Many thanks for Justin's advice for assigning the same number of PP and PME ranks in each run (30/6 in 5.1.1 and 27/9 in 2019.3). Sorry I am not familiar with these kind of settings, can I ask how to do this exactly? e.g. how to change "gmx mdrun -deffnm md_0_1 -cpi -append" ?
------------------ Original ------------------ From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 17, 2020 00:57 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re:Re:Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1? I have re-run the MD, with only 2 ps in both version. Indeed, the Version 2019 is far slower than the Version 5.1.1. Version 2019 needs 114.111 hours to complete 1 ns, while Version 5.1.1 only needs 6.362 hours to complete 1 ns. The new logs files are at https://github.com/lanselibai/gromacs-20200116 The MD is run on our HPC cluster. So I personally could not compile it. Is there still some way to get equivalent performance for the Version 2019? ------------------ Original ------------------ From: "ZHANG Cheng"<272699...@qq.com>; Date: Thu, Jan 16, 2020 07:58 AM To: "ZHANG Cheng"<272699...@qq.com>;"gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re:Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1? Hi Justin, what kind of information should I look at in the log files? They are too big to paste here. Would it be possible if you can see them at https://github.com/lanselibai/gromacs-20200115 ? Thank you! ------------------ Original ------------------ From: "ZHANG Cheng"<272699...@qq.com>; Date: Thu, Jan 16, 2020 03:38 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1? I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and production run, respectively. Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can do in the "VERSION 2019.3" so as to accelerate the MD? I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html The commands I used are listed below. gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce -inter -ignh -merge interactive gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1 gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05 (Afterwards, using the HPC to run) gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr gerun mdrun_mpi -v -deffnm em gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro gerun mdrun_mpi -deffnm nvt gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro gerun mdrun_mpi -deffnm npt gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro gmx mdrun -deffnm md_0_1 -cpi -append -- 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.