[gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?
Quyen V. Vu
vuqv.phys at gmail.com
Fri Jan 17 12:49:20 CET 2020
He said he ran a nearly identical simulation on two versions of gromacs but
I didn't think so,
in 2019.3 logs:
There are: 117860 Atoms
Atom distribution over 27 domains: av 4365 stddev 75 min 4289 max 4626
and 5.1 logs:
There are: 127790 Atoms
Atom distribution over 30 domains: av 4259 stddev 90 min 4193 max 4370
On Thu, Jan 16, 2020 at 11:37 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/16/20 11:57 AM, ZHANG Cheng wrote:
> > 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?
> >
>
> Try assigning the same number of PP and PME ranks in each run (30/6 in
> 5.1.1 and 27/9 in 2019.3). You're losing a lot of performance in
> communicating PME forces in the 2019.3 run. You may also want to try
> version 2020 to see if automatic detection has improved.
>
> -Justin
>
> >
> >
> > ------------------ Original ------------------
> > From: "ZHANG Cheng"<272699575 at qq.com>;
> > Date: Thu, Jan 16, 2020 07:58 AM
> > To: "ZHANG Cheng"<272699575 at qq.com>;"gromacs.org_gmx-users"<
> gromacs.org_gmx-users at 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"<272699575 at qq.com>;
> > Date: Thu, Jan 16, 2020 03:38 AM
> > To: "gromacs.org_gmx-users"<
> gromacs.org_gmx-users at maillist.sys.kth.se>;
> > Cc: "ZHANG Cheng"<272699575 at 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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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