[FLASH-USERS] MORE nodes MORE time on HPC
Hansen, Eddie
ehansen at pas.rochester.edu
Fri Jun 17 15:26:12 EDT 2022
Hello,
Just to add to Ryan's very helpful insights, the Grid_advanceDiffusion routine is the main routine for all implicit diffusion solves (thermal conduction and radiation transport). FLASH effectively just sets up or defines the diffusion problems and the HYPRE library does all the hard work.
It's not surprising that with 20 radiation groups, the code spends a lot of time here. But with more cores taking longer, it does seem like the version of HYPRE you have might not be parallelized.
--
Eddie Hansen | Research Scientist
Flash Center for Computational Science
Dept. of Physics and Astronomy
University of Rochester, Rochester, NY
Cell 607-341-6126 | flash.rochester.edu
(he / him / his)
________________________________
From: flash-users <flash-users-bounces at flash.rochester.edu> on behalf of Ryan Farber <rjfarber at umich.edu>
Sent: Friday, June 17, 2022 3:12:30 PM
To: 赵旭 <xuzhao1994 at sjtu.edu.cn>
Cc: flash-users <flash-users at flash.rochester.edu>
Subject: Re: [FLASH-USERS] MORE nodes MORE time on HPC
Hi Zhao,
I'll admit I haven't used the modules you're using so I can't say much on the performance you've observing vs expected. My guess is that there are versions of HYPRE with and without parallel support and possibly yours is operating without parallel support?
If you check towards the end of the log files it specifies the percentage of time different routines took up. For the one node case, 47% of the evolution time is spent in "RadTrans" most of which occurs in "Grid_advanceDiffusion" of which most of that time is spent in gr_hypre_solve (~27% of total walltime) next most expensive is sourceTerms (37% total walltime) most of which is spent in EnergyDeposition -> Transport Rays.
In the two node case, the logfile shows that 74% of the simulation time is spent in RadTrans, mostly (again) in "Grid_advanceDiffusion" and (again) most of which is spent in gr_hypreSolve (~66%). Given that about twice the amount of time is spent there compared to the one node case, there's likely some MPI_BCAST or MPI_ALLREDUCE or other parallel inefficiencies occurring there. Possibly related to the code not handling well cylindrical geometry (just speculating).
Looking into those routines may provide future elucidation but I'd start by exploring your hypre package. Best of luck!
Best,
--------
Ryan
On Fri, Jun 17, 2022 at 3:27 PM 赵旭 <xuzhao1994 at sjtu.edu.cn<mailto:xuzhao1994 at sjtu.edu.cn>> wrote:
Hi Ryan，
Thank you for you reply.
Please find attached log file for case 1) - 1node.log and case 2) - 2nodes.log.
The setup flag is
./setup -auto $SM_dir -2d +cylindrical -nxb=16 -nyb=16 -maxblocks=1000 +hdf5typeio species=Cham,Fuel,Cone +mtmmmt +laser +pm4dev +uhd3t +mgd mgd_meshgroups=20 -objdir=~/zx/FLASH4.6.2/data/$Data_dir -parfile=$par_dir
and the .par is also attached
is is the AMR mesh caused the problem?
> "(e.g., if you've written a lot of MPI_BCAST or MPI_ALL_REDUCE calls) "
I dont write anything to the source code, I only changed run parameters for targets and lasers, etc.
Best,
Zhao Xu
----- 原始邮件 -----
发件人: "Ryan Farber" <rjfarber at umich.edu<mailto:rjfarber at umich.edu>>
收件人: "赵旭" <xuzhao1994 at sjtu.edu.cn<mailto:xuzhao1994 at sjtu.edu.cn>>
抄送: "flash-users" <flash-users at flash.rochester.edu<mailto:flash-users at flash.rochester.edu>>
发送时间: 星期五, 2022年 6 月 17日 下午 5:31:46
主题: Re: [FLASH-USERS] MORE nodes MORE time on HPC
Hi Zhao,
I'm having some trouble understanding exactly the cases you're comparing.
If you attach logfiles for each case, that should clear things up.
More generally, using more than one node / more processors increases the
communication time so if your problem doesn't scale well (e.g., if you've
written a lot of MPI_BCAST or MPI_ALL_REDUCE calls) then using more
processors can result in a slower solution time.
Best,
--------
Ryan
On Fri, Jun 17, 2022 at 7:19 AM 赵旭 <xuzhao1994 at sjtu.edu.cn<mailto:xuzhao1994 at sjtu.edu.cn>> wrote:
> Dear all,
>
> sorry about the typo,
>
> '' the results show that in case 2) it takes double or even more time than
> 1) ''
>
> that is when i use more than 1 node, it spends more time.
>
>
> ----- 原始邮件 -----
> 发件人: "赵旭" <xuzhao1994 at sjtu.edu.cn<mailto:xuzhao1994 at sjtu.edu.cn>>
> 收件人: "flash-users" <flash-users at flash.rochester.edu<mailto:flash-users at flash.rochester.edu>>
> 发送时间: 星期五, 2022年 6 月 17日 上午 11:39:48
> 主题: [FLASH-USERS] MORE nodes MORE time on HPC
>
> Dear FLASH user & developers,
>
> I have a question about running FLASH code on HPC. I am running a modified
> laserslab case (changed .par and initBlock.F90 for laser and target) from
> the default one. I tried that
> 1) running on 1 nodes with 40 cores (1 nodes contains 40 cores) and
> 2) running on 2 nodes with 80 cores with the same setup and parameters in
> 1)
>
> the results show that in case 1) it takes double or even more time than
> 1), and this seems counter intuitive. Because if I run a case with larger
> simulation box or with fine resolution I have to using more cores.
>
> I tried two HPC, as a) 1 nodes = 40 cores with total 192G memory, and b) 1
> nodes = 64 cores total 512G memory. It takes 2 times in 2 nodes in a) and
> nearly 5 times in 2 nodes in b)
>
> I dont know if this problem comes from the setting related to HPC (like
> mpi and hypre version , or job systerm) or setting related to FLASH
> code(like in some source code files)
>
> I use gcc 7.5, python3.8, mpich 3.3.2, hypre 2.11.2, hdf5 1.10.5.
>
> both HPCs use slurm job systerm and like below
>
> #!/bin/bash
>
> #SBATCH --job-name= # Name
> #SBATCH --partition=64c512g # cpu
> #SBATCH -n 128 # total cpu
> #SBATCH --ntasks-per-node=64 # cpu/node
> #SBATCH --output=%j.out
> #SBATCH --error=%j.err
>
> mpirun ./flash4 >laser_slab.log
>
> I would appreciate any help.
>
> Thanks !
>
> --
> Zhao Xu
> Laboratory for Laser Plasmas (MoE)
> Shanghai Jiao Tong University
> 800 Dongchuan Rd, Shanghai 200240
> _______________________________________________
> flash-users mailing list
> flash-users at flash.rochester.edu<mailto:flash-users at flash.rochester.edu>
>
> For list info, including unsubscribe:
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> --
> Zhao Xu
> Laboratory for Laser Plasmas (MoE)
> Shanghai Jiao Tong University
> 800 Dongchuan Rd, Shanghai 200240
> _______________________________________________
> flash-users mailing list
> flash-users at flash.rochester.edu<mailto:flash-users at flash.rochester.edu>
>
> For list info, including unsubscribe:
> https://flash.rochester.edu/mailman/listinfo/flash-users
>
--
Zhao Xu
Laboratory for Laser Plasmas (MoE)
Shanghai Jiao Tong University
800 Dongchuan Rd, Shanghai 200240
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