[gmx-users] REMD
Hi, I have some doubt regarding REMD simulation. 1. In the .mdp file of each replica is it necessary to keep the gen-temp constant? as example: 300 k is the lowest temp of REMD simulation. Is it necessary to keep the gen-temp=300 in each replica. 2. Is it necessary to provide -replex flag during the equilbration phase of REMD simulation -- 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] Regarding OH, HH vector distribution
Thanks Sir, I did like that only, Now how can I make the distribution plot for these vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. But results is not proper. Can you suggest me regarding this? Thank you On Tue, Jul 30, 2019, 17:27 David van der Spoel wrote: > Den 2019-07-30 kl. 07:55, skrev Omkar Singh: > > Hi, > > I did by "gmx gangle ..." command. But I am not getting good result, > > because I have a doubt in ndx file. Can you help me for making ndx > file. > > How should I select the atom for vectors. > For OH it should be > 1 2 > 1 3 > 4 5 > 4 6 > 7 8 > 7 9 > etc., assuming a three particle water model with atoms O H H. > For HH it should be > 2 3 > 5 6 > 8 9 > etc. > A simple script would do it. The dipole vector is somewhat harder. > > Thanks > > > > On Mon, Jul 29, 2019, 22:50 David van der Spoel > > wrote: > > > >> Den 2019-07-29 kl. 18:26, skrev Omkar Singh: > >>> Hi, > >>> Meaning is that If I want to calculate angle between OH, HH and dip > >> vector > >>> with positive Z-axis. How can I make index file for this issue? And is > it > >>> possible that the angle distribution of these vectors for bulk water > >>> aproximatly linear. Hope now question is clear. > >> Probably. Check gmx gangle -g2 z > >>> > >>> Thanks > >>> > >>> On Mon, Jul 29, 2019, 16:33 David van der Spoel > >>> wrote: > >>> > Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > > Hello everyone, > > Is it possible that the probability distribution of HH, OH vector for > bulk > > water is approximately linear? > > > What do you mean? > > -- > 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. > > >> > >> > >> -- > >> 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. > >> > > > -- > 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.
Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm
On Tue, Jul 30, 2019 at 3:29 PM Carlos Navarro
wrote:
>
> Hi all,
> First of all, thanks for all your valuable inputs!!.
> I tried Szilárd suggestion (multi simulations) with the following commands
> (using a single node):
>
> EXE="mpirun -np 4 gmx_mpi mdrun "
>
> cd $WORKDIR0
> #$DO_PARALLEL
> $EXE -s 4q.tpr -deffnm 4q -dlb yes -resethway -multidir 1 2 3 4
> And I noticed that the performance went from 37,32,23,22 ns/day to ~42
> ns/day in all four simulations. I check that the 80 processors were been
> used a 100% of the time, while the gpu was used about a 50% (from a 70%
> when running a single simulation in the node where I obtain a performance
> of ~50 ns/day).
Great!
Note that optimizing hardware utilization doesn't always maximize performance.
Also, manual launches with pinoffset/pinstride will give exactly the
same performance as the multi runs *if* you get the affinities right.
In your original commands you tried to use 20 of the 80 threads/rank,
but you offset the runs only by 10 (hardware threads) which means that
runs were overlapping and interfering with each other as well as
ending up under-utilizing the hardware.
> So overall I'm quite happy with the performance I'm getting now; and
> honestly, I don't know if at some point I can get the same performance
> (running 4 jobs) that I'm getting running just one.
No, but you _may_ get a bit more aggregate performance if you run 8
concurrent jobs. Also, you cna try 1 thread per core ("mpirun -np 4
gmx mdrun_mpi -multi 4 -ntomp 10 -pin on to use only half of the
threads),
Cheers,
--
Szilárd
> Best regards,
> Carlos
>
> ——
> Carlos Navarro Retamal
> Bioinformatic Engineering. PhD.
> Postdoctoral Researcher in Center of Bioinformatics and Molecular
> Simulations
> Universidad de Talca
> Av. Lircay S/N, Talca, Chile
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
> On July 29, 2019 at 6:11:31 PM, Mark Abraham (mark.j.abra...@gmail.com)
> wrote:
>
> Hi,
>
> Yes and the -nmpi I copied from Carlos's post is ineffective - use -ntmpi
>
> Mark
>
>
> On Mon., 29 Jul. 2019, 15:15 Justin Lemkul, wrote:
>
> >
> >
> > On 7/29/19 8:46 AM, Carlos Navarro wrote:
> > > Hi Mark,
> > > I tried that before, but unfortunately in that case (removing
> —gres=gpu:1
> > > and including in each line the -gpu_id flag) for some reason the jobs
> are
> > > run one at a time (one after the other), so I can’t use properly the
> > whole
> > > node.
> > >
> >
> > You need to run all but the last mdrun process in the background (&).
> >
> > -Justin
> >
> > > ——
> > > Carlos Navarro Retamal
> > > Bioinformatic Engineering. PhD.
> > > Postdoctoral Researcher in Center of Bioinformatics and Molecular
> > > Simulations
> > > Universidad de Talca
> > > Av. Lircay S/N, Talca, Chile
> > > E: carlos.navarr...@gmail.com or cnava...@utalca.cl
> > >
> > > On July 29, 2019 at 11:48:21 AM, Mark Abraham (mark.j.abra...@gmail.com)
> > > wrote:
> > >
> > > Hi,
> > >
> > > When you use
> > >
> > > DO_PARALLEL=" srun --exclusive -n 1 --gres=gpu:1 "
> > >
> > > then the environment seems to make sure only one GPU is visible. (The
> log
> > > files report only finding one GPU.) But it's probably the same GPU in
> > each
> > > case, with three remaining idle. I would suggest not using --gres unless
> > > you can specify *which* of the four available GPUs each run can use.
> > >
> > > Otherwise, don't use --gres and use the facilities built into GROMACS,
> > e.g.
> > >
> > > $DO_PARALLEL $EXE -s eq6.tpr -deffnm eq6-20 -nmpi 1 -pin on -pinoffset 0
> > > -ntomp 20 -gpu_id 0
> > > $DO_PARALLEL $EXE -s eq6.tpr -deffnm eq6-20 -nmpi 1 -pin on -pinoffset
> 10
> > > -ntomp 20 -gpu_id 1
> > > $DO_PARALLEL $EXE -s eq6.tpr -deffnm eq6-20 -nmpi 1 -pin on -pinoffset
> 20
> > > -ntomp 20 -gpu_id 2
> > > etc.
> > >
> > > Mark
> > >
> > > On Mon, 29 Jul 2019 at 11:34, Carlos Navarro > >
> > > wrote:
> > >
> > >> Hi Szilárd,
> > >> To answer your questions:
> > >> **are you trying to run multiple simulations concurrently on the same
> > >> node or are you trying to strong-scale?
> > >> I'm trying to run multiple simulations on the same node at the same
> > time.
> > >>
> > >> ** what are you simulating?
> > >> Regular and CompEl simulations
> > >>
> > >> ** can you provide log files of the runs?
> > >> In the following link are some logs files:
> > >> https://www.dropbox.com/s/7q249vbqqwf5r03/Archive.zip?dl=0.
> > >> In short, alone.log -> single run in the node (using 1 gpu).
> > >> multi1/2/3/4.log ->4 independent simulations ran at the same time in a
> > >> single node. In all cases, 20 cpus are used.
> > >> Best regards,
> > >> Carlos
> > >>
> > >> El jue., 25 jul. 2019 a las 10:59, Szilárd Páll (<
> > pall.szil...@gmail.com>)
> > >> escribió:
> > >>
> > >>> Hi,
> > >>>
> > >>> It is not clear to me how are you trying to set up your runs, so
> > >>> please provide some details:
> > >>> - are you trying to run multiple simulations concurrently on the same
> > >>> node or are you trying to
[gmx-users] clashes after energy minimization - Ser2 multiple copies
Hi all I have been having trouble setting up a peptide+water simulation system due to the appearance of clashes in an energy minimization. Trying to pin down the origin of the problem I have found that a minimum system that reproduces my problem is a box with multiple copies of an unblocked serine dipeptide, which I am simulating using a combination of an Amber force field and TIP3P water. I have created a gist in case anyone could please help. https://gist.github.com/daviddesancho/00b23264fed0b6d20ec4e26e7d7810e7 At some point in the minimization, the energy drops asymptotically (also, the forces become massive, ~1e+07). Surprisingly, this does not occur when the number of copies of the dipeptide is N=1, 2 or 3. The resulting minimized structure has a cycle formed by atoms in the C-terminal serine, and one of the carboxylic oxygens overlaps with the alcoholic hydrogen. So far, I have been able to reproduce this with different force fields from the Amber family and the drop in the energy seems easy to rationalize, based on the parameters. The sidechain hydrogen (HG) and oxygen (OC1) have opposite charges, while the hydrogen has 0 sigma and epsilon. Hence the interaction energy of the hydrogen will be zero and the Coulomb term will be maximized for r_OH=0. No surprise, then that they attract each other. But why do they clash only when there are 4 molecules around? I have checked different box sizes and initial configurations to no avail. Also, adding water and ions to neutralize the box and increase charge screening does not change the outcome qualitatively (although it makes the visualization trickier). As always, all help greatly appreciated, 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] performance issues running gromacs with more than 1 gpu card in slurm
Hi all, First of all, thanks for all your valuable inputs!!. I tried Szilárd suggestion (multi simulations) with the following commands (using a single node): EXE="mpirun -np 4 gmx_mpi mdrun " cd $WORKDIR0 #$DO_PARALLEL $EXE -s 4q.tpr -deffnm 4q -dlb yes -resethway -multidir 1 2 3 4 And I noticed that the performance went from 37,32,23,22 ns/day to ~42 ns/day in all four simulations. I check that the 80 processors were been used a 100% of the time, while the gpu was used about a 50% (from a 70% when running a single simulation in the node where I obtain a performance of ~50 ns/day). So overall I'm quite happy with the performance I'm getting now; and honestly, I don't know if at some point I can get the same performance (running 4 jobs) that I'm getting running just one. Best regards, Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center of Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca, Chile E: carlos.navarr...@gmail.com or cnava...@utalca.cl On July 29, 2019 at 6:11:31 PM, Mark Abraham (mark.j.abra...@gmail.com) wrote: Hi, Yes and the -nmpi I copied from Carlos's post is ineffective - use -ntmpi Mark On Mon., 29 Jul. 2019, 15:15 Justin Lemkul, wrote: > > > On 7/29/19 8:46 AM, Carlos Navarro wrote: > > Hi Mark, > > I tried that before, but unfortunately in that case (removing —gres=gpu:1 > > and including in each line the -gpu_id flag) for some reason the jobs are > > run one at a time (one after the other), so I can’t use properly the > whole > > node. > > > > You need to run all but the last mdrun process in the background (&). > > -Justin > > > —— > > Carlos Navarro Retamal > > Bioinformatic Engineering. PhD. > > Postdoctoral Researcher in Center of Bioinformatics and Molecular > > Simulations > > Universidad de Talca > > Av. Lircay S/N, Talca, Chile > > E: carlos.navarr...@gmail.com or cnava...@utalca.cl > > > > On July 29, 2019 at 11:48:21 AM, Mark Abraham (mark.j.abra...@gmail.com) > > wrote: > > > > Hi, > > > > When you use > > > > DO_PARALLEL=" srun --exclusive -n 1 --gres=gpu:1 " > > > > then the environment seems to make sure only one GPU is visible. (The log > > files report only finding one GPU.) But it's probably the same GPU in > each > > case, with three remaining idle. I would suggest not using --gres unless > > you can specify *which* of the four available GPUs each run can use. > > > > Otherwise, don't use --gres and use the facilities built into GROMACS, > e.g. > > > > $DO_PARALLEL $EXE -s eq6.tpr -deffnm eq6-20 -nmpi 1 -pin on -pinoffset 0 > > -ntomp 20 -gpu_id 0 > > $DO_PARALLEL $EXE -s eq6.tpr -deffnm eq6-20 -nmpi 1 -pin on -pinoffset 10 > > -ntomp 20 -gpu_id 1 > > $DO_PARALLEL $EXE -s eq6.tpr -deffnm eq6-20 -nmpi 1 -pin on -pinoffset 20 > > -ntomp 20 -gpu_id 2 > > etc. > > > > Mark > > > > On Mon, 29 Jul 2019 at 11:34, Carlos Navarro > > > wrote: > > > >> Hi Szilárd, > >> To answer your questions: > >> **are you trying to run multiple simulations concurrently on the same > >> node or are you trying to strong-scale? > >> I'm trying to run multiple simulations on the same node at the same > time. > >> > >> ** what are you simulating? > >> Regular and CompEl simulations > >> > >> ** can you provide log files of the runs? > >> In the following link are some logs files: > >> https://www.dropbox.com/s/7q249vbqqwf5r03/Archive.zip?dl=0. > >> In short, alone.log -> single run in the node (using 1 gpu). > >> multi1/2/3/4.log ->4 independent simulations ran at the same time in a > >> single node. In all cases, 20 cpus are used. > >> Best regards, > >> Carlos > >> > >> El jue., 25 jul. 2019 a las 10:59, Szilárd Páll (< > pall.szil...@gmail.com>) > >> escribió: > >> > >>> Hi, > >>> > >>> It is not clear to me how are you trying to set up your runs, so > >>> please provide some details: > >>> - are you trying to run multiple simulations concurrently on the same > >>> node or are you trying to strong-scale? > >>> - what are you simulating? > >>> - can you provide log files of the runs? > >>> > >>> Cheers, > >>> > >>> -- > >>> Szilárd > >>> > >>> On Tue, Jul 23, 2019 at 1:34 AM Carlos Navarro > >>> wrote: > No one can give me an idea of what can be happening? Or how I can > > solve > >>> it? > Best regards, > Carlos > > —— > Carlos Navarro Retamal > Bioinformatic Engineering. PhD. > Postdoctoral Researcher in Center of Bioinformatics and Molecular > Simulations > Universidad de Talca > Av. Lircay S/N, Talca, Chile > E: carlos.navarr...@gmail.com or cnava...@utalca.cl > > On July 19, 2019 at 2:20:41 PM, Carlos Navarro ( > >>> carlos.navarr...@gmail.com) > wrote: > > Dear gmx-users, > I’m currently working in a server where each node posses 40 physical > >>> cores > (40 threads) and 4 Nvidia-V100. > When I launch a single job (1 simulation using a single gpu card) I > >> get a > performance
Re: [gmx-users] Regarding OH, HH vector distribution
Den 2019-07-30 kl. 07:55, skrev Omkar Singh: Hi, I did by "gmx gangle ..." command. But I am not getting good result, because I have a doubt in ndx file. Can you help me for making ndx file. How should I select the atom for vectors. For OH it should be 1 2 1 3 4 5 4 6 7 8 7 9 etc., assuming a three particle water model with atoms O H H. For HH it should be 2 3 5 6 8 9 etc. A simple script would do it. The dipole vector is somewhat harder. Thanks On Mon, Jul 29, 2019, 22:50 David van der Spoel wrote: Den 2019-07-29 kl. 18:26, skrev Omkar Singh: Hi, Meaning is that If I want to calculate angle between OH, HH and dip vector with positive Z-axis. How can I make index file for this issue? And is it possible that the angle distribution of these vectors for bulk water aproximatly linear. Hope now question is clear. Probably. Check gmx gangle -g2 z Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel wrote: Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- 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. -- 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. -- 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.
Re: [gmx-users] simulation on 2 gpus
Kevin, Mark, thanks for sharing advices and experience. I am facing some strange behaviour trying to run with the two gpus: there are some combinations that "simply" make the system crash (the workstation turns off after few seconds of running); in particular the following runs: gmx mdrun -deffnm run (-gpu_id 01) -pin on which produces the following log "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: 10.10 Running on 1 node with total 32 cores, 64 logical cores, 2 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] GPU info: Number of GPUs detected: 2 #0: NVIDIA GeForce RTX 2080 Ti, compute cap.: 7.5, ECC: no, stat: compatible #1: NVIDIA GeForce RTX 2080 Ti, compute cap.: 7.5, ECC: no, stat: compatible ... Using 16 MPI threads Using 4 OpenMP threads per tMPI thread On host pcpharm018 2 GPUs selected for this run. Mapping of GPU IDs to the 16 GPU tasks in the 16 ranks on this node: PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1 PP tasks will do (non-perturbed) short-ranged and most bonded interactions on the GPU Pinning threads with an auto-selected logical core stride of 1" Running the following command seems to work without crashing, with 1 tmpi and 32 omp threads on 1 gpu only: gmx mdrun -deffnm run -gpu_id 01 -pin on -pinstride 1 -pinoffset 32 -ntmpi 1. The most efficient way to run a single run seems to be produced by: gmx mdrun -deffnm run -gpu_id 0 -ntmpi 1 -ntomp 28 which makes 86 ns/day for a system of about 100K atoms (1000 res. protein with membrane and water). I also tried to run two independent simulations, and again with the following commands the system crashes: gmx mdrun -deffnm run1 -gpu_id 1 -pin on -pinstride 1 -pinoffset 32 -ntomp 32 -ntmpi 1 gmx mdrun -deffnm run0 -gpu_id 0 -pin on -pinstride 1 -pinoffset 0 -ntomp 32 -ntmpi 1 with the log "Running on 1 node with total 32 cores, 64 logical cores, 2 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] GPU info: Number of GPUs detected: 2 #0: NVIDIA GeForce RTX 2080 Ti, compute cap.: 7.5, ECC: no, stat: compatible #1: NVIDIA GeForce RTX 2080 Ti, compute cap.: 7.5, ECC: no, stat: compatible ... Using 1 MPI thread
