On 1/15/20 6:58 PM, ZHANG Cheng wrote:
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 ?
It doesn't look like either of those runs actually finished, and you have very frequent restarts from checkpoint files, so I don't see performance statistics. Relevant information will be printed in an obvious summary at the end of the output.
Try running a very short simulation with each version that runs to completion and look at the end of the .log file.
Also note that at least in version 5.1, you are not compiling GROMACS for maximum performance.
-Justin
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
-- ================================================== 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.
