Re: [gmx-users] Drude force field
On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi wrote: > Thank you Dr. Lemkel, > > I don't have ions in my simulation. It's a neutral system with a protein in > membrane bilayer with solvent. > I have downloaded the force field (Drude FF for charmm FF in Gromacs > format). to run the simulation with charmm FF in "Gromacs 2019.3". > However, it seems the format of the file does not match with the current > version. > > In the web, > > Compile and install as you would any other (post-5.0) GROMACS version. If > you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will > not be accessible.* > > There are 5.0 and 5.1 series of Gromacs versions. Which one should I use? > > Or, it there a way to modify the force field format to use the current > version of Gromacs?, Then I will modify the format. > > Read the information at the previous link more carefully. You cannot use any released version of GROMACS. You must use the developmental version as instructed in that link. -Justin > > On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > > > > > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > > Dear users, > > > > > > I want to run a simulation with a polarizable force field. > > > > > > How and where can I get Drude force field for the current version of > > > Gromacs? > > > > Everything you need to know: > > > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > > > The implementation is not complete. If your system has ions, do not use > > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or > > OpenMM. The Drude model is still considered experimental, hence it is > > not officially supported yet. There have been a lot of snags along the > > way (mostly in my time to get the code up to par for official inclusion). > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > == > > > > -- > > 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. > -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] Xeon Gold + RTX 5000
Perfect, thanks a lot! We are less constrained by cost, so we'll go straight to 2080Ti. You guys already saved us a few grand here. ;) Alex On 7/17/2019 7:34 PM, Moir, Michael (MMoir) wrote: Alex, The motherboard I am using with the 9900K is the ASUS WS Z390 PRO. The PRO version has the extra PCIe controller. I am using two RTX 1070ti GPUs, and I can hear everyone snorting with derision, but with this configuration I get performance with 100,000 atoms of about 72 ns/day with 2019.1 which is adequate for my needs. I’ll upgrade to the 2080ti when the price drops to <$1000. Another tip is to get the highest speed memory that the motherboard will handle. It doesn’t make a huge difference, maybe 2-3% over the cheapest memory but it is something that is easy and low cost to do. Mike Sent from my iPhone On Jul 17, 2019, at 11:16 AM, Alex wrote: Gentlemen, thank you both! Michael, would you be able to suggest a specific motherboard that removes the bottleneck? We aren't really limited by price in this case and would prefer to get every bit of benefit out of the processing components, if possible. Thanks, Alex On 7/17/2019 10:44 AM, Moir, Michael (MMoir) wrote: This is not quite true. I certainly observed this degradation in performance using the 9900K with two GPUs as Szilárd states using a motherboard with one PCIe controller, but the limitation is from the motherboard not from the CPU. It is possible to obtain a motherboard that contains two PCIe controllers which overcomes this obstacle for not a whole lot more money. Mike -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Szilárd Páll Sent: Wednesday, July 17, 2019 8:14 AM To: Discussion list for GROMACS users Subject: [**EXTERNAL**] Re: [gmx-users] Xeon Gold + RTX 5000 Hi Alex, I've not had a chance to test the new 3rd gen Ryzen CPUs, but all public benchmarks out there point to the fact that they are a major improvement over the previous generation Ryzen -- which were already quite competitive for GPU-accelerated GROMACS runs compared to Intel, especially in perf/price. One caveat for dual-GPU setups on the i9 9900 or the Ryzen 3900X is that they don't have enough PCI lanes for peak CPU-GPU transfer (x8 for both of the GPUs) which will lead to a slightly less performance (I'd estimate <5-10%) in particular compared to i) having a single GPU plugged in into the machine ii) compare to CPUs like Threadripper or the i9 79xx series processors which have more PCIe lanes. However, if throughput is the goal, the ideal use-case especially for small simulation systems like <=50k atoms is to run e.g. 2 runs / GPU, hence 4 runs on a 2-GPU system case in which the impact of the aforementioned limitation will be further decreased. Cheers, -- Szilárd On Tue, Jul 16, 2019 at 7:18 PM Alex wrote: That is excellent information, thank you. None of us have dealt with AMD CPUs in a while, so would the combination of a Ryzen 3900X and two Quadro 2080 Ti be a good choice? Again, thanks! Alex On 7/16/2019 8:41 AM, Szilárd Páll wrote: Hi Alex, On Mon, Jul 15, 2019 at 8:53 PM Alex wrote: Hi all and especially Szilard! My glorious management asked me to post this here. One of our group members, an ex-NAMD guy, wants to use Gromacs for biophysics and the following basics have been spec'ed for him: CPU: Xeon Gold 6244 GPU: RTX 5000 or 6000 I'll be surprised if he runs systems with more than 50K particles. Could you please comment on whether this is a cost-efficient and reasonably powerful setup? Your past suggestions have been invaluable for us. That will be reasonably fast, but cost efficiency will be awful, to be honest: - that CPU is a ~$3000 part and won't perform much better than a $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which would be significantly faster. - Quadro cards also pretty low in bang for buck: a 2080 Ti will be close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit slower for at least another 1.5x less. Single run at a time or possibly multiple? The proposed (or any 8+ core) workstation CPU is fast enough in the majority of the simulations to pair well with two of those GPUs if used for two concurrent simulations. If that's a relevant use-case, I'd recommend two 2070 Super or 2080 cards. Cheers, -- Szilárd Thank you, Alex -- 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
Re: [gmx-users] Drude force field
I've got the following Error. It seems this version of Gromacs does not recognize the Drude force field format distributed by MacKerell. There are additional Terms like [anisotropic_polarization] , etc.. Gromacs read this as a residue name. Program gmx, VERSION 5.0.7 Source code file: /data/cluster/apps/gromacs/source/gromacs-5.0.7/src/gromacs/gmxpreprocess/resall.c, line: 488 Fatal error: in .rtp file in residue anisotropic_polarization at line: DBR6 BR6C6C1C5 1.8000 0.6000 0.6000 On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > Dear users, > > > > I want to run a simulation with a polarizable force field. > > > > How and where can I get Drude force field for the current version of > > Gromacs? > > Everything you need to know: > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > The implementation is not complete. If your system has ions, do not use > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or > OpenMM. The Drude model is still considered experimental, hence it is > not officially supported yet. There have been a lot of snags along the > way (mostly in my time to get the code up to par for official inclusion). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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.
Re: [gmx-users] Xeon Gold + RTX 5000
Alex, The motherboard I am using with the 9900K is the ASUS WS Z390 PRO. The PRO version has the extra PCIe controller. I am using two RTX 1070ti GPUs, and I can hear everyone snorting with derision, but with this configuration I get performance with 100,000 atoms of about 72 ns/day with 2019.1 which is adequate for my needs. I’ll upgrade to the 2080ti when the price drops to <$1000. Another tip is to get the highest speed memory that the motherboard will handle. It doesn’t make a huge difference, maybe 2-3% over the cheapest memory but it is something that is easy and low cost to do. Mike Sent from my iPhone > On Jul 17, 2019, at 11:16 AM, Alex wrote: > > Gentlemen, thank you both! > > Michael, would you be able to suggest a specific motherboard that removes the > bottleneck? We aren't really limited by price in this case and would prefer > to get every bit of benefit out of the processing components, if possible. > > Thanks, > > Alex > >> On 7/17/2019 10:44 AM, Moir, Michael (MMoir) wrote: >> This is not quite true. I certainly observed this degradation in >> performance using the 9900K with two GPUs as Szilárd states using a >> motherboard with one PCIe controller, but the limitation is from the >> motherboard not from the CPU. It is possible to obtain a motherboard that >> contains two PCIe controllers which overcomes this obstacle for not a whole >> lot more money. >> >> Mike >> >> -Original Message- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> On Behalf Of Szilárd Páll >> Sent: Wednesday, July 17, 2019 8:14 AM >> To: Discussion list for GROMACS users >> Subject: [**EXTERNAL**] Re: [gmx-users] Xeon Gold + RTX 5000 >> >> Hi Alex, >> >> I've not had a chance to test the new 3rd gen Ryzen CPUs, but all >> public benchmarks out there point to the fact that they are a major >> improvement over the previous generation Ryzen -- which were already >> quite competitive for GPU-accelerated GROMACS runs compared to Intel, >> especially in perf/price. >> >> One caveat for dual-GPU setups on the i9 9900 or the Ryzen 3900X is >> that they don't have enough PCI lanes for peak CPU-GPU transfer (x8 >> for both of the GPUs) which will lead to a slightly less performance >> (I'd estimate <5-10%) in particular compared to i) having a single GPU >> plugged in into the machine ii) compare to CPUs like Threadripper or >> the i9 79xx series processors which have more PCIe lanes. >> >> However, if throughput is the goal, the ideal use-case especially for >> small simulation systems like <=50k atoms is to run e.g. 2 runs / GPU, >> hence 4 runs on a 2-GPU system case in which the impact of the >> aforementioned limitation will be further decreased. >> >> Cheers, >> -- >> Szilárd >> >> >>> On Tue, Jul 16, 2019 at 7:18 PM Alex wrote: >>> That is excellent information, thank you. None of us have dealt with AMD >>> CPUs in a while, so would the combination of a Ryzen 3900X and two >>> Quadro 2080 Ti be a good choice? >>> >>> Again, thanks! >>> >>> Alex >>> >>> On 7/16/2019 8:41 AM, Szilárd Páll wrote: Hi Alex, > On Mon, Jul 15, 2019 at 8:53 PM Alex wrote: > Hi all and especially Szilard! > > My glorious management asked me to post this here. One of our group > members, an ex-NAMD guy, wants to use Gromacs for biophysics and the > following basics have been spec'ed for him: > > CPU: Xeon Gold 6244 > GPU: RTX 5000 or 6000 > > I'll be surprised if he runs systems with more than 50K particles. Could > you please comment on whether this is a cost-efficient and reasonably > powerful setup? Your past suggestions have been invaluable for us. That will be reasonably fast, but cost efficiency will be awful, to be honest: - that CPU is a ~$3000 part and won't perform much better than a $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which would be significantly faster. - Quadro cards also pretty low in bang for buck: a 2080 Ti will be close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit slower for at least another 1.5x less. Single run at a time or possibly multiple? The proposed (or any 8+ core) workstation CPU is fast enough in the majority of the simulations to pair well with two of those GPUs if used for two concurrent simulations. If that's a relevant use-case, I'd recommend two 2070 Super or 2080 cards. Cheers, -- Szilárd > Thank you, > > Alex > -- > 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. >>> -- >>>
Re: [gmx-users] Drude force field
Thank you Dr. Lemkel, I don't have ions in my simulation. It's a neutral system with a protein in membrane bilayer with solvent. I have downloaded the force field (Drude FF for charmm FF in Gromacs format). to run the simulation with charmm FF in "Gromacs 2019.3". However, it seems the format of the file does not match with the current version. In the web, Compile and install as you would any other (post-5.0) GROMACS version. If you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will not be accessible.* There are 5.0 and 5.1 series of Gromacs versions. Which one should I use? Or, it there a way to modify the force field format to use the current version of Gromacs?, Then I will modify the format. On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > Dear users, > > > > I want to run a simulation with a polarizable force field. > > > > How and where can I get Drude force field for the current version of > > Gromacs? > > Everything you need to know: > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > The implementation is not complete. If your system has ions, do not use > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or > OpenMM. The Drude model is still considered experimental, hence it is > not officially supported yet. There have been a lot of snags along the > way (mostly in my time to get the code up to par for official inclusion). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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.
Re: [gmx-users] Drude force field
Thank you. On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > Dear users, > > > > I want to run a simulation with a polarizable force field. > > > > How and where can I get Drude force field for the current version of > > Gromacs? > > Everything you need to know: > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > The implementation is not complete. If your system has ions, do not use > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or > OpenMM. The Drude model is still considered experimental, hence it is > not officially supported yet. There have been a lot of snags along the > way (mostly in my time to get the code up to par for official inclusion). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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.
Re: [gmx-users] Drude force field
On 7/17/19 8:39 PM, Myunggi Yi wrote: Dear users, I want to run a simulation with a polarizable force field. How and where can I get Drude force field for the current version of Gromacs? Everything you need to know: http://mackerell.umaryland.edu/charmm_drude_ff.shtml The implementation is not complete. If your system has ions, do not use GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or OpenMM. The Drude model is still considered experimental, hence it is not officially supported yet. There have been a lot of snags along the way (mostly in my time to get the code up to par for official inclusion). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
[gmx-users] Drude force field
Dear users, I want to run a simulation with a polarizable force field. How and where can I get Drude force field for the current version of Gromacs? Thank you. -- 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.
Re: [gmx-users] Xeon Gold + RTX 5000
Certainly. When I get home this evening I will post the information. Mike -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Alex Sent: Wednesday, July 17, 2019 11:16 AM To: gmx-us...@gromacs.org Subject: [**EXTERNAL**] Re: [gmx-users] Xeon Gold + RTX 5000 Gentlemen, thank you both! Michael, would you be able to suggest a specific motherboard that removes the bottleneck? We aren't really limited by price in this case and would prefer to get every bit of benefit out of the processing components, if possible. Thanks, Alex On 7/17/2019 10:44 AM, Moir, Michael (MMoir) wrote: > This is not quite true. I certainly observed this degradation in performance > using the 9900K with two GPUs as Szilárd states using a motherboard with one > PCIe controller, but the limitation is from the motherboard not from the CPU. > It is possible to obtain a motherboard that contains two PCIe controllers > which overcomes this obstacle for not a whole lot more money. > > Mike > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > On Behalf Of Szilárd Páll > Sent: Wednesday, July 17, 2019 8:14 AM > To: Discussion list for GROMACS users > Subject: [**EXTERNAL**] Re: [gmx-users] Xeon Gold + RTX 5000 > > Hi Alex, > > I've not had a chance to test the new 3rd gen Ryzen CPUs, but all > public benchmarks out there point to the fact that they are a major > improvement over the previous generation Ryzen -- which were already > quite competitive for GPU-accelerated GROMACS runs compared to Intel, > especially in perf/price. > > One caveat for dual-GPU setups on the i9 9900 or the Ryzen 3900X is > that they don't have enough PCI lanes for peak CPU-GPU transfer (x8 > for both of the GPUs) which will lead to a slightly less performance > (I'd estimate <5-10%) in particular compared to i) having a single GPU > plugged in into the machine ii) compare to CPUs like Threadripper or > the i9 79xx series processors which have more PCIe lanes. > > However, if throughput is the goal, the ideal use-case especially for > small simulation systems like <=50k atoms is to run e.g. 2 runs / GPU, > hence 4 runs on a 2-GPU system case in which the impact of the > aforementioned limitation will be further decreased. > > Cheers, > -- > Szilárd > > > On Tue, Jul 16, 2019 at 7:18 PM Alex wrote: >> That is excellent information, thank you. None of us have dealt with AMD >> CPUs in a while, so would the combination of a Ryzen 3900X and two >> Quadro 2080 Ti be a good choice? >> >> Again, thanks! >> >> Alex >> >> >> On 7/16/2019 8:41 AM, Szilárd Páll wrote: >>> Hi Alex, >>> >>> On Mon, Jul 15, 2019 at 8:53 PM Alex wrote: Hi all and especially Szilard! My glorious management asked me to post this here. One of our group members, an ex-NAMD guy, wants to use Gromacs for biophysics and the following basics have been spec'ed for him: CPU: Xeon Gold 6244 GPU: RTX 5000 or 6000 I'll be surprised if he runs systems with more than 50K particles. Could you please comment on whether this is a cost-efficient and reasonably powerful setup? Your past suggestions have been invaluable for us. >>> That will be reasonably fast, but cost efficiency will be awful, to be >>> honest: >>> - that CPU is a ~$3000 part and won't perform much better than a >>> $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which >>> would be significantly faster. >>> - Quadro cards also pretty low in bang for buck: a 2080 Ti will be >>> close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit >>> slower for at least another 1.5x less. >>> >>> Single run at a time or possibly multiple? The proposed (or any 8+ >>> core) workstation CPU is fast enough in the majority of the >>> simulations to pair well with two of those GPUs if used for two >>> concurrent simulations. If that's a relevant use-case, I'd recommend >>> two 2070 Super or 2080 cards. >>> >>> Cheers, >>> -- >>> Szilárd >>> >>> Thank you, Alex -- 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
Re: [gmx-users] Xeon Gold + RTX 5000
Gentlemen, thank you both! Michael, would you be able to suggest a specific motherboard that removes the bottleneck? We aren't really limited by price in this case and would prefer to get every bit of benefit out of the processing components, if possible. Thanks, Alex On 7/17/2019 10:44 AM, Moir, Michael (MMoir) wrote: This is not quite true. I certainly observed this degradation in performance using the 9900K with two GPUs as Szilárd states using a motherboard with one PCIe controller, but the limitation is from the motherboard not from the CPU. It is possible to obtain a motherboard that contains two PCIe controllers which overcomes this obstacle for not a whole lot more money. Mike -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Szilárd Páll Sent: Wednesday, July 17, 2019 8:14 AM To: Discussion list for GROMACS users Subject: [**EXTERNAL**] Re: [gmx-users] Xeon Gold + RTX 5000 Hi Alex, I've not had a chance to test the new 3rd gen Ryzen CPUs, but all public benchmarks out there point to the fact that they are a major improvement over the previous generation Ryzen -- which were already quite competitive for GPU-accelerated GROMACS runs compared to Intel, especially in perf/price. One caveat for dual-GPU setups on the i9 9900 or the Ryzen 3900X is that they don't have enough PCI lanes for peak CPU-GPU transfer (x8 for both of the GPUs) which will lead to a slightly less performance (I'd estimate <5-10%) in particular compared to i) having a single GPU plugged in into the machine ii) compare to CPUs like Threadripper or the i9 79xx series processors which have more PCIe lanes. However, if throughput is the goal, the ideal use-case especially for small simulation systems like <=50k atoms is to run e.g. 2 runs / GPU, hence 4 runs on a 2-GPU system case in which the impact of the aforementioned limitation will be further decreased. Cheers, -- Szilárd On Tue, Jul 16, 2019 at 7:18 PM Alex wrote: That is excellent information, thank you. None of us have dealt with AMD CPUs in a while, so would the combination of a Ryzen 3900X and two Quadro 2080 Ti be a good choice? Again, thanks! Alex On 7/16/2019 8:41 AM, Szilárd Páll wrote: Hi Alex, On Mon, Jul 15, 2019 at 8:53 PM Alex wrote: Hi all and especially Szilard! My glorious management asked me to post this here. One of our group members, an ex-NAMD guy, wants to use Gromacs for biophysics and the following basics have been spec'ed for him: CPU: Xeon Gold 6244 GPU: RTX 5000 or 6000 I'll be surprised if he runs systems with more than 50K particles. Could you please comment on whether this is a cost-efficient and reasonably powerful setup? Your past suggestions have been invaluable for us. That will be reasonably fast, but cost efficiency will be awful, to be honest: - that CPU is a ~$3000 part and won't perform much better than a $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which would be significantly faster. - Quadro cards also pretty low in bang for buck: a 2080 Ti will be close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit slower for at least another 1.5x less. Single run at a time or possibly multiple? The proposed (or any 8+ core) workstation CPU is fast enough in the majority of the simulations to pair well with two of those GPUs if used for two concurrent simulations. If that's a relevant use-case, I'd recommend two 2070 Super or 2080 cards. Cheers, -- Szilárd Thank you, Alex -- 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. -- 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.
[gmx-users] make manual fails
hi,so I say:prompt> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_C_COMPILER=gcc-7 -DCMAKE_CXX_COMPILER=g++-7 -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=/home/michael/local/gromacs-2019-3-bin -DGMX_BUILD_MANUAL=onprompt> make -j 4prompt> make install prompt> make manualmanual cannot be built because Sphinx expected minimum version 1.6.1 is not available although I seem to have version 1.8.4 (see below) prompt> apt policy python-sphinx python-sphinx: Installed: 1.8.4-1 Candidate: 1.8.4-1 Version table: *** 1.8.4-1 500 500 http://ftp.at.debian.org/debian buster/main amd64 Packages 500 http://ftp.at.debian.org/debian buster/main i386 Packages 100 /var/lib/dpkg/status anybody else seen this issue?cheers,michael === Why be happy when you could be normal? -- 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.
Re: [gmx-users] Xeon Gold + RTX 5000
This is not quite true. I certainly observed this degradation in performance using the 9900K with two GPUs as Szilárd states using a motherboard with one PCIe controller, but the limitation is from the motherboard not from the CPU. It is possible to obtain a motherboard that contains two PCIe controllers which overcomes this obstacle for not a whole lot more money. Mike -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Szilárd Páll Sent: Wednesday, July 17, 2019 8:14 AM To: Discussion list for GROMACS users Subject: [**EXTERNAL**] Re: [gmx-users] Xeon Gold + RTX 5000 Hi Alex, I've not had a chance to test the new 3rd gen Ryzen CPUs, but all public benchmarks out there point to the fact that they are a major improvement over the previous generation Ryzen -- which were already quite competitive for GPU-accelerated GROMACS runs compared to Intel, especially in perf/price. One caveat for dual-GPU setups on the i9 9900 or the Ryzen 3900X is that they don't have enough PCI lanes for peak CPU-GPU transfer (x8 for both of the GPUs) which will lead to a slightly less performance (I'd estimate <5-10%) in particular compared to i) having a single GPU plugged in into the machine ii) compare to CPUs like Threadripper or the i9 79xx series processors which have more PCIe lanes. However, if throughput is the goal, the ideal use-case especially for small simulation systems like <=50k atoms is to run e.g. 2 runs / GPU, hence 4 runs on a 2-GPU system case in which the impact of the aforementioned limitation will be further decreased. Cheers, -- Szilárd On Tue, Jul 16, 2019 at 7:18 PM Alex wrote: > > That is excellent information, thank you. None of us have dealt with AMD > CPUs in a while, so would the combination of a Ryzen 3900X and two > Quadro 2080 Ti be a good choice? > > Again, thanks! > > Alex > > > On 7/16/2019 8:41 AM, Szilárd Páll wrote: > > Hi Alex, > > > > On Mon, Jul 15, 2019 at 8:53 PM Alex wrote: > >> Hi all and especially Szilard! > >> > >> My glorious management asked me to post this here. One of our group > >> members, an ex-NAMD guy, wants to use Gromacs for biophysics and the > >> following basics have been spec'ed for him: > >> > >> CPU: Xeon Gold 6244 > >> GPU: RTX 5000 or 6000 > >> > >> I'll be surprised if he runs systems with more than 50K particles. Could > >> you please comment on whether this is a cost-efficient and reasonably > >> powerful setup? Your past suggestions have been invaluable for us. > > That will be reasonably fast, but cost efficiency will be awful, to be > > honest: > > - that CPU is a ~$3000 part and won't perform much better than a > > $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which > > would be significantly faster. > > - Quadro cards also pretty low in bang for buck: a 2080 Ti will be > > close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit > > slower for at least another 1.5x less. > > > > Single run at a time or possibly multiple? The proposed (or any 8+ > > core) workstation CPU is fast enough in the majority of the > > simulations to pair well with two of those GPUs if used for two > > concurrent simulations. If that's a relevant use-case, I'd recommend > > two 2070 Super or 2080 cards. > > > > Cheers, > > -- > > Szilárd > > > > > >> Thank you, > >> > >> Alex > >> -- > >> 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. -- 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.
Re: [gmx-users] Xeon Gold + RTX 5000
Hi Alex, I've not had a chance to test the new 3rd gen Ryzen CPUs, but all public benchmarks out there point to the fact that they are a major improvement over the previous generation Ryzen -- which were already quite competitive for GPU-accelerated GROMACS runs compared to Intel, especially in perf/price. One caveat for dual-GPU setups on the i9 9900 or the Ryzen 3900X is that they don't have enough PCI lanes for peak CPU-GPU transfer (x8 for both of the GPUs) which will lead to a slightly less performance (I'd estimate <5-10%) in particular compared to i) having a single GPU plugged in into the machine ii) compare to CPUs like Threadripper or the i9 79xx series processors which have more PCIe lanes. However, if throughput is the goal, the ideal use-case especially for small simulation systems like <=50k atoms is to run e.g. 2 runs / GPU, hence 4 runs on a 2-GPU system case in which the impact of the aforementioned limitation will be further decreased. Cheers, -- Szilárd On Tue, Jul 16, 2019 at 7:18 PM Alex wrote: > > That is excellent information, thank you. None of us have dealt with AMD > CPUs in a while, so would the combination of a Ryzen 3900X and two > Quadro 2080 Ti be a good choice? > > Again, thanks! > > Alex > > > On 7/16/2019 8:41 AM, Szilárd Páll wrote: > > Hi Alex, > > > > On Mon, Jul 15, 2019 at 8:53 PM Alex wrote: > >> Hi all and especially Szilard! > >> > >> My glorious management asked me to post this here. One of our group > >> members, an ex-NAMD guy, wants to use Gromacs for biophysics and the > >> following basics have been spec'ed for him: > >> > >> CPU: Xeon Gold 6244 > >> GPU: RTX 5000 or 6000 > >> > >> I'll be surprised if he runs systems with more than 50K particles. Could > >> you please comment on whether this is a cost-efficient and reasonably > >> powerful setup? Your past suggestions have been invaluable for us. > > That will be reasonably fast, but cost efficiency will be awful, to be > > honest: > > - that CPU is a ~$3000 part and won't perform much better than a > > $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which > > would be significantly faster. > > - Quadro cards also pretty low in bang for buck: a 2080 Ti will be > > close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit > > slower for at least another 1.5x less. > > > > Single run at a time or possibly multiple? The proposed (or any 8+ > > core) workstation CPU is fast enough in the majority of the > > simulations to pair well with two of those GPUs if used for two > > concurrent simulations. If that's a relevant use-case, I'd recommend > > two 2070 Super or 2080 cards. > > > > Cheers, > > -- > > Szilárd > > > > > >> Thank you, > >> > >> Alex > >> -- > >> 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.
Re: [gmx-users] decreased performance with free energy
Hi, Lower performe especially with GPUs is not unexpected, but what you report is unusually large. I suggest you post your mdp and log file, perhaps there are some things to improve. -- Szilárd On Wed, Jul 17, 2019 at 3:47 PM David de Sancho wrote: > Hi all > I have been doing some testing for Hamiltonian replica exchange using > Gromacs 2018.3 on a relatively simple system with 3000 atoms in a cubic > box. > For the modified hamiltonian I have simply modified the water interactions > by generating a typeB atom in the force field ffnonbonded.itp with > different parameters file and then creating a number of tpr files for > different lambda values as defined in the mdp files. The only difference > between mdp files for a simple NVT run and for the HREX runs are the > following lines: > > > ; H-REPLEX > > free-energy = yes > > init-lambda-state = 0 > > nstdhdl = 0 > > vdw_lambdas = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 > > I have tested for performance in the same machine and compared the standard > NVT run performance (~175 ns/day in 8 cores) with that for the free energy > tpr file (6.2 ns/day). > Is this performance loss what you would expect or are there any immediate > changes you can suggest to improve things? I have found a relatively old > post on this on Gromacs developers (https://redmine.gromacs.org/issues/742 > ), > but I am not sure whether it is the exact same problem. > Thanks, > > David > -- > 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.
Re: [gmx-users] rtx 2080 gpu
On Wed, Jul 17, 2019 at 2:13 PM Stefano Guglielmo < stefano.guglie...@unito.it> wrote: > Hi Benson, > thanks for your answer and sorry for my delay: in the meantime I had to > restore the OS. I obviously re-installed NVIDIA driver (430.64) and CUDA > 10.1, I re-compiled Gromacs 2019.2 with the following command: > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_SIMD=AVX2_256 -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DREGRESSIONTEST_DOWNLOAD=ON > > I did make test and I got 100% passed. but this is the log file: > > GROMACS: gmx mdrun, version 2019.2 > Executable: /usr/local/gromacs/bin/gmx > Data prefix: /usr/local/gromacs > Working dir: /home/stefano/CB2 > Process ID: 117020 > Command line: > gmx mdrun -deffnm cb2_trz2c3ohene -ntmpi 1 -pin on > > GROMACS version:2019.2 > Precision: single > Memory model: 64 bit > MPI library:thread_mpi > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) > GPU support:CUDA > SIMD instructions: AVX2_256 > FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128 > RDTSCP usage: enabled > TNG support:enabled > Hwloc support: disabled > Tracing support:disabled > C compiler: /usr/bin/cc GNU 4.8.5 > C compiler flags:-mavx2 -mfma -O3 -DNDEBUG -funroll-all-loops > -fexcess-precision=fast > C++ compiler: /usr/bin/c++ GNU 4.8.5 > C++ compiler flags: -mavx2 -mfma-std=c++11 -O3 -DNDEBUG > -funroll-all-loops -fexcess-precision=fast > CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler > driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on > Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1, > V10.1.168 > CUDA compiler > > flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;;; > > ;-mavx2;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; > CUDA driver:10.10 > CUDA runtime: N/A > > NOTE: Detection of GPUs failed. The API reported: > unknown error > GROMACS cannot run tasks on a GPU. > > Running on 1 node with total 32 cores, 64 logical cores, 0 compatible GPUs > Hardware detected: > CPU info: > Vendor: AMD > Brand: AMD Ryzen Threadripper 2990WX 32-Core Processor > Family: 23 Model: 8 Stepping: 2 > Features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf > misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp > sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 > Hardware topology: Basic > Sockets, cores, and logical processors: > Socket 0: [ 0 32] [ 1 33] [ 2 34] [ 3 35] [ 4 36] [ > 5 37] [ 6 38] [ 7 39] [ 16 48] [ 17 49] [ 18 50] [ 19 51] [ > 20 52] [ 21 53] [ 22 54] [ 23 55] [ 8 40] [ 9 41] [ 10 42] > [ 11 43] [ 12 44] [ 13 45] [ 14 46] [ 15 47] [ 24 56] [ 25 > 57] [ 26 58] [ 27 59] [ 28 60] [ 29 61] [ 30 62] [ 31 63] > > Do you have any suggestions? > > PS: I set SIMD option to AVX2_256 with an AMD Ryzen Threadripper 2990WX > 32-Core Processor: do you think it is a good idea? > In general, I suggest you stick to the defaults (which is not AVX2_128), this will typically be faster, in particular in CPU-only runs. The difference may not be significant in GPU-accelerated runs and (in some no too common cases it can even be a little bit faster with AVX2_256). Cheers, -- Szilárd > > Thanks again > Stefano > > Il giorno mer 10 lug 2019 alle ore 08:13 Benson Muite < > benson_mu...@emailplus.org> ha scritto: > > > Hi Stefano, > > > > What was your compilation command? (it may be helpful to add SIMD > > support appropriate to your processor > > > > > http://manual.gromacs.org/documentation/current/install-guide/index.html#simd-support > > ) > > > > Did you run make test after compiling? > > > > Benson > > > > On 7/10/19 1:18 AM, Stefano Guglielmo wrote: > > > Dear all, > > > I have a centOS machine equipped with two RTX 2080 cards, with nvidia > > > drivers 430.2; I installed cuda toolkit 10-1. when executing mdrun the > > log > > > reported the following message: > > > > > > GROMACS version:2019.2 > > > Precision: single > > > Memory model: 64 bit > > > MPI library:thread_mpi > > > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) > > > GPU support:CUDA > > > SIMD instructions: NONE > > > FFT library:fftw-3.3.8 > > > RDTSCP usage: disabled > > > TNG support:enabled > > > Hwloc support: disabled > > > Tracing support:disabled > > > C compiler: /usr/bin/cc GNU 4.8.5 > > > C compiler flags:-O3 -DNDEBUG -funroll-all-loops > > > -fexcess-precision=fast > > > C++ compiler:
Re: [gmx-users] rtx 2080 gpu
On Wed, Jul 10, 2019 at 2:18 AM Stefano Guglielmo < stefano.guglie...@unito.it> wrote: > Dear all, > I have a centOS machine equipped with two RTX 2080 cards, with nvidia > drivers 430.2; I installed cuda toolkit 10-1. when executing mdrun the log > reported the following message: > > GROMACS version:2019.2 > Precision: single > Memory model: 64 bit > MPI library:thread_mpi > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) > GPU support:CUDA > SIMD instructions: NONE > FFT library:fftw-3.3.8 > RDTSCP usage: disabled > TNG support:enabled > Hwloc support: disabled > Tracing support:disabled > C compiler: /usr/bin/cc GNU 4.8.5 > C compiler flags:-O3 -DNDEBUG -funroll-all-loops > -fexcess-precision=fast > C++ compiler: /usr/bin/c++ GNU 4.8.5 > C++ compiler flags: -std=c++11 -O3 -DNDEBUG -funroll-all-loops > -fexcess-precision=fast > CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler > driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on > Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1, > V10.1.168 > CUDA compiler > > flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;;; > ;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; > CUDA driver:10.20 > CUDA runtime: N/A > ˆˆˆ Something was not correct about your CUDA runtime installation. -- Szilárd > > NOTE: Detection of GPUs failed. The API reported: > unknown error > GROMACS cannot run tasks on a GPU. > > Does anyone have any suggestions? > Thanks in advance > Stefano > > > > -- > Stefano GUGLIELMO PhD > Assistant Professor of Medicinal Chemistry > Department of Drug Science and Technology > Via P. Giuria 9 > 10125 Turin, ITALY > ph. +39 (0)11 6707178 > -- > 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.
[gmx-users] decreased performance with free energy
Hi all I have been doing some testing for Hamiltonian replica exchange using Gromacs 2018.3 on a relatively simple system with 3000 atoms in a cubic box. For the modified hamiltonian I have simply modified the water interactions by generating a typeB atom in the force field ffnonbonded.itp with different parameters file and then creating a number of tpr files for different lambda values as defined in the mdp files. The only difference between mdp files for a simple NVT run and for the HREX runs are the following lines: > ; H-REPLEX > free-energy = yes > init-lambda-state = 0 > nstdhdl = 0 > vdw_lambdas = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 I have tested for performance in the same machine and compared the standard NVT run performance (~175 ns/day in 8 cores) with that for the free energy tpr file (6.2 ns/day). Is this performance loss what you would expect or are there any immediate changes you can suggest to improve things? I have found a relatively old post on this on Gromacs developers (https://redmine.gromacs.org/issues/742), but I am not sure whether it is the exact same problem. Thanks, David -- 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.
Re: [gmx-users] rtx 2080 gpu
Hi Benson, thanks for your answer and sorry for my delay: in the meantime I had to restore the OS. I obviously re-installed NVIDIA driver (430.64) and CUDA 10.1, I re-compiled Gromacs 2019.2 with the following command: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_SIMD=AVX2_256 -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DREGRESSIONTEST_DOWNLOAD=ON I did make test and I got 100% passed. but this is the log file: GROMACS: gmx mdrun, version 2019.2 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/stefano/CB2 Process ID: 117020 Command line: gmx mdrun -deffnm cb2_trz2c3ohene -ntmpi 1 -pin on GROMACS version:2019.2 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support:CUDA SIMD instructions: AVX2_256 FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128 RDTSCP usage: enabled TNG support:enabled Hwloc support: disabled Tracing support:disabled C compiler: /usr/bin/cc GNU 4.8.5 C compiler flags:-mavx2 -mfma -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 4.8.5 C++ compiler flags: -mavx2 -mfma-std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1, V10.1.168 CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;;; ;-mavx2;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; CUDA driver:10.10 CUDA runtime: N/A NOTE: Detection of GPUs failed. The API reported: unknown error GROMACS cannot run tasks on a GPU. Running on 1 node with total 32 cores, 64 logical cores, 0 compatible GPUs Hardware detected: CPU info: Vendor: AMD Brand: AMD Ryzen Threadripper 2990WX 32-Core Processor Family: 23 Model: 8 Stepping: 2 Features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 Hardware topology: Basic Sockets, cores, and logical processors: Socket 0: [ 0 32] [ 1 33] [ 2 34] [ 3 35] [ 4 36] [ 5 37] [ 6 38] [ 7 39] [ 16 48] [ 17 49] [ 18 50] [ 19 51] [ 20 52] [ 21 53] [ 22 54] [ 23 55] [ 8 40] [ 9 41] [ 10 42] [ 11 43] [ 12 44] [ 13 45] [ 14 46] [ 15 47] [ 24 56] [ 25 57] [ 26 58] [ 27 59] [ 28 60] [ 29 61] [ 30 62] [ 31 63] Do you have any suggestions? PS: I set SIMD option to AVX2_256 with an AMD Ryzen Threadripper 2990WX 32-Core Processor: do you think it is a good idea? Thanks again Stefano Il giorno mer 10 lug 2019 alle ore 08:13 Benson Muite < benson_mu...@emailplus.org> ha scritto: > Hi Stefano, > > What was your compilation command? (it may be helpful to add SIMD > support appropriate to your processor > > http://manual.gromacs.org/documentation/current/install-guide/index.html#simd-support > ) > > Did you run make test after compiling? > > Benson > > On 7/10/19 1:18 AM, Stefano Guglielmo wrote: > > Dear all, > > I have a centOS machine equipped with two RTX 2080 cards, with nvidia > > drivers 430.2; I installed cuda toolkit 10-1. when executing mdrun the > log > > reported the following message: > > > > GROMACS version:2019.2 > > Precision: single > > Memory model: 64 bit > > MPI library:thread_mpi > > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) > > GPU support:CUDA > > SIMD instructions: NONE > > FFT library:fftw-3.3.8 > > RDTSCP usage: disabled > > TNG support:enabled > > Hwloc support: disabled > > Tracing support:disabled > > C compiler: /usr/bin/cc GNU 4.8.5 > > C compiler flags:-O3 -DNDEBUG -funroll-all-loops > > -fexcess-precision=fast > > C++ compiler: /usr/bin/c++ GNU 4.8.5 > > C++ compiler flags: -std=c++11 -O3 -DNDEBUG -funroll-all-loops > > -fexcess-precision=fast > > CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda > compiler > > driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on > > Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1, > V10.1.168 > > CUDA compiler > > >
Re: [gmx-users] heat capacity collection
Thank you David, but I just had an issue with output file. I wanted to have heat-capacities as a data file, which I guess gromacs does not provide a separate output file for that. So I could mange to do that with my own script (calculating heat capacity from energy and temperature outpute data). On Tue, Jul 16, 2019 at 9:32 PM David van der Spoel wrote: > Den 2019-07-16 kl. 13:30, skrev Amin Rouy: > > Hi everyone, > > > > I try to collect the heat capacities from my set of simulations. I see > that > > the heat capacity through gmx energy -fluct_props does not provide an > > output file with the heat capacities. > > Any suggestion how can I collect them (or how to do with an script)? > > > > thanks > > > What kind of systems are these? > I have quite a few reference data for liquids on > http://virtualchemistry.org > These were done using the gmx dos program that computes quantum > corrections but this is not entirely trivial. > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > 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.
