[gmx-users] scaling of replica exchange
Dear all, I am making some tests to start using replica exchange molecular dynamics on my system in water. The setup is ok (i.e. one replica alone runs correctly), but I am not able to parallelize the REMD. Details follow: - the test is on 8 temperatures, so 8 replicas - Gromacs version 4.5.3 - One replica alone, in 30 minutes with 256 processors, makes 52500 steps. 8 replicas with 256x8 = 2048 processors, make 300 (!!) steps each = 2400 in total (I arrived to these numbers just to see some update of the log file: since I am running on a big cluster, I can not use more than half an hour for tests with less than 512 processors) - I am using mpirun with options -np 256 -s md_.tpr -multi 8 -replex 1000 Do you have any idea? Thanks in advance Valeria -- 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] scaling of replica exchange
Sorry Luca, my mistake in writing. I used actually 2048. Valeria On Wed, 23 Feb 2011, Luca wrote: Hi Valeria, Dear all, I am making some tests to start using replica exchange molecular dynamics on my system in water. The setup is ok (i.e. one replica alone runs correctly), but I am not able to parallelize the REMD. Details follow: - the test is on 8 temperatures, so 8 replicas - Gromacs version 4.5.3 - One replica alone, in 30 minutes with 256 processors, makes 52500 steps. 8 replicas with 256x8 = 2048 processors, make 300 (!!) steps each = 2400 in total (I arrived to these numbers just to see some update of the log file: since I am running on a big cluster, I can not use more than half an hour for tests with less than 512 processors) - I am using mpirun with options -np 256 -s md_.tpr -multi 8 -replex 1000 I think that with this option you are using 256/8=32 cpu for each replica. If you want use 256 for each replica you cna try set up -np option equal to 256x8 = 2048. Luca Do you have any idea? Thanks in advance Valeria -- 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] scaling of replica exchange
Thank you Mark. I found one message of this month concerning this topic, and there are some small suggestions. I don't think that such a changes can restore a factor of 26, but it could be worth to try to see what happens. I will let you know. Valeria On Wed, 23 Feb 2011, Mark Abraham wrote: On 02/23/11, Valeria Losasso wrote: Dear all, I am making some tests to start using replica exchange molecular dynamics on my system in water. The setup is ok (i.e. one replica alone runs correctly), but I am not able to parallelize the REMD. Details follow: - the test is on 8 temperatures, so 8 replicas - Gromacs version 4.5.3 - One replica alone, in 30 minutes with 256 processors, makes 52500 steps. 8 replicas with 256x8 = 2048 processors, make 300 (!!) steps each = 2400 in total (I arrived to these numbers just to see some update of the log file: since I am running on a big cluster, I can not use more than half an hour for tests with less than 512 processors) - I am using mpirun with options -np 256 -s md_.tpr -multi 8 -replex 1000 There have been two threads on this topic in the last month or so, please check the archives. The implementation of multi-simulations scales poorly. The scaling of replica-exchange itself is not great either. I have a working version under final development that scales much better. Watch this space. 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
[gmx-users] g_cluster: optimal cutoff
Dear all, for my cluster analysis I am using the g_cluster tool with the gromos method. The problem is that I have to compare the results for system of different lengths, and of course the result of the cluster analysis changes according to the cutoff chosen. So what will be a great choice in this case? I was thinking about different possibilities, namely: i) choosing - as it is quite frequent in the literature - an arbitrary cutoff (like the default 0.1), but using the same for different systems would be probably not suitable... ii) looking for every case at the RMSD distribution and choosing the minimum value between the two peaks - in this case the cutoff would vary for every system; iii) choosing for every system the cutoff that allows to have in the largest cluster the 50% of the structures, and also in this case the cutoff would be different for the different cases... Any hint? Thanks a lot, Valeria Valeria Losasso v.losa...@grs-sim.de German Research School for Simulation Sciences GmbH 52425 Jülich | Germany Tel +49 2461 61 8934 Web www.grs-sim.de Members: Forschungszentrum Jülich GmbH | RWTH Aachen University Registered in the commercial register of the local court of Düren (Amtsgericht Düren) under registration number HRB 5268 Registered office: Jülich Executive board: Prof. Marek Behr Ph.D. | Dr. Norbert Drewes -- 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] g_cluster: optimal cutoff
Dear all, for my cluster analysis I am using the g_cluster tool with the gromos method. The problem is that I have to compare the results for system of different lengths, and of course the result of the cluster analysis changes according to the cutoff chosen. So what will be a great choice in this case? I was thinking about different possibilities, namely: i) choosing - as it is quite frequent in the literature - an arbitrary cutoff (like the default 0.1), but using the same for different systems would be probably not suitable... ii) looking for every case at the RMSD distribution and choosing the minimum value between the two peaks - in this case the cutoff would vary for every system; iii) choosing for every system the cutoff that allows to have in the largest cluster the 50% of the structures, and also in this case the cutoff would be different for the different cases... Any hint? Thanks a lot, Valeria -- 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
