GEOS-5

Running the GEOS-5 SBU Benchmark: Difference between revisions

← Older editNewer edit →
mNo edit summary
Re-add text for one-day in comment
Line 106: Line 106:
These effectively let you change whatever you want - useful for debugging, etc. For example, you can set your timers in ~/.esma_base.mk.
These effectively let you change whatever you want - useful for debugging, etc. For example, you can set your timers in ~/.esma_base.mk.


-->


==Benchmark Run==
==Test Build with One-Day Run==


The full benchmark run is a run of 5-days using a portable version of the GEOS-5 boundary conditions. This will use space and cores. For effective benchmarking of I/O, it's recommended to run on less congested than nobackup.
To make sure all works, we will first try setting up a simple one-day experiment.


===Learn to love tcsh===
===Learn to love tcsh===


One preliminary note is that GEOS-5 is, in many ways, a collection of csh/tcsh scripts. If things start going wrong, the answer can often be "change your shell to tcsh and try". Yes, it's not bash/fish/zsh, but it is what it is. I don't think it's entirely necessary for just this automated work, but it could happen.
One preliminary note is that GEOS-5 is, in many ways, a collection of csh/tcsh scripts. If things start going wrong, the answer can often be "change your shell to tcsh and try". Yes, it's not bash/fish/zsh, but it is what it is. I don't think it's entirely necessary for just this automated work, but it could happen.
===Setting up a one-day experiment===
Go into the model application directory and do a couple of preliminary commands:
$ cd $ESMADIR/src/Applications/GEOSgcm_App
Now you can run <tt>create_expt.py</tt>:
<nowiki>$ ~mathomp4/bin/create_exp.py -h
usage: create_expt.py [-h] [-v] [-q] [--expdsc EXPDSC] [--expdir EXPDIR]
                      [--horz {a,b,c,d,e,c12,c24,c48,c90,c180,c360,c720,c1440,c2880}]
                      [--vert {72,132}] [--ocean {o1,o2,o3}] [--land {1,2}]
                      [--runoff {yes,no}] [--gocart {A,C}]
                      [--emission {MERRA2,PIESA,CMIP,NR,MERRA2-DD,OPS}]
                      [--history HISTORY] [--account ACCOUNT] [--gpu]
                      expid
Utility to quickly create experiment. At present, it creates an experiment in
the same manner as gcm_setup would with home and experiment directories as
usual.
positional arguments:
  expid                Experiment ID
optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose        Verbose output
  -q, --quiet          Quietly Setup Experiment (no printing)
  --expdsc EXPDSC      Experiment Description (Default: same as expid)
  --expdir EXPDIR      Experiment Directory Root *NOT CONTAINING EXPID*
                        (Default is what is in ~/.EXPDIRroot:
                        /discover/nobackup/mathomp4 )
  --horz {a,b,c,d,e,c12,c24,c48,c90,c180,c360,c720,c1440,c2880}
                        Horizontal Resolution (Default: c48 on clusters, c12
                        on desktop)
  --vert {72,132}      Vertical Resolution (Default: 72)
  --ocean {o1,o2,o3}    Data Ocean Resolution (Default: o1)
  --land {1,2}          Land Surface Model (Default: 1)
  --runoff {yes,no}    Runoff Routing Model (Default: no)
  --gocart {A,C}        GOCART aerosols: Actual (A) or Climatological (C)
                        (Default: A on clusters, C on desktops)
  --emission {MERRA2,PIESA,CMIP,NR,MERRA2-DD,OPS}
                        GOCART Emissions to use (Default: MERRA2)
  --history HISTORY    History Template (Default: Current)
  --account ACCOUNT    Account Number to Use (Default: g0620 at NCCS, g26141
                        at NAS)
  --gpu                Setup Experiment to use GPUs</nowiki>
This is a script that attempts to ease setting up a GEOS-5 AGCM run. It has some "smarts" in that it will detect from an experiment ID some information, but you can be explicit (to the point you can specify impossible experiments too).
Your first choice is where you'd like to run the experiment. $NOBACKUP or other disks with space are vital. For example, if you'd like to run the experiment in /discover/nobackup/username/experiment-name, then run the script with --expdir /discover/nobackup/username. To actually create the experiment, run the script and choose a C48 horizontal resolution:
$ ~mathomp4/bin/create_expt.py test-1day-expt --horz c48 --account <ACCOUNTID> --expdir /discover/nobackup/username
Horizontal resolution c48 passed in
Using c48 horizontal resolution
Assuming default vertical resolution of 72
Using 72 vertical resolution
Assuming default ocean resolution of o1
Using o1 ocean resolution
Using actual aerosols
  Running gcm_setup...done.
Experiment is located in directory: /discover/nobackup/username/test-1day-expt
If you don't pass in an account-id, you'll get the default of g0620 (the developer's account).
===Run a one-day test===
To run a test one-day run, go to the experiment directory:
<nowiki>$ cd /discover/nobackup/mathomp4/test-1day-expt
total 96M
-rwxr-xr-x 1 mathomp4 g0620 96M Feb 13 11:11 GEOSgcm.x*
-rwxr-xr-x 1 mathomp4 g0620 573 Feb 13 14:47 CAP.rc*
-rwxr-xr-x 1 mathomp4 g0620 364 Feb 13 14:47 fvcore_layout.rc*
-rw-r--r-- 1 mathomp4 g0620 25K Feb 13 14:47 AGCM.rc
-rwxr-xr-x 1 mathomp4 g0620 21K Feb 13 14:47 gcm_run.j*
-rw-r--r-- 1 mathomp4 g0620 61K Feb 13 14:47 HISTORY.rc
drwxr-xr-x 2 mathomp4 g0620 512 Feb 13 14:47 post/
drwxr-xr-x 2 mathomp4 g0620 512 Feb 13 14:47 plot/
drwxr-xr-x 2 mathomp4 g0620 512 Feb 13 14:47 archive/
drwxr-xr-x 2 mathomp4 g0620 512 Feb 13 14:47 regress/
drwxr-xr-x 2 mathomp4 g0620 512 Feb 13 14:47 convert/
drwxr-xr-x 2 mathomp4 g0620 512 Feb 13 14:47 forecasts/
drwxr-xr-x 2 mathomp4 g0620 16K Feb 13 14:47 RC/
Directory: /discover/nobackup/mathomp4/test-1day-expt</nowiki>
Now you'll run another script called <tt>makeoneday.bash</tt> that edits some .rc files, edits run scripts, as well as linking in some example restarts and sets up the model to stop after one day (with no options). Note: these restarts are write-protected, so if you want to run a multi-year run, don't use this script!
<nowiki>$ ~mathomp4/bin/makeoneday.bash
Using Heracles-5_0 directories
Making one-day experiment
Restoring AGCM.rc.save to AGCM.rc...
Copying AGCM.rc to AGCM.rc.save...
Restoring CAP.rc.save to CAP.rc...
Copying CAP.rc to CAP.rc.save...
Restoring HISTORY.rc.save to HISTORY.rc...
Copying HISTORY.rc to HISTORY.rc.save...
Restoring gcm_run.j.save to gcm_run.j...
Copying gcm_run.j to gcm_run.j.save...
Restoring regress/gcm_regress.j.save to regress/gcm_regress.j...
Copying regress/gcm_regress.j to regress/gcm_regress.j.save...
Restoring RC/GEOS_ChemGridComp.rc.save to RC/GEOS_ChemGridComp.rc...
Copying RC/GEOS_ChemGridComp.rc to RC/GEOS_ChemGridComp.rc.save...
DYN_INTERNAL_RESTART_TYPE not found. Assuming NC4
Found fvcore_internal_rst. Assuming you have needed restarts!
Changes made to CAP.rc:
9,10c9,10
< JOB_SGMT:    00000015 000000
< NUM_SGMT:    20
---
> JOB_SGMT:    00000001 000000
> NUM_SGMT:    1
25c25
< MAPL_ENABLE_TIMERS: NO
---
> MAPL_ENABLE_TIMERS: YES
Changes made to gcm_run.j:
7c7
< #PBS -l walltime=12:00:00
---
> #PBS -l walltime=0:15:00
11a12
> #SBATCH --mail-type=ALL
260c261
< if($numrs == 0) then
---
> if($numrs == 1) then
433a435
> exit
</nowiki>
At this point, you should be able to <tt>sbatch gcm_run.j</tt> and the model should run a day.
-->
==Benchmark Run==
The full benchmark run is a run of 5-days using a portable version of the GEOS-5 boundary conditions. This will use space and cores. For effective benchmarking of I/O, it's recommended to run on less congested than nobackup.


===Setting up benchmark experiment===
===Setting up benchmark experiment===
Retrieved from "https://geos5.org/wiki/index.php?title=Running_the_GEOS-5_SBU_Benchmark"