up for inaccurate PME calculations with this. Use 0.1 - 0.12 unless you've got some compelling reason to decrease your accuracy. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Moeed Shahamat Graduate Student (Materials Modeling Research Group) McGill University- Department of Chemical Engineering Montreal, Quebec H3A 2B2, Canada Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php Web:http://mmrg.chemeng.mcgill.ca/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] number of DD cells
On 05/03/11, Justin A. Lemkul jalem...@vt.edu wrote: Moeed wrote: Hello, I am attempting to increase the density using NPT. As I increase the pressure to compress the system after some steps simulation crashes. I thought maybe its becasue I am compressing too fast but even when I take a stepwise approach to compress gradually the same error comes up. The density at the point of crash is about 30 SI while I need 650 which is the actual density. Topology file is generated successfully and also I did EM before MD. Initial box size is 30 nm. As suggested in the link below I reduced the size to 20 nm (there are 2500 atoms in the system ) but the same error appears. http://lists.gromacs.org/pipermail/gmx-users/2009-April/041488.html I also tried less -np from 7 to 4 but no success. Can you please tell me what this exclamation mark mean which I get at times in parallel trials.(vol 0.99 !) Domain decomposition relies on dividing your system up into reliably-sized domains in order to communicate force, coordinate, energy, etc. information. If something happens to skew or annihilate these domains, the algorithm crashes. The exclamation marks indicate (in a general sense) that the DD algorithm has detected something dangerously wrong. If you're trying to make drastic changes to the size or dimensions of your system, DD is a bad choice and you'll likely have to use particle decomposition (mdrun -pd). Or during compression, do regular and frequent grompp -t .trr -e .edr restarts so that the DD information in the checkpoint file is not propagated, and so you can do a new DD based on the current volume. Mark snip fourierspacing = 0.3 You're setting yourself up for inaccurate PME calculations with this. Use 0.1 - 0.12 unless you've got some compelling reason to decrease your accuracy. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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
Re: [gmx-users] number of DD cells
On 27/12/2010 7:51 AM, Poojari, Chetan wrote: Hi, I am following umbrella sampling tutorial for my membrane protein system. While running continuous pulling simulation (mdrun). under step five: Generating Configurations of the tutorial. I get the below error. The system ran initially but corrupted very soon with warning The X-size of the box (4.800448) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.20) I am using 64 cores with -npme = 16. I haven't set any -dds. My system box size is 6 x 6 x 12 nm That's a large box deformation... 6nm to 4.8nm. I'd say your system is probably blowing up, and that -dds 0.6 is hiding the symptoms. Try running on fewer processors to see whether when the DD box size is larger whether you get other explosion symptoms. Mark -- 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
RE: [gmx-users] number of DD cells
Hi Mark, I ran on 48 processors.the error is: The X-size of the box (5.312040) times the triclinic skew factor (1.00) is smaller than the number of DD cells (6) times the smallest allowed cell size (0.885281) Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham [mark.abra...@anu.edu.au] Sent: 27 December 2010 00:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] number of DD cells On 27/12/2010 7:51 AM, Poojari, Chetan wrote: Hi, I am following umbrella sampling tutorial for my membrane protein system. While running continuous pulling simulation (mdrun). under step five: Generating Configurations of the tutorial. I get the below error. The system ran initially but corrupted very soon with warning The X-size of the box (4.800448) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.20) I am using 64 cores with -npme = 16. I haven't set any -dds. My system box size is 6 x 6 x 12 nm That's a large box deformation... 6nm to 4.8nm. I'd say your system is probably blowing up, and that -dds 0.6 is hiding the symptoms. Try running on fewer processors to see whether when the DD box size is larger whether you get other explosion symptoms. Mark -- 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 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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
Re: [gmx-users] number of DD cells
Poojari, Chetan wrote: Hi Mark, I ran on 48 processors.the error is: The X-size of the box (5.312040) times the triclinic skew factor (1.00) is smaller than the number of DD cells (6) times the smallest allowed cell size (0.885281) I would say this further confirms Mark's suspicions. Whatever you're doing to the system is causing it to rapidly collapse, a behavior that is now independent of the number of DD cells. -Justin Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham [mark.abra...@anu.edu.au] Sent: 27 December 2010 00:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] number of DD cells On 27/12/2010 7:51 AM, Poojari, Chetan wrote: Hi, I am following umbrella sampling tutorial for my membrane protein system. While running continuous pulling simulation (mdrun). under step five: Generating Configurations of the tutorial. I get the below error. The system ran initially but corrupted very soon with warning The X-size of the box (4.800448) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.20) I am using 64 cores with -npme = 16. I haven't set any -dds. My system box size is 6 x 6 x 12 nm That's a large box deformation... 6nm to 4.8nm. I'd say your system is probably blowing up, and that -dds 0.6 is hiding the symptoms. Try running on fewer processors to see whether when the DD box size is larger whether you get other explosion symptoms. Mark -- 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 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
