Running the GEOS-5 SBU Benchmark
Build and install the model
First, untar the model tarball (in $NOBACKUP!!!):
$ tar xf Heracles-UNSTABLE-MPT-Benchmark.2017Feb13.tar.gz
Next, set up ESMADIR:
$ setenv ESMADIR <directory-to>/Heracles-UNSTABLE-MPT-Benchmark/GEOSagcm
it is just below the src/ directory.
Go into the src/ directory of your model. Following above:
$ cd $ESMADIR/src
Setup the environment by sourcing the g5_modules file:
$ source g5_modules
To build the model, you have one of two choices. First, you can use the parallel_build.csh script to submit a PBS job that compiles the model:
$ ./parallel_build.csh
or you can interactively build the model using:
$ make install
To capture the install log, we recommend tee'ing the output to a file:
$ make install |& tee make.install.log (on tcsh) $ make install 2>&1 | tee make.install.log (on bash)
Note you can also build in parallel interactively with:
$ make -j8 pinstall |& tee make.pinstall.log (on tcsh)
where N is the number of parallel processes. From testing, 8 jobs is about as much as is useful. You can use more, but no benefit will accrue.
By default, the Intel Fortran compiler (ifort) is used for the build process. For other compilers, contact matthew.thompson@nasa.gov for instructions to use GCC or PGI compilers.
Monitor build process
The build can be monitored using the utility gmh.pl in the directory Config. From the src directory:
$ Config/gmh.pl -Av make.install.log
outputs the build status as
--------
Packages
--------
>>>> Fatal Error .... Ignored Error
[ok] Config
[ok] GMAO_Shared
[ok] | GMAO_mpeu
[ok] | | mpi0
[ok] | GMAO_pilgrim
[ok] | GMAO_gfio
[ok] | | r4
[ok] | | r8
[ok] | GMAO_perllib
[ok] | MAPL_cfio
[ok] | | r4
[ok] | | r8
[ok] | MAPL_Base
[ok] | | TeX
[ok] | GEOS_Shared
[ 1] .... .... Chem_Base
[ok] | Chem_Shared
[ok] | GMAO_etc
[ok] | GMAO_hermes
[ 2] .... .... GFDL_fms
[ok] | GEOS_Util
[ok] | | post
-------
Summary
-------
IGNORED mpp_comm_sma.d mpp_transmit_sma.d Chem_AodMod.d (3 files in 2 packages)
All 22 packages compiled successfully.
In case of errors, gmh summarizes exactly where it happens by indicating the package where it occured. Caveat: it does not work in parallel (output is scrambled). So, if the parallel build fails, rerun it sequentially (it will go quickly and die in the same place) and run gmh on the output for a summary.
Run the model
Setting up an experiment
Go into the model application directory and do a couple of preliminary commands:
$ cd $ESMADIR/src/Applications/GEOSgcm_App $ echo $NOBACKUP > ~/.HOMDIRroot $ echo $NOBACKUP > ~/.EXPDIRroot
These echos set up some defaults. While they both don't have to be in the same location, it's highly recommended they are. Also, make sure they are in a nobackup directory.
Now you can run create_expt.py:
$ ~mathomp4/bin/create_exp.py -h
usage: create_expt.py [-h] [-v] [-q] [--expdsc EXPDSC]
[--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)
--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
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).
Run a one-day test
To run the job, first change to the experiment directory you specified in the above gcm_setup. Then, copy a set of restarts to model directory. Sample restarts are provided on Discover (at /discover/nobackup/mathomp4/Restarts-G10) and Pleiades (at /nobackup/gmao_SIteam/ModelData/Restarts-G10/).
Then, edit CAP.rc:
JOB_SGMT should be 1 day (00000001 000000) NUM_SGMT should be 1
and gcm_run.j by inserting "exit" after
$RUN_CMD $NPES ./GEOSgcm.x set rc = $status echo Status = $rc
A script that can automate these processes is:
#!/bin/bash
sed -i'.orig' -e '/^JOB_SGMT:/ s/000000[0-9][0-9]/00000001/' \
-e '/^NUM_SGMT:/ s/[0-9][0-9]*/1/' \
-e '/^MAPL_ENABLE_TIMERS:/ s/NO/YES/' CAP.rc
sed -i'.orig' -e '/^echo Sta/ a exit' \
-e '/^#PBS -j oe/ a #PBS -m abe\n#PBS -M email@myserver.com' \
-e '/^ if(-e $EXPDIR\/$rst ) \/bin/ s/cp/ln -s/' gcm_run.j
Note: This script also sets up email notification as well as linking restarts to the scratch/ directory rather than copying (which is nice if running at high-res).
Compare to a "correct" run by using cmpscratch
a. If all success, runs are bit-identical b. If not => "What is correct?"