[gmx-users] PME nodes
Hi all, There must be something I don't fully understand, by running grompp on a system, I get this: Estimate for the relative computational load of the PME mesh part: 0.32 Good, that's approximately 1/3, or a 2:1 PP:PME ratio, which is the recommended value for a dodecahedral box. But then I run the dynamics with mdrun_mpi -np 8 (different cores in a single physical machine) and I get: Initializing Domain Decomposition on 8 nodes [...] Using 0 separate PME nodes I would have expected at least 2 nodes (3:1, 0.25) to be used for PME, so there's obviously something wrong in my assumption. Should I be looking somewhere in the output to find out why? Would it be better to try to get some dedicated PME node(s) (even in a single machine)? Thanks, Ignacio -- 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] PME nodes
According to the manual, mdrun does not dedicate PME nodes unless -np 11 You can manually specify dedicated PME nodes using -npme, but it is highly system dependent on whether this will be faster on lowcore systems. Also the estimate given by grompp may not be optimal during runtime. You'll have to repeat runs on different node combinations or use g_tune_pme to discover the optimal PME:PP ratio for your particular system. On 2012-05-31 04:11:15AM -0700, Ignacio Fernández Galván wrote: Hi all, There must be something I don't fully understand, by running grompp on a system, I get this: Estimate for the relative computational load of the PME mesh part: 0.32 Good, that's approximately 1/3, or a 2:1 PP:PME ratio, which is the recommended value for a dodecahedral box. But then I run the dynamics with mdrun_mpi -np 8 (different cores in a single physical machine) and I get: Initializing Domain Decomposition on 8 nodes [...] Using 0 separate PME nodes I would have expected at least 2 nodes (3:1, 0.25) to be used for PME, so there's obviously something wrong in my assumption. Should I be looking somewhere in the output to find out why? Would it be better to try to get some dedicated PME node(s) (even in a single machine)? Thanks, Ignacio -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] PME nodes
On 31/05/2012 9:11 PM, Ignacio Fernández Galván wrote: Hi all, There must be something I don't fully understand, by running grompp on a system, I get this: Estimate for the relative computational load of the PME mesh part: 0.32 Good, that's approximately 1/3, or a 2:1 PP:PME ratio, which is the recommended value for a dodecahedral box. But then I run the dynamics with mdrun_mpi -np 8 (different cores in a single physical machine) and I get: Initializing Domain Decomposition on 8 nodes [...] Using 0 separate PME nodes I would have expected at least 2 nodes (3:1, 0.25) to be used for PME, so there's obviously something wrong in my assumption. Should I be looking somewhere in the output to find out why? Would it be better to try to get some dedicated PME node(s) (even in a single machine)? Generally mdrun does pretty well, given the constraints you've set for it. Here, you've implicitly let it choose (with mdrun -npme -1), and with fewer than a minimum number of nodes (10, in 4.5.5) it doesn't bother, since the book-keeping would be too costly. Otherwise, you can investigate the reasons for the choices mdrun made from the output in the .log file. You can try mdrun -npme 2 or 3 if you like, but it's likely not faster or might even refuse to run. See manual 3.17, also. 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] PME nodes
On Jun 6, 2009, at 1:20 PM, XAvier Periole wrote: On Jun 6, 2009, at 1:08 PM, Justin A. Lemkul wrote: XAvier Periole wrote: Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best. I'd appreciate if some of you could post their experience in that matter. I mean the number of pme nodes as compared the total number of CPUs used. I think this info as been discussed recently on the list but the archive is not accessible. It may matter that I have a system containing about 7 atoms, a protein in a bilayer. Some advice that I got from Berk long ago has worked beautifully for me. You want a 3:1 PP:PME balance for a regular triclinic cell (grompp will report the relative PME load as 25% if your parameters create such a balance), 2:1 for an octahedron. My scaling has been great using this information, without having to alter -rdd, -rcon, etc. Thanks for the info. I got more or less to that ratio. Although a 2:1 PP:PME sometimes is better. However my problem now is to get 256 CPUs more efficient (ns/day) than 128 CPUs. The communications become a limiting factor ... can't get it to go faster! The system might be small, but not sure. I'll take a look at the CVS tool. There is also a version for gromacs 4.0.x available for download at www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/ Regards, Carsten -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] PME nodes
Hello, How can I compile the g_tune_pme program available at: http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/ Many thanks, Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] PME nodes
Hi, it's written at the begin of the .c file: * You can compile this tool using the Gromacs Makefile from the * share/gromacs/template directory, just replace 'template' by 'g_tune_pme' * where needed. To enable shell completions for g_tune_pme, just * copy the provided completion.* files to your Gromacs bin directory. Carsten On Jun 8, 2009, at 12:48 PM, Andrei Neamtu wrote: Hello, How can I compile the g_tune_pme program available at: http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/ Many thanks, Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 mailing listgmx-users@gromacs.org http://lists.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] PME nodes
Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best. I'd appreciate if some of you could post their experience in that matter. I mean the number of pme nodes as compared the total number of CPUs used. I think this info as been discussed recently on the list but the archive is not accessible. It may matter that I have a system containing about 7 atoms, a protein in a bilayer. Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] PME nodes
XAvier Periole wrote: Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best. I'd appreciate if some of you could post their experience in that matter. I mean the number of pme nodes as compared the total number of CPUs used. I think this info as been discussed recently on the list but the archive is not accessible. It may matter that I have a system containing about 7 atoms, a protein in a bilayer. g_tunepme in the CVS is your friend here. Carsten Kutzner is the author of this program. Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] PME nodes
XAvier Periole wrote: Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best. I'd appreciate if some of you could post their experience in that matter. I mean the number of pme nodes as compared the total number of CPUs used. I think this info as been discussed recently on the list but the archive is not accessible. It may matter that I have a system containing about 7 atoms, a protein in a bilayer. Some advice that I got from Berk long ago has worked beautifully for me. You want a 3:1 PP:PME balance for a regular triclinic cell (grompp will report the relative PME load as 25% if your parameters create such a balance), 2:1 for an octahedron. My scaling has been great using this information, without having to alter -rdd, -rcon, etc. -Justin Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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
Re: [gmx-users] PME nodes
On Jun 6, 2009, at 1:08 PM, Justin A. Lemkul wrote: XAvier Periole wrote: Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best. I'd appreciate if some of you could post their experience in that matter. I mean the number of pme nodes as compared the total number of CPUs used. I think this info as been discussed recently on the list but the archive is not accessible. It may matter that I have a system containing about 7 atoms, a protein in a bilayer. Some advice that I got from Berk long ago has worked beautifully for me. You want a 3:1 PP:PME balance for a regular triclinic cell (grompp will report the relative PME load as 25% if your parameters create such a balance), 2:1 for an octahedron. My scaling has been great using this information, without having to alter -rdd, -rcon, etc. Thanks for the info. I got more or less to that ratio. Although a 2:1 PP:PME sometimes is better. However my problem now is to get 256 CPUs more efficient (ns/day) than 128 CPUs. The communications become a limiting factor ... can't get it to go faster! The system might be small, but not sure. I'll take a look at the CVS tool. XAvier. -Justin Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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 mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] PME nodes
XAvier Periole wrote: On Jun 6, 2009, at 1:08 PM, Justin A. Lemkul wrote: XAvier Periole wrote: Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best. I'd appreciate if some of you could post their experience in that matter. I mean the number of pme nodes as compared the total number of CPUs used. I think this info as been discussed recently on the list but the archive is not accessible. It may matter that I have a system containing about 7 atoms, a protein in a bilayer. Some advice that I got from Berk long ago has worked beautifully for me. You want a 3:1 PP:PME balance for a regular triclinic cell (grompp will report the relative PME load as 25% if your parameters create such a balance), 2:1 for an octahedron. My scaling has been great using this information, without having to alter -rdd, -rcon, etc. Thanks for the info. I got more or less to that ratio. Although a 2:1 PP:PME sometimes is better. However my problem now is to get 256 CPUs more efficient (ns/day) than 128 CPUs. The communications become a limiting factor ... can't get it to go faster! The system might be small, but not sure. Depends a lot on the interconnect and the ratio atoms/node. You may also want to play with cut-offs, the tool will help you with this. I'll take a look at the CVS tool. XAvier. -Justin Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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 mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
