Re: [gmx-users] Domain decomposition error while running coarse grained simulations on cluster
On 9/3/19 12:21 PM, Avijeet Kulshrestha wrote: Hi Justin, Thanks for replying to my query. Please see the error message below of log file. I have user-defined bonded, angle potential which I am providing by supplying tabulated data. I have position restraint also on backbone atoms of the protein that is only in the equilibration steps. *This is the error message of the log file. * Initializing Domain Decomposition on 8 ranks Dynamic load balancing: off Minimum cell size due to atom displacement: 0.546 nm Initial maximum inter charge-group distances: two-body bonded interactions: 12.145 nm, LJ-14, atoms 11 568 Here's your problem. You have pairs defined that are in excess of 12 nm, but they are assigned to a 1-4 interaction, so atoms that should be separated by three bonds. The user-defined potential shouldn't matter here unless you've added [pairs] to the topology. -Justin multi-body bonded interactions: 1.124 nm, G96Angle, atoms 3767 3770 Minimum cell size due to bonded interactions: 13.359 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 1.360 nm Estimated maximum distance required for P-LINCS: 1.360 nm Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 16.699 nm The maximum allowed number of cells is: X 0 Y 0 Z 1 --- Program: gmx mdrun, version 2018.6 Source file: src/gromacs/domdec/domdec.cpp (line 6594) MPI rank:0 (out of 8) Fatal error: There is no domain decomposition for 8 ranks that is compatible with the given box and a minimum cell size of 16.6989 nm Change the number of ranks or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition Please let me know what I can do to rectify it. On Mon, 2 Sep 2019 at 12:25, < 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: simulation termination problem (Prabir Khatua) 2. Re: wham analysis (Justin Lemkul) 3. Re: Domain decomposition error while running coarse grained simulations on cluster (Justin Lemkul) 4. Re: mdrun error (Justin Lemkul) 5. regarding changing the scale from ps to ns (sudha bhagwati) -- Message: 1 Date: Sun, 1 Sep 2019 12:10:04 -0500 From: Prabir Khatua To: gmx-us...@gromacs.org Subject: Re: [gmx-users] simulation termination problem Message-ID: < caobzxoogmnzmky8ddreyhfh7cjm9ycppo3fg6dmoe5fn-mg...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Thanks Justin. The problem has been fixed. On Fri, Aug 30, 2019 at 7:31 AM Justin Lemkul wrote: On 8/29/19 12:31 PM, Prabir Khatua wrote: Hello Gromacs users, I am trying to simulate a system of atom size 3,58,973 in gromacs 5.1.5. However, my simulation is being terminated in between with the following error. File input/output error: Cannot rename checkpoint file; maybe you are out of disk space? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I did not find any solution with respect to the error I was having in the mentioned website. What I found was related to memory issue. I do not know whether this is the same issue. The issue is not related to memory, it is (potentially) related to disk space. Do you have enough space on the filesystem to write output files? This can also happen sometimes when the filesystem blips. There's not much you can do about that except complain to your sysadmin about integrity of the filesystem. -Justin Please note that I was successfully able to run another simulation of a system having relatively less number of atoms with same script. The run command that I used for the simulation was mpirun -np 48 gmx_mpi mdrun -ntomp 1 -deffnm npt I ran both the simulations on two nodes having 24 cpu cores in each one of the nodes. I am also not able to figure out one issue. The log file of the system where the simulation was successfully completed showed Running on 2 nodes with total 48 cores, 48 logical cores, 0 compatible GPUs Cores per node: 24 Logical cores per node: 24 Compatible GPUs per node: 0 However, in the unsuccessful case, the log file showed Running on 1 node with total 24 cores, 24
Re: [gmx-users] The problem of utilizing multiple GPU
Hello Mark Abraham, Thank you very much for your reply. I will definitely check the webinar and gromacs document. But now I am confused and expect an direct solution. The workstation should have 18 cores each with 4 hyperthreads. The output of "lscpu" reads: Architecture: x86_64 CPU op-mode(s):32-bit, 64-bit Byte Order:Little Endian CPU(s):72 On-line CPU(s) list: 0-71 Thread(s) per core:2 Core(s) per socket:18 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family:6 Model: 85 Model name:Intel(R) Xeon(R) Gold 6150 CPU @ 2.70GHz Stepping: 4 CPU MHz: 2701.000 CPU max MHz: 2701. CPU min MHz: 1200. BogoMIPS: 5400.00 Virtualization:VT-x L1d cache: 32K L1i cache: 32K L2 cache: 1024K L3 cache: 25344K NUMA node0 CPU(s): 0-17,36-53 NUMA node1 CPU(s): 18-35,54-71 Now I don't want to do multiple simulations and just want to run a single simulation. When assigning the simulation to only one GPU (gmx mdrun -v -gpu_id 0 -deffnm md), the simulation performance is 90 ns/day. However, when I don't assign the GPU but let all GPU work by: gmx mdrun -v -deffnm md The simulation performance is only 2 ns/day. So what is correct command to make a full use of all GPUs and achieve the best performance (which I expect should be much higher than 90 ns/day with only one GPU)? Could you give me further suggestions and help? Best regards, Yeping -- From:Mark Abraham Sent At:2019 Sep. 4 (Wed.) 19:10 To:gromacs ; 孙业平 Cc:gromacs.org_gmx-users Subject:Re: [gmx-users] The problem of utilizing multiple GPU Hi, On Wed, 4 Sep 2019 at 12:54, sunyeping wrote: Dear everyone, I am trying to do simulation with a workstation with 72 core and 8 geforce 1080 GPUs. 72 cores, or just 36 cores each with two hyperthreads? (it matters because you might not want to share cores between simulations, which is what you'd get if you just assigned 9 hyperthreads per GPU and 1 GPU per simulation). When I do not assign a certain GPU with the command: gmx mdrun -v -deffnm md all GPUs are used and but the utilization of each GPU is extremely low (only 1-2 %), and the simulation will be finished after several months. Yep. Too many workers for not enough work means everyone spends time more time coordinating than working. This is likely to improve in GROMACS 2020 (beta out shortly). In contrast, when I assign the simulation task to only one GPU: gmx mdrun -v -gpu_id 0 -deffnm md the GPU utilization can reach 60-70%, and the simulation can be finished within a week. Even when I use only two GPU: Utilization is only a proxy - what you actually want to measure is the rate of simulation ie. ns/day. gmx mdrun -v -gpu_id 0,2 -deffnm md the GPU utilizations are very low and the simulation is very slow. That could be for a variety of reasons, which you could diagnose by looking at the performance report at the end of the log file, and comparing different runs. I think I may missuse the GPU for gromacs simulation. Could you tell me what is the correct way to use multiple GPUs? If you're happy running multiple simulations, then the easiest thing to do is to use the existing multi-simulation support to do mpirun -np 8 gmx_mpi -multidir dir0 dir1 dir2 ... dir7 and let mdrun handle the details. Otherwise you have to get involved in assigning a subset of the CPU cores and GPUs to each job that both runs fast and does not conflict. See the documentation for GROMACS for the version you're running e.g. http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node. You probably want to check out this webinar tomorrow https://bioexcel.eu/webinar-more-bang-for-your-buck-improved-use-of-gpu-nodes-for-gromacs-2018-2019-09-05/. Mark Best regards -- 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] Question about the pulling code
Dear All, I want to pulling a ligand out of the binding pocket using Gromacs 2019. The pulling code was: pull= yes pull_ncoords= 1 pull_coord1_type= umbrella pull_coord1_geometry= direction pull_ngroups= 1 pull_group1_name= Ligand pull_coord1_dim = Y N N pull-coord1-vec = 1 0 0 pull_coord1_rate= 0.0005 pull_coord1_k = 830 I think the reaction coordinate had been defined by COM of the pulling group (i.e the ligand) and the pulling direction vector (i.e 1 0 0), but why still need to provide two groups for pull_coord1_groups ? If provided, then the reaction coordinate was also defined by the COM of the two groups, is this right? How should I set up my pulling code with "pull_coord1_geometry= direction". Any suggestion would be appreciated! Best regards Sting -- 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] how to define a pair
Hi, I am performed a all-atom simulation of a membrane-protein system (the starting structure received from CHARMM-GUI server, using charmm36 FF). #include "toppar/charmm36.itp" [ defaults ]; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 2 yes 1.0 1.0 I want to add a pair between list of two atoms, say 10-500 (CA atoms). Lets say the distance between them is 0.800 nm. So I define my pairs in the following way, 10 500 1 (4*2.5*0.800**6) (4*2.5*0.800**12) ; where 2.5 is my epsilon. I get some error when I run the simulation (infinite force, exploding simulation). I suspect my definition of C6 and C12 is wrong. Any suggestions would be useful. -manuel -- 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] how to define a pair
Hi, I am performed a all-atom simulation of a membrane-protein system (the starting structure received from CHARMM-GUI server, using charmm36 FF). #include "toppar/charmm36.itp" [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 I want to add a pair between list of two atoms, say 10-500 (CA atoms). Lets say the distance between them is 0.800 nm. So I define my pairs in the following way, 10 500 1 (4*2.5*0.800**6) (4*2.5*0.800**12) ; where 2.5 is my epsilon. I get some error when I run the simulation (infinite force, exploding simulation). I suspect my definition of C6 and C12 is wrong. Any suggestions would be useful -manuel -- 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] The problem of utilizing multiple GPU
Hi, On Wed, 4 Sep 2019 at 12:54, sunyeping wrote: > Dear everyone, > > I am trying to do simulation with a workstation with 72 core and 8 geforce > 1080 GPUs. > 72 cores, or just 36 cores each with two hyperthreads? (it matters because you might not want to share cores between simulations, which is what you'd get if you just assigned 9 hyperthreads per GPU and 1 GPU per simulation). > When I do not assign a certain GPU with the command: > gmx mdrun -v -deffnm md > all GPUs are used and but the utilization of each GPU is extremely low > (only 1-2 %), and the simulation will be finished after several months. > Yep. Too many workers for not enough work means everyone spends time more time coordinating than working. This is likely to improve in GROMACS 2020 (beta out shortly). In contrast, when I assign the simulation task to only one GPU: > gmx mdrun -v -gpu_id 0 -deffnm md > the GPU utilization can reach 60-70%, and the simulation can be finished > within a week. Even when I use only two GPU: > Utilization is only a proxy - what you actually want to measure is the rate of simulation ie. ns/day. gmx mdrun -v -gpu_id 0,2 -deffnm md > > the GPU utilizations are very low and the simulation is very slow. > That could be for a variety of reasons, which you could diagnose by looking at the performance report at the end of the log file, and comparing different runs. > I think I may missuse the GPU for gromacs simulation. Could you tell me > what is the correct way to use multiple GPUs? > If you're happy running multiple simulations, then the easiest thing to do is to use the existing multi-simulation support to do mpirun -np 8 gmx_mpi -multidir dir0 dir1 dir2 ... dir7 and let mdrun handle the details. Otherwise you have to get involved in assigning a subset of the CPU cores and GPUs to each job that both runs fast and does not conflict. See the documentation for GROMACS for the version you're running e.g. http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node . You probably want to check out this webinar tomorrow https://bioexcel.eu/webinar-more-bang-for-your-buck-improved-use-of-gpu-nodes-for-gromacs-2018-2019-09-05/ . Mark > Best regards > -- > 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] The problem of utilizing multiple GPU
Dear everyone, I am trying to do simulation with a workstation with 72 core and 8 geforce 1080 GPUs. When I do not assign a certain GPU with the command: gmx mdrun -v -deffnm md all GPUs are used and but the utilization of each GPU is extremely low (only 1-2 %), and the simulation will be finished after several months. In contrast, when I assign the simulation task to only one GPU: gmx mdrun -v -gpu_id 0 -deffnm md the GPU utilization can reach 60-70%, and the simulation can be finished within a week. Even when I use only two GPU: gmx mdrun -v -gpu_id 0,2 -deffnm md the GPU utilizations are very low and the simulation is very slow. I think I may missuse the GPU for gromacs simulation. Could you tell me what is the correct way to use multiple GPUs? Best regards -- 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] REMD-error
Thank you for your email sir. On Wed, Sep 4, 2019 at 2:42 PM Mark Abraham wrote: > Hi, > > On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in > > > wrote: > > > Respected Mark Abraham, > > The command-line and the job > > submission script is given below > > > > #!/bin/bash > > #SBATCH -n 130 # Number of cores > > > > Per the docs, this is a guide to sbatch about how many (MPI) tasks you want > to run. It's not a core request. > > #SBATCH -N 5 # no of nodes > > > > This requires a certain number of nodes. So to implement both your > instructions, MPI has to start 26 tasks per node. That would make sense if > you had nodes with a multiple 26 cores. My guess is that your nodes have a > multiple of 16 cores, based on the error message. MPI saw that you asked to > allocate more tasks on cores than available cores, and decided not to set a > number of OpenMP threads per MPI task, so that fell back on a default, > which produced 16, which GROMACS can see doesn't make sense. > > If you want to use -N and -n, then you need to make a choice that makes > sense for the number of cores per node. Easier might be to use -n 130 and > -c 2 to express what I assume is your intent to have 2 cores per MPI task. > Now slurm+MPI can pass that message along properly to OpenMP. > > Your other message about -ntomp can only have come from running gmx_mpi_d > -ntmpi, so just a typo we don't need to worry about further. > > Mark > > #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM > > #SBATCH -p cpu # Partition to submit to > > #SBATCH -o hostname_%j.out # File to which STDOUT will be written > > #SBATCH -e hostname_%j.err # File to which STDERR will be written > > #loading gromacs > > module load gromacs/2018.4 > > #specifying work_dir > > WORKDIR=/home/chm_bratin/GMX_Projects/REMD/4wbu-REMD-inst-clust_1/stage-1 > > > > > > mpirun -np 130 gmx_mpi_d mdrun -v -s remd_nvt_next2.tpr -multidir equil0 > > equil1 equil2 equil3 equil4 equil5 equil6 equil7 equil8 equil9 equil10 > > equil11 equil12 equil13 equil14 equil15 equil16 equil17 equil18 equil19 > > equil20 equil21 equil22 equil23 equil24 equil25 equil26 equil27 equil28 > > equil29 equil30 equil31 equil32 equil33 equil34 equil35 equil36 equil37 > > equil38 equil39 equil40 equil41 equil42 equil43 equil44 equil45 equil46 > > equil47 equil48 equil49 equil50 equil51 equil52 equil53 equil54 equil55 > > equil56 equil57 equil58 equil59 equil60 equil61 equil62 equil63 equil64 > > -deffnm remd_nvt -cpi remd_nvt.cpt -append > > > > On Wed, Sep 4, 2019 at 2:13 PM Mark Abraham > > wrote: > > > > > Hi, > > > > > > We need to see your command line in order to have a chance of helping. > > > > > > Mark > > > > > > On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das < > > 177cy500.bra...@nitk.edu.in > > > > > > > wrote: > > > > > > > Dear all, > > > > I am running one REMD simulation with 65 replicas. I am > > using > > > > 130 cores for the simulation. I am getting the following error. > > > > > > > > Fatal error: > > > > Your choice of number of MPI ranks and amount of resources results in > > > using > > > > 16 > > > > OpenMP threads per rank, which is most likely inefficient. The > optimum > > is > > > > usually between 1 and 6 threads per rank. If you want to run with > this > > > > setup, > > > > specify the -ntomp option. But we suggest to change the number of MPI > > > > ranks. > > > > > > > > when I am using -ntomp option ...it is throwing another error > > > > > > > > Fatal error: > > > > Setting the number of thread-MPI ranks is only supported with > > thread-MPI > > > > and > > > > GROMACS was compiled without thread-MPI > > > > > > > > > > > > while GROMACS is compiled with threated-MPI... > > > > > > > > plerase help me in this regard. > > > > -- > > > > 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 > >
[gmx-users] Channelrhodopsin topology
Hello everyone, I got some troubles with topology setup for channelrhodopsin setup in membrane. It is first such difficult system I met at my short scientific way and in fact it blocks my progress. I am not sure if gromacs mailing list is the way I should call for help, but perhaps I will find some answers here. Channelrhodopsin consists of protein, ligand (retinal) bounded to protein and there should be membrane. I want to make simulations in charmm ff. I found nice topology created by prof. Jochen Hub, but unfortunatly it is in amber ff. I have attached protein to membrane via charmm-gui, but I had to cut off the retinal (charmm gui couldn't handle ligand conected to protein). So I get nice structure and topology for both protein and membrane. Later I wanted to add retinal to the system - I made it manually, by coppying coordinates to gro file and getting topology to retinal from swiss-param. There are two problems - one is retinal and protein lives on their own. They do't see each other. On tail of retinal and tail of Lys296 (to which retinal is connected) there are too many hydrgens instead of bond. I just deleted it manually, but still I don't have parameters for this particular atoms. I don't know where to find them, how to get them. Also I have some mess in topology, beacuse some parts come from charmm-gui and retinal from swiss param. Any ideas how to make nice and managable topology files? And how should I connect retinal with lys296? With best regards, Wiktor -- 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] REMD-error
Hi, On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Respected Mark Abraham, > The command-line and the job > submission script is given below > > #!/bin/bash > #SBATCH -n 130 # Number of cores > Per the docs, this is a guide to sbatch about how many (MPI) tasks you want to run. It's not a core request. #SBATCH -N 5 # no of nodes > This requires a certain number of nodes. So to implement both your instructions, MPI has to start 26 tasks per node. That would make sense if you had nodes with a multiple 26 cores. My guess is that your nodes have a multiple of 16 cores, based on the error message. MPI saw that you asked to allocate more tasks on cores than available cores, and decided not to set a number of OpenMP threads per MPI task, so that fell back on a default, which produced 16, which GROMACS can see doesn't make sense. If you want to use -N and -n, then you need to make a choice that makes sense for the number of cores per node. Easier might be to use -n 130 and -c 2 to express what I assume is your intent to have 2 cores per MPI task. Now slurm+MPI can pass that message along properly to OpenMP. Your other message about -ntomp can only have come from running gmx_mpi_d -ntmpi, so just a typo we don't need to worry about further. Mark #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM > #SBATCH -p cpu # Partition to submit to > #SBATCH -o hostname_%j.out # File to which STDOUT will be written > #SBATCH -e hostname_%j.err # File to which STDERR will be written > #loading gromacs > module load gromacs/2018.4 > #specifying work_dir > WORKDIR=/home/chm_bratin/GMX_Projects/REMD/4wbu-REMD-inst-clust_1/stage-1 > > > mpirun -np 130 gmx_mpi_d mdrun -v -s remd_nvt_next2.tpr -multidir equil0 > equil1 equil2 equil3 equil4 equil5 equil6 equil7 equil8 equil9 equil10 > equil11 equil12 equil13 equil14 equil15 equil16 equil17 equil18 equil19 > equil20 equil21 equil22 equil23 equil24 equil25 equil26 equil27 equil28 > equil29 equil30 equil31 equil32 equil33 equil34 equil35 equil36 equil37 > equil38 equil39 equil40 equil41 equil42 equil43 equil44 equil45 equil46 > equil47 equil48 equil49 equil50 equil51 equil52 equil53 equil54 equil55 > equil56 equil57 equil58 equil59 equil60 equil61 equil62 equil63 equil64 > -deffnm remd_nvt -cpi remd_nvt.cpt -append > > On Wed, Sep 4, 2019 at 2:13 PM Mark Abraham > wrote: > > > Hi, > > > > We need to see your command line in order to have a chance of helping. > > > > Mark > > > > On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das < > 177cy500.bra...@nitk.edu.in > > > > > wrote: > > > > > Dear all, > > > I am running one REMD simulation with 65 replicas. I am > using > > > 130 cores for the simulation. I am getting the following error. > > > > > > Fatal error: > > > Your choice of number of MPI ranks and amount of resources results in > > using > > > 16 > > > OpenMP threads per rank, which is most likely inefficient. The optimum > is > > > usually between 1 and 6 threads per rank. If you want to run with this > > > setup, > > > specify the -ntomp option. But we suggest to change the number of MPI > > > ranks. > > > > > > when I am using -ntomp option ...it is throwing another error > > > > > > Fatal error: > > > Setting the number of thread-MPI ranks is only supported with > thread-MPI > > > and > > > GROMACS was compiled without thread-MPI > > > > > > > > > while GROMACS is compiled with threated-MPI... > > > > > > plerase help me in this regard. > > > -- > > > 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
Re: [gmx-users] REMD-error
Respected Mark Abraham, The command-line and the job submission script is given below #!/bin/bash #SBATCH -n 130 # Number of cores #SBATCH -N 5 # no of nodes #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM #SBATCH -p cpu # Partition to submit to #SBATCH -o hostname_%j.out # File to which STDOUT will be written #SBATCH -e hostname_%j.err # File to which STDERR will be written #loading gromacs module load gromacs/2018.4 #specifying work_dir WORKDIR=/home/chm_bratin/GMX_Projects/REMD/4wbu-REMD-inst-clust_1/stage-1 mpirun -np 130 gmx_mpi_d mdrun -v -s remd_nvt_next2.tpr -multidir equil0 equil1 equil2 equil3 equil4 equil5 equil6 equil7 equil8 equil9 equil10 equil11 equil12 equil13 equil14 equil15 equil16 equil17 equil18 equil19 equil20 equil21 equil22 equil23 equil24 equil25 equil26 equil27 equil28 equil29 equil30 equil31 equil32 equil33 equil34 equil35 equil36 equil37 equil38 equil39 equil40 equil41 equil42 equil43 equil44 equil45 equil46 equil47 equil48 equil49 equil50 equil51 equil52 equil53 equil54 equil55 equil56 equil57 equil58 equil59 equil60 equil61 equil62 equil63 equil64 -deffnm remd_nvt -cpi remd_nvt.cpt -append On Wed, Sep 4, 2019 at 2:13 PM Mark Abraham wrote: > Hi, > > We need to see your command line in order to have a chance of helping. > > Mark > > On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das <177cy500.bra...@nitk.edu.in > > > wrote: > > > Dear all, > > I am running one REMD simulation with 65 replicas. I am using > > 130 cores for the simulation. I am getting the following error. > > > > Fatal error: > > Your choice of number of MPI ranks and amount of resources results in > using > > 16 > > OpenMP threads per rank, which is most likely inefficient. The optimum is > > usually between 1 and 6 threads per rank. If you want to run with this > > setup, > > specify the -ntomp option. But we suggest to change the number of MPI > > ranks. > > > > when I am using -ntomp option ...it is throwing another error > > > > Fatal error: > > Setting the number of thread-MPI ranks is only supported with thread-MPI > > and > > GROMACS was compiled without thread-MPI > > > > > > while GROMACS is compiled with threated-MPI... > > > > plerase help me in this regard. > > -- > > 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] REMD-error
Hi, We need to see your command line in order to have a chance of helping. Mark On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Dear all, > I am running one REMD simulation with 65 replicas. I am using > 130 cores for the simulation. I am getting the following error. > > Fatal error: > Your choice of number of MPI ranks and amount of resources results in using > 16 > OpenMP threads per rank, which is most likely inefficient. The optimum is > usually between 1 and 6 threads per rank. If you want to run with this > setup, > specify the -ntomp option. But we suggest to change the number of MPI > ranks. > > when I am using -ntomp option ...it is throwing another error > > Fatal error: > Setting the number of thread-MPI ranks is only supported with thread-MPI > and > GROMACS was compiled without thread-MPI > > > while GROMACS is compiled with threated-MPI... > > plerase help me in this regard. > -- > 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.
