BTW, forgot to mention that you may not loose much _aggregate_ performance by over-subscribing cores. I have not tried recently, but last time I checked even with with multiple (single-threaded) ranks per core you *should* get about the same aggregate performance. Just turn off pinning (which will be done by default) and preferably run # ranks multiple of the core count and it should run fine.
-- Szilárd On Sat, Apr 15, 2017 at 3:03 PM, Мижээ Батсайхан <b.mijidd...@gmail.com> wrote: > Dear gmx users, > > Thank you very much for your useful discussions. > > Best regards, > Mijee > > On Sat, Apr 15, 2017 at 7:00 PM, < > gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > >> Send gromacs.org_gmx-users mailing list submissions to >> gromacs.org_gmx-users@maillist.sys.kth.se >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or, via email, send a message with subject or body 'help' to >> gromacs.org_gmx-users-requ...@maillist.sys.kth.se >> >> You can reach the person managing the list at >> gromacs.org_gmx-users-ow...@maillist.sys.kth.se >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of gromacs.org_gmx-users digest..." >> >> >> Today's Topics: >> >> 1. Re: Replica exchange simulations more than number of >> processor (Thomas Piggot) >> 2. Re: Replica exchange simulations more than number of >> processor (Christopher Neale) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 14 Apr 2017 20:06:29 +0100 >> From: Thomas Piggot <t.pig...@soton.ac.uk> >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Replica exchange simulations more than number >> of processor >> Message-ID: <339c3321-fd12-7318-43b6-b41433f58...@soton.ac.uk> >> Content-Type: text/plain; charset=gbk; format=flowed >> >> Have you thought about a more selective scaling of the interactions >> (i.e. HREX with only scalings applied for certain bits of the protein, >> not the complete thing as in REST2) so as to reduce the protein >> hydrophobicity at the lower lambda's? I've seen this selective scaling >> work well in other types of system to counteract broadly similar types >> of sampling issues at lower lambda's. >> >> Just a thought, it might not work well for what you are doing, >> >> Cheers >> >> Tom >> >> On 14/04/17 19:27, Christopher Neale wrote: >> > In REST2, the protein becomes way too hydrophobic as lambda is >> decreased. Just run a standard simulation at 300K, another at 600K and then >> another one at 300K with REST2 lambda=0.5 and you'll see what I mean. >> > >> > REST has a hidden barrier corresponding to the point at which water >> becomes a theta solvent and the exchange is very poor across that boundary, >> with globular replicas staying at higher lambda and extended replicas >> staying at lower lambda. However, with REST2, there is no such hidden >> barrier because water never gets anywhere near being a theta solvent. So in >> REST2 you get good exchange for all the wrong reasons. >> > >> > Work continues.... >> > >> > >> > ________________________________________ >> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas >> Piggot <t.pig...@soton.ac.uk> >> > Sent: 14 April 2017 14:16:26 >> > To: gmx-us...@gromacs.org >> > Subject: Re: [gmx-users] Replica exchange simulations more than number >> of processor >> > >> > Hi Chris, >> > >> > This is interesting. Do you have an idea why the sampling at low lambda >> > values isn't very good? >> > >> > Cheers >> > >> > Tom >> > >> > On 14/04/17 17:40, Christopher Neale wrote: >> >> What I have is only my own personal unpublished data. But add to that >> the number of years since REST2 came out and the low number of papers in >> which anybody did something useful with it and I'd say that suggests many >> others have tried and run into the same issues that I did (or maybe I'm >> just not reading the right papers, so please correct me if I am wrong). >> When my desired use failed I fell back to trp-cage folding in water and >> found the same things, so it's not like REST2 only fails for some exotic >> systems. Running 3 entirely separate repeats of regular T-REMD and 3 of >> REST2, I found that overall T-REMD is of similar or perhaps better >> efficiency (even though it has more replicas) compared to REST2. It's an >> on/off area of research for me, attempting to fix REST, but I still don't >> have a good answer for it. >> >> >> >> >> >> ________________________________________ >> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Szil?rd >> P?ll <pall.szil...@gmail.com> >> >> Sent: 14 April 2017 12:26:41 >> >> To: Discussion list for GROMACS users >> >> Subject: Re: [gmx-users] Replica exchange simulations more than number >> of processor >> >> >> >> On Fri, Apr 14, 2017 at 5:51 PM, Christopher Neale < >> >> chris.ne...@alum.utoronto.ca> wrote: >> >> >> >>> Just my 2 cents: REST2 doesn't work. The random walk is much better >> than >> >>> REST but the sampling efficiency at low lambda is now poor. >> >> Interesting. Is there any (published) data you could point to that >> supports >> >> this? >> >> >> >> >> >>> Your mileage may vary, but be aware that REST2 is not necessarily >> going to >> >>> be useful for all systems. >> >>> ________________________________________ >> >>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas >> >>> Piggot <t.pig...@soton.ac.uk> >> >>> Sent: 14 April 2017 09:23:35 >> >>> To: gmx-us...@gromacs.org >> >>> Subject: Re: [gmx-users] Replica exchange simulations more than number >> of >> >>> processor >> >>> >> >>> In addition, using another technique like REST2 may substantially >> reduce >> >>> the numbers of replica's you need. Still, more compute is definitely >> >>> recommended if you can get it. >> >>> >> >>> Cheers >> >>> >> >>> Tom >> >>> >> >>> On 14/04/17 12:48, Smith, Micholas D. wrote: >> >>>> You can try over assignment of cores, but that will be horribly slow. >> Or >> >>> use more than 1 node (if you can get it). >> >>>> =================== >> >>>> Micholas Dean Smith, PhD. >> >>>> Post-doctoral Research Associate >> >>>> University of Tennessee/Oak Ridge National Laboratory >> >>>> Center for Molecular Biophysics >> >>>> >> >>>> ________________________________________ >> >>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of ????? >> >>> ????????? <b.mijidd...@gmail.com> >> >>>> Sent: Friday, April 14, 2017 4:16 AM >> >>>> To: gromacs.org_gmx-users@maillist.sys.kth.se >> >>>> Subject: [gmx-users] Replica exchange simulations more than number of >> >>> processor >> >>>> Dear gmx users, >> >>>> >> >>>> I would like to simulate folding of a peptides. I have only 12 core >> >>>> processor, and I assumed the number of replica using temperature >> >>> generator >> >>>> as following link >> >>>> http://folding.bmc.uu.se/remd/. >> >>>> >> >>>> The number of replica is about 60. How can I solve this problem? Can >> you >> >>>> advice me, please? >> >>>> >> >>>> Best regards, >> >>>> Mijee >> >>>> -- >> >>>> Gromacs Users mailing list >> >>>> >> >>>> * Please search the archive at http://www.gromacs.org/Support >> >>> /Mailing_Lists/GMX-Users_List before posting! >> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>>> >> >>>> * For (un)subscribe requests visit >> >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >>> send a mail to gmx-users-requ...@gromacs.org. >> >>> -- >> >>> Dr Thomas Piggot >> >>> Visiting Fellow >> >>> University of Southampton, UK. >> >>> >> >>> -- >> >>> Gromacs Users mailing list >> >>> >> >>> * Please search the archive at http://www.gromacs.org/Support >> >>> /Mailing_Lists/GMX-Users_List before posting! >> >>> >> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>> >> >>> * For (un)subscribe requests visit >> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >>> send a mail to gmx-users-requ...@gromacs.org. >> >>> -- >> >>> Gromacs Users mailing list >> >>> >> >>> * Please search the archive at http://www.gromacs.org/Support >> >>> /Mailing_Lists/GMX-Users_List before posting! >> >>> >> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>> >> >>> * For (un)subscribe requests visit >> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >>> send a mail to gmx-users-requ...@gromacs.org. >> >>> >> >> -- >> >> Gromacs Users mailing list >> >> >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> * For (un)subscribe requests visit >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- >> > Dr Thomas Piggot >> > Visiting Fellow >> > University of Southampton, UK. >> > >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> -- >> Dr Thomas Piggot >> Visiting Fellow >> University of Southampton, UK. >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 14 Apr 2017 19:23:06 +0000 >> From: Christopher Neale <chris.ne...@alum.utoronto.ca> >> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> >> Subject: Re: [gmx-users] Replica exchange simulations more than number >> of processor >> Message-ID: >> <SN2PR03MB2301C9C82BC8E629AC3F313CC5050@SN2PR03MB2301. >> namprd03.prod.outlook.com> >> >> Content-Type: text/plain; charset="gb2312" >> >> Dear Thomas: >> >> Thanks for the suggestion. I have a way foward, I'm just being selective >> about what I share at this point. This thread got a bit side-tracked from >> my reason for posting, which was simply to help a user with a single >> 12-core node to realize that dedicating it to a 6-month REST2 simulation >> might not be a good idea. >> ________________________________________ >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas >> Piggot <t.pig...@soton.ac.uk> >> Sent: 14 April 2017 15:06:29 >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Replica exchange simulations more than number of >> processor >> >> Have you thought about a more selective scaling of the interactions >> (i.e. HREX with only scalings applied for certain bits of the protein, >> not the complete thing as in REST2) so as to reduce the protein >> hydrophobicity at the lower lambda's? I've seen this selective scaling >> work well in other types of system to counteract broadly similar types >> of sampling issues at lower lambda's. >> >> Just a thought, it might not work well for what you are doing, >> >> Cheers >> >> Tom >> >> On 14/04/17 19:27, Christopher Neale wrote: >> > In REST2, the protein becomes way too hydrophobic as lambda is >> decreased. Just run a standard simulation at 300K, another at 600K and then >> another one at 300K with REST2 lambda=0.5 and you'll see what I mean. >> > >> > REST has a hidden barrier corresponding to the point at which water >> becomes a theta solvent and the exchange is very poor across that boundary, >> with globular replicas staying at higher lambda and extended replicas >> staying at lower lambda. However, with REST2, there is no such hidden >> barrier because water never gets anywhere near being a theta solvent. So in >> REST2 you get good exchange for all the wrong reasons. >> > >> > Work continues.... >> > >> > >> > ________________________________________ >> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas >> Piggot <t.pig...@soton.ac.uk> >> > Sent: 14 April 2017 14:16:26 >> > To: gmx-us...@gromacs.org >> > Subject: Re: [gmx-users] Replica exchange simulations more than number >> of processor >> > >> > Hi Chris, >> > >> > This is interesting. Do you have an idea why the sampling at low lambda >> > values isn't very good? >> > >> > Cheers >> > >> > Tom >> > >> > On 14/04/17 17:40, Christopher Neale wrote: >> >> What I have is only my own personal unpublished data. But add to that >> the number of years since REST2 came out and the low number of papers in >> which anybody did something useful with it and I'd say that suggests many >> others have tried and run into the same issues that I did (or maybe I'm >> just not reading the right papers, so please correct me if I am wrong). >> When my desired use failed I fell back to trp-cage folding in water and >> found the same things, so it's not like REST2 only fails for some exotic >> systems. Running 3 entirely separate repeats of regular T-REMD and 3 of >> REST2, I found that overall T-REMD is of similar or perhaps better >> efficiency (even though it has more replicas) compared to REST2. It's an >> on/off area of research for me, attempting to fix REST, but I still don't >> have a good answer for it. >> >> >> >> >> >> ________________________________________ >> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Szil?rd >> P?ll <pall.szil...@gmail.com> >> >> Sent: 14 April 2017 12:26:41 >> >> To: Discussion list for GROMACS users >> >> Subject: Re: [gmx-users] Replica exchange simulations more than number >> of processor >> >> >> >> On Fri, Apr 14, 2017 at 5:51 PM, Christopher Neale < >> >> chris.ne...@alum.utoronto.ca> wrote: >> >> >> >>> Just my 2 cents: REST2 doesn't work. The random walk is much better >> than >> >>> REST but the sampling efficiency at low lambda is now poor. >> >> Interesting. Is there any (published) data you could point to that >> supports >> >> this? >> >> >> >> >> >>> Your mileage may vary, but be aware that REST2 is not necessarily >> going to >> >>> be useful for all systems. >> >>> ________________________________________ >> >>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas >> >>> Piggot <t.pig...@soton.ac.uk> >> >>> Sent: 14 April 2017 09:23:35 >> >>> To: gmx-us...@gromacs.org >> >>> Subject: Re: [gmx-users] Replica exchange simulations more than number >> of >> >>> processor >> >>> >> >>> In addition, using another technique like REST2 may substantially >> reduce >> >>> the numbers of replica's you need. Still, more compute is definitely >> >>> recommended if you can get it. >> >>> >> >>> Cheers >> >>> >> >>> Tom >> >>> >> >>> On 14/04/17 12:48, Smith, Micholas D. wrote: >> >>>> You can try over assignment of cores, but that will be horribly slow. >> Or >> >>> use more than 1 node (if you can get it). >> >>>> =================== >> >>>> Micholas Dean Smith, PhD. >> >>>> Post-doctoral Research Associate >> >>>> University of Tennessee/Oak Ridge National Laboratory >> >>>> Center for Molecular Biophysics >> >>>> >> >>>> ________________________________________ >> >>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of ????? >> >>> ????????? <b.mijidd...@gmail.com> >> >>>> Sent: Friday, April 14, 2017 4:16 AM >> >>>> To: gromacs.org_gmx-users@maillist.sys.kth.se >> >>>> Subject: [gmx-users] Replica exchange simulations more than number of >> >>> processor >> >>>> Dear gmx users, >> >>>> >> >>>> I would like to simulate folding of a peptides. I have only 12 core >> >>>> processor, and I assumed the number of replica using temperature >> >>> generator >> >>>> as following link >> >>>> http://folding.bmc.uu.se/remd/. >> >>>> >> >>>> The number of replica is about 60. How can I solve this problem? Can >> you >> >>>> advice me, please? >> >>>> >> >>>> Best regards, >> >>>> Mijee >> >>>> -- >> >>>> Gromacs Users mailing list >> >>>> >> >>>> * Please search the archive at http://www.gromacs.org/Support >> >>> /Mailing_Lists/GMX-Users_List before posting! >> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>>> >> >>>> * For (un)subscribe requests visit >> >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >>> send a mail to gmx-users-requ...@gromacs.org. >> >>> -- >> >>> Dr Thomas Piggot >> >>> Visiting Fellow >> >>> University of Southampton, UK. >> >>> >> >>> -- >> >>> Gromacs Users mailing list >> >>> >> >>> * Please search the archive at http://www.gromacs.org/Support >> >>> /Mailing_Lists/GMX-Users_List before posting! >> >>> >> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>> >> >>> * For (un)subscribe requests visit >> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >>> send a mail to gmx-users-requ...@gromacs.org. >> >>> -- >> >>> Gromacs Users mailing list >> >>> >> >>> * Please search the archive at http://www.gromacs.org/Support >> >>> /Mailing_Lists/GMX-Users_List before posting! >> >>> >> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>> >> >>> * For (un)subscribe requests visit >> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >>> send a mail to gmx-users-requ...@gromacs.org. >> >>> >> >> -- >> >> Gromacs Users mailing list >> >> >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> * For (un)subscribe requests visit >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- >> > Dr Thomas Piggot >> > Visiting Fellow >> > University of Southampton, UK. >> > >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> -- >> Dr Thomas Piggot >> Visiting Fellow >> University of Southampton, UK. >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> ------------------------------ >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> End of gromacs.org_gmx-users Digest, Vol 156, Issue 73 >> ****************************************************** >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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