[gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

[Justin Lemkul]

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:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Date:&nbsp;Thu, Jan 16, 2020 03:38 AM
> To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
> Cc:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Subject:&nbsp;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&nbsp; -f Fab.pdb -o Fab_processed.gro -water spce&nbsp; -inter&nbsp; -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

-- 
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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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