Christoph, Actually, once i got the <mdrun> <opts>-nt 8</opts> </mdrun>
into the settings.xml file, it all start moving along faster. Thank you so much for your help!! On Friday, April 2, 2021 at 11:19:13 PM UTC-4 Christoph Junghans wrote: > > > On Fri, Apr 2, 2021, 20:58 Satyen Dhamankar <[email protected]> wrote: > >> Christoph, >> >> I also ran some ibi tests on the urea-water tutorial example. >> I am running into the same issues. The IBI is running at an incredibly >> slow pace. From what I have gathered, it seems to be a problem when you >> have more than one bead type in the coarse-grained system that IBI gets >> incredibly slow. I have heard that tabulated potentials are incredibly slow >> in GMX... Could that be a contributing factor? >> > Tabulated interactions are slow but not more than a factor 2. > More bead types means more energy groups and that could be the issue, but > for multiple tables you need multiple energy groups. > You could try an older gromacs version... > But not many other users have reported that issue before, so I would > investigate more why gromacs is slow first. > > Christoph > >> >> On Friday, April 2, 2021 at 3:10:49 PM UTC-4 Satyen Dhamankar wrote: >> >>> Christoph, >>> >>> Thank you for the advice. >>> I have added -nt 12 in the following manner: >>> >>> <inverse> >>> <!-- 200*0.00831451 gromacs units --> >>> <kBT>1.66290</kBT> >>> <!-- use gromacs as simulation program --> >>> <program>gromacs</program> >>> <!-- gromacs specific options --> >>> <gromacs> >>> <!-- trash so many frames at the beginning --> >>> <equi_time>20</equi_time> >>> <!-- grid for table*.xvg !--> >>> <table_bins>0.002</table_bins> >>> <!-- cut the potential at this value (gromacs bug) --> >>> <pot_max>1000000</pot_max> >>> <!-- extend the tables to this value --> >>> <table_end>2.5</table_end> >>> <mdrun.opts>-nt 12</mdrun.opts> >>> </gromacs> >>> >>> however, i am getting the same message: >>> "Running on 1 node with total 28 cores, 28 logical cores" >>> and also runs on them >>> "Initializing Domain Decomposition on 28 ranks" >>> >>> I have attached my settings.xml file to this document (the only change i >>> have made is the -nt 12 part). >>> >>> >>> Speaking of, I made the change and wrote -nt 8 in the methanol tutorial, >>> and that one worked fine... >>> On Friday, April 2, 2021 at 10:20:55 AM UTC-4 Christoph Junghans wrote: >>> >>>> On Fri, Apr 2, 2021 at 7:16 AM Satyen Dhamankar <[email protected]> >>>> wrote: >>>> > >>>> > The gromacs run. It is strange because the spce ibi did not take as >>>> long. >>>> > I have attached my md.log file. After 2.5 hours, only 11999 steps >>>> were completed for a 3000 molecule simulation... >>>> Hmm, that might be more a question for the gromacs user mailing list. >>>> >>>> From your md.log, I see that Gromacs detected 28 cores >>>> "Running on 1 node with total 28 cores, 28 logical cores" >>>> and also runs on them >>>> "Initializing Domain Decomposition on 28 ranks" >>>> >>>> However you only requested 12 cores in your batch script: >>>> #SBATCH --ntasks-per-node=12 >>>> >>>> If the other cores are used by another user that could lead to >>>> performance problems as gromacs always runs as slow as the slowest >>>> core. >>>> gromacs has an option to limit the number cores, I believe "-nt 12", >>>> which you can hand over to gromacs from the xml file using >>>> cg.inverse.gromacs.mdrun.opts. >>>> >>>> Christoph >>>> >>>> > >>>> > On Friday, April 2, 2021 at 8:47:18 AM UTC-4 Christoph Junghans >>>> wrote: >>>> >> >>>> >> On Thu, Apr 1, 2021 at 21:57 Satyen Dhamankar <[email protected]> >>>> wrote: >>>> >>> >>>> >>> Hello, >>>> >>> >>>> >>> I have been running the propane IBI tutorial for propane. The IBI >>>> for propane takes quite some time to run. Step_001 has taken more than an >>>> hour to complete. >>>> >>> >>>> >>> This is the slurm script I have used to run this job: >>>> >>> >>>> >>> #!/bin/bash >>>> >>> # >>>> >>> #SBATCH --job-name=R1.5-CG # create a short name for your job >>>> >>> #SBATCH --qos=vshort # _quality of service_ >>>> >>> #SBATCH --nodes=1 # node count >>>> >>> #SBATCH --ntasks-per-node=12 # number of tasks per node >>>> >>> #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if >>>> multi-threaded tasks) >>>> >>> #SBATCH --mem=10GB # total memory requested >>>> >>> ##SBATCH --mem-per-cpu=4G # memory per cpu-core (4G per cpu-core is >>>> default) >>>> >>> #SBATCH --gres=gpu:1 # number of gpurs per node >>>> >>> #SBATCH --time=2:30:00 # total run time limit (HH:MM:SS) >>>> >>> #SBATCH --mail-type=all # send email on job start, end, and fail >>>> >>> module purge >>>> >>> module load intel/19.0/64/19.0.5.281 # for running gromacs >>>> >>> module load rh/devtoolset/7 >>>> >>> module load intel-mkl/2019.5/5/64 >>>> >>> module load cmake/3.x >>>> >>> # run the job >>>> >>> set -e >>>> >>> # keep track of the last executed command >>>> >>> trap 'last_command=$current_command; current_command=$BASH_COMMAND' >>>> DEBUG >>>> >>> # echo an error message before exiting >>>> >>> #trap 'echo "\"${last_command\" command filed with exit code $?." ' >>>> EXIT >>>> >>> bash run.sh >>>> >>> >>>> >>> Is taking such a long time for a sample IBI run normal? >>>> >> >>>> >> Where does it get stuck? In the gromacs run or after that? >>>> >> >>>> >> Christoph >>>> >>> >>>> >>> -- >>>> >>> Join us on Slack: https://join.slack.com/t/votca/signup >>>> >>> --- >>>> >>> You received this message because you are subscribed to the Google >>>> Groups "votca" group. >>>> >>> To unsubscribe from this group and stop receiving emails from it, >>>> send an email to [email protected]. >>>> >>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/votca/dadf2e09-20dd-4e63-8eaf-f748a3d390a3n%40googlegroups.com. >>>> >>>> >>>> >> >>>> >> -- >>>> >> Christoph Junghans >>>> >> Web: http://www.compphys.de >>>> > >>>> > -- >>>> > Join us on Slack: https://join.slack.com/t/votca/signup >>>> > --- >>>> > You received this message because you are subscribed to the Google >>>> Groups "votca" group. >>>> > To unsubscribe from this group and stop receiving emails from it, >>>> send an email to [email protected]. >>>> > To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/votca/0847a33c-636b-4a09-82c0-4fdd5a63c1e5n%40googlegroups.com. >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> Christoph Junghans >>>> Web: http://www.compphys.de >>>> >>> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/75b980dd-748f-4cfd-b0fc-b9a5ccb0741cn%40googlegroups.com >> >> <https://groups.google.com/d/msgid/votca/75b980dd-748f-4cfd-b0fc-b9a5ccb0741cn%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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