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Introduction

OpenIFS is an ECMWF led project which provides an easy-to-use, exportable version of the IFS system in use at ECMWF for operational weather forecasting. The project aims to develop and promote research, teaching and training on numerical weather prediction (NWP) and NWP-related topics with academic and research institutions.

In this tutorial, OpenIFS has been pre-installed and pre-compiled for you. If you want to learn more about how OpenIFS can be downloaded, configured and installed, please see the OpenIFS website at: http://software.ecmwf.int/oifs/.

In this tutorial...

What you will do:

Connect to the ECMWF HPC Facility
Explore installed OpenIFS files
Run T21 model forecast
Verify the model works in serial (1 process) and parallel (2 tasks & 2 threads)
Carry out acceptance test
Use the model namelist to change settings
Explore model output data (GRIB)

At the end of this tutorial, you will:

have learnt about how OpenIFS is installed and organised,
have run it at T21 resolution and know how to run it serially (1 process) and in parallel with both MPI & OpenMP,
know how to use grib tools to look at model output.

Connecting to the ECMWF HPC Facilities

In this tutorial, and throughout the entire workshop, you will use a one of the Cray XC40 computers which is are part of the ECMWF's high-performance computing facility (HPCF).

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title	Tasks - Connect to HPCF

Start the Mobaxterm application and open a local terminal
Login to the RACC using ssh -X cluster.act.rdg.ac.uk
On the cluster type the command: ssh troifsX@ecaccess.ecmwf.int Note: Instead of troifsX you should use your ECMWF training user-ID
You will be prompted for the hostname with a choice between ecgate, cca and ccb. You should select ccb.
When you have completed your work you can disconnect from ccb by typing exit at the command prompt.

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The following tasks need to be carried out only once in order to set up the training accounts and the OpenIFS 43r3 model.

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Type the following command:

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title	Tasks - Start interactive session

% qsub -I -q df -l EC_total_tasks=6 -l EC_job_tmpdir=10G -l EC_memory_per_task=2G
qsub: waiting for job 7215630.ccbpar to start
qsub: job 7215630.ccbpar ready

The changed command line prompt indicates that we have switched from the login node to a pre/post-processing node.

You can close the interactive session by typing exit which will bring you back to the login node.

On the ECMWF HPCF an interactive session will last for 48 hrs by default, unless the walltime is specified using an additional directive.

OpenIFS directories

In this section we:

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Set up training account - do this only once after the first login

After the first login type the following command: /home/ectrain/troifs0/setup-cray/my43
Log out of the training account by typing exit
Login once more using ssh troifsX@ecaccess.ecmwf.int
Type the following command: get43

The actions above will ensure that your training account receives required scripts and shell configuration files.

The last command will copy the model binaries and input files to your account for version 43r3.

Instead of using the login nodes of the HPCF we will use an interactive session to ask for computing resources and fast temporary disk. This also allows to run parallel jobs in the terminal window.

Type the following command:

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Carry out the tasks above to connect to ccb and start an

Type the command: cd perm/oifs43r3

Type the command: source ./oifs-config.ccb.sh

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title	Tasks - Set OpenIFS environment

Start interactive session

The oifs-config.ccb.sh file sets a number of Unix shell environment variables which define the type of OpenIFS compiled installation and location of files.

Make sure you type the source command before you run the model otherwise OpenIFS will not run correctly.

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% qsub -I -q df -l EC_total_tasks=6 -l EC_job_tmpdir=10G -l EC_memory_per_task=2G
qsub: waiting for job 7215630.ccbpar to start
qsub: job 7215630.ccbpar ready

The changed command line prompt indicates that we have switched from the login node to a pre/post-processing node.

Important: After completing your work you need to close the interactive session by typing exit which will bring you back to the login node.

On the ECMWF HPCF an interactive session will last for 48 hrs by default, unless the walltime is specified using an additional directive.

OpenIFS directories

In this section we:

Set the OpenIFS environment
Examine the OpenIFS installation

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title	Tasks - Examine the oifs43r3 directory

Make sure you are in the directory: ~/perm/oifs43r3/
List the files in this directory using the ls command

The directory contains a number of text files and directories:

Code Block
% ls CHANGES CITE COPYING LICENSE NOTICE README READMEs/ bin/ examples/ fcm/ make/ python/ src/ t21test/

Directories:

src - contains all the source code for the model and supporting programs.
make - contains the build configuration files for the FCM compile command. Object files and executables will be in this directory organised according to the type of build (OIFS_BUILD environment variable).
t21test - self contained T21 model run for verifying the installation is correct.
ifsdata - contains additional input files for the model e.g. climatologies. Available as separate tarfiles.

Note:

OpenIFS has been precompiled on the HPCF.
All source code has been removed due to licensing restrictions.
OpenIFS builds 'out-of-source'; this means object (.o) files and executables (binary files) are not mixed with the source code.
The README file contains information about software requirements, setting up the local compilation environment, and where to get help and support.

OpenIFS T21 test forecasts

In this section of the tutorial, we will run the pre-compiled OpenIFS model on a simple T21 forecast.

You will:

learn about OpenIFS input and output files.
learn some switches to control OpenIFS.
learn how to run the model in parallel.
learn how to run the acceptability test.

Set OpenIFS environment

Carry out the tasks above to connect to ccb and start an interactive session
Change into the model's main directory: cd perm/oifs43r3
Type the command: source ./oifs-config.ccb.sh

The oifs-config.ccb.sh script sets a number of Unix shell environment variables which define the type of OpenIFS compiled installation and location of files. These settings are specific to version 43r3.

If you do not run this setup script (or alternatively include its content in your Unix shell configuration file) then OpenIFS will not run correctly.

For more information on how to configure OpenIFS, please see the OpenIFS website: http://software.ecmwf.int/oifs/.

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bgColor	#f0f0ff
title	Tasks - Examine the oifs43r3 directory

Make sure you are in the directory: ~/perm/oifs43r3/
List the files in this directory using the ls command

The directory contains a number of text files and directories:

Code Block
% ls bin/ COPYING LICENSE oifs-config.ccb.sh READMEs/ CHANGES examples/ make/ python/ src/ CITE fcm/ NOTICE README t21test/

Directories:

src - contains all the source code for the model and supporting programs.
make - contains the build configuration files for the FCM compile command. Object files and executables will be in this directory organised according to the type of build (OIFS_BUILD environment variable).
t21test - self contained T21 model run for verifying the installation is correct.
ifsdata - contains additional input files for the model e.g. climatologies. Available as separate tarfiles.

Note:

OpenIFS has been precompiled on the HPCF.
All source code has been removed due to licensing restrictions.
OpenIFS builds 'out-of-source'; this means object (.o) files and executables (binary files) are not mixed with the source code.
The README file contains information about software requirements, setting up the local compilation environment, and where to get help and support.

OpenIFS T21 test forecasts

In this section of the tutorial, we will run the pre-compiled OpenIFS model on a simple T21 forecast.

You will:

learn about OpenIFS input and output files.
learn some switches to control OpenIFS.
learn how to run the model in parallel.
learn how to run the acceptability test.

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title
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title	Tasks - Examine t21test directory

Make sure you are in the directory: $PERM~/perm/oifs43r3/t21test
List the files in this directory.

The directory t21test contains a number of files:

Code Block
% ls t21test ICMGGepc8 ICMGGepc8INIUAICMGGepc8INIT ICMSHepc8INIT ifsdatajob namelists ICMGGepc8INIT ICMSHepc8 ref_021_0072 ICMGGepc8INIUA ifsdata/ README namelists job ref_021_0144run.ppn

Files beginning with 'ICM'.
These are the input files for this T21 experiment. They are in GRIB format. Do not move them from this directory. OpenIFS expects to find its input files in the same directory as the main executable.

epc8 - this is the Experiment ID. Experiments IDs are used at ECMWF and initial conditions provided by ECMWF will always have an expt id.
ICMGGepc8 - 'GG' indicates these contain gridpoint fields.
ICMSHepc8 - 'SH' indicates these contains spherical harmonic fields.

job
Simple shell Shell script to run the model. Described in more detail below.

run.ppn
Simple shell script which calls job in an interactive shell environment.

ifsdata
Climate data fields used for T21 test integration. You should not move or rename this directory as the model will expect to find the climate files it needs in a directory of this name.

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title	Tasks - Run model

Run the model:

% ./jobrun.ppn

What happens?

The model fails. Look at the standard output (or in the NODE_001.01 file when it is created) and find the subroutine traceback. Near the top of the traceback you will find the error messages.

Whenever the model fails, it will produce this traceback (controlled by DR_HOOK=1 in the job file).

Single process test

Copy the file namelists to fort.4 and run the model with a single task and single thread by executing the job script:

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title	Tasks - Run the model as a single process

Code Block
% cp namelists fort.4 % ./run.ppn

The model will expect to find a file called fort.4 in the same directory as the executable. This script copies the executable from make/opt/bin.

If the run works you will see output like:

	Tasks - Run the model as a single process

Copy the file namelists to fort.4 and run the model with a single task and single thread by executing the job script:

Code Block
% cp namelists fort.4 % ./run.ppn

The model will expect to find a file called fort.4 in the same directory as the executable. This script copies the executable from make/cce-opt/oifs/bin.

If the run works you will see output like:

Code Block

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  17:09:08 STEP    1 H=   0:10 +CPU=  0.276
           STEP    1 :## EC_MEMINFO    1 ccbppn01     309     206       0     16530     190    16080    1188     35807   61171      0.2   0.0 s/p
  17:09:08 STEP    2 H=   0:20 +CPU=  0.280
           STEP    2 :## EC_MEMINFO    1 ccbppn01     309     206       0     16530     190    16011    1188     35740   61170      0.2   0.0 s/p
  17:09:08 STEP    3 H=   0:30 +CPU=  0.268
           STEP    3 :## EC_MEMINFO    1 ccbppn01     309     206       0     16530     190    16008    1188     35734   61170      0.2   0.0 s/p
  17:09:09 STEP    4 H=   0:40 +CPU=  0.264
           STEP    4 :## EC_MEMINFO    1 ccbppn01     309     206       0     16530     190    15966    1188     35695   61170      0.2   0.0 s/p
  17:09:09 STEP    5 H=   0:50 +CPU=  0.268
           STEP    5 :## EC_MEMINFO    1 ccbppn01     309     206

Code Block

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signal_drhook(SIGSYS=31): New handler installed at 0x4d06cf; old preserved at 0x0
MPL_BUFFER_METHOD:  2           0
     16530   16:03:46 STEP 190   0 H=16008   0:00 +CPU= 1188  3.598
   16:03:4635734 STEP  61171  1 H=   0:10 +CPU=.2   0.5350 s/p
   1617:0309:4709 STEP    26 H=   01:2000 +CPU=  0.537004
   16:03:48 STEP         STEP    6 :## EC_MEMINFO   3 H=1 ccbppn01  0:30 +CPU=  0.537
309   16:03:48 STEP 206   4 H=   0:40  +CPU=  0.527
 16530  16:03:49 STEP  190  5 H= 16008  0:50 +CPU= 1188 0.526
   16:03:49 STEP35734   61171 6  H=   1:00 +CPU=0.2   0.5300 s/p

This test runs only 6 a small number of timesteps.

Model output

The model writes its output to a several files.

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title	Tasks - Examine model output

Look at the output from the model in the NODE_001.01 file from this successful run. Note the output of the model namelists and the statistics printed at the end. IFS has very comprehensive logging output which is useful for debugging and understanding the model's performance.

Look at the grib output files using the grib commands.

Parallel runs

These next short tests verify the model works correctly with either OpenMP parallel threading, MPI tasks and both and follow on from the serial tests above.

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bgColor	#f0f0ff
title	Tasks - Enable OpenMP

Edit the file run.ppn and change the line: export NTHREADS=1 to NTHREADS=42

Run ./run.ppn as above.

Do the reported CPU times change?

Use the grib_ls command to look at grib output files - what do you notice?

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Code Block
NUMBER OF THREADS 42

to verify the model ran with 4 OpenMP threads.

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title	Tasks - Enable MPI

Edit the file run.ppn and change NTHREADS back to 1.

Change the line: NPROC=1 to NPROC=42.

Also, edit the fort.4 file and change NPROC to 42.

Rerun the job:
./run.ppn

Do the reported CPU times change?

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Look in the NODE_001.01 output file for the line: "NUMBER OF TASKS 2NPROC = 2" to verify that two MPI tasks was used.

Mixed mode: OpenMP/MPI

The model can also be set to use NPROC=4 and 2 and NTHREADS=4 to 2 to use a total of 4 processes. However, this would require a computer with at least 16 4 cores.

Acceptance testing

The final step is to check the model is producing the numerical answers within acceptable limits, even if it runs the short tests above without failing. OpenIFS includes code that will compute internal statistical norms and compare against numbers supplied by ECMWF. The file: ref_021_0144 in the t21test directory contains statistical norms computed by the model run at ECMWF.

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title	Task - run acceptance test

To do the acceptance test, edit the namelists in fort.4 and look for the NAMCT0 namelist:

Code Block
&NAMCT0 LREFOUT=false, NSTOP=6,

change the number of timesteps to 72 to run the model for 12 hours (assuming you have not changed the default timestep of 10mins at T21) and set the variable LREFOUT to TRUE:

Code Block
&NAMCT0 LREFOUT=true, NSTOP=72,

With LREFOUT=true, at the last timestep OpenIFS will read the ref_021_0144 file and produce a new file: res_021_0144 (note the similar filenames!). The contents of the file should be similar to:

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As long as the model reports 'calculations are correct' and the error is less than a few percent then the model is behaving satisfactorily in your compilation and run environment.

How to control model output

In this section, the main NAMELIST variables that control the output of the model are presented.

If you have time, try changing the variables, run the model and using the grib_ls and grib_dump commands to view the output grib file contents.

How to control output frequency

The namelist variables that determine the output from the model as it runs are:

Namelist : `NAMCT0`

NFPOS - this should be set =2 in order to turn on model output and diagnostics.

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NPOSTS & NHISTS - these are integer arrays that control the write times of the history files. They can be used for non-regular output intervals.

Examples

Regular output at fixed timesteps

NFRHIS=4, NFRPOS=4, NPOSTS=0, NHISTS=0,

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Note
For this to work correctly, `NFRHIS * timestep` must equal an integer number of hours. The GRIB output will not work correctly if this isn't the case.

Non-regular output

NFRHIS=1,
NFRPOS=1,
NHISTS(0)=3,
NHISTS(1:3)=0,-3,-9,
NPOSTS(0)=-3,
NPOSTS(1:3)=0,-3,-9,

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In this example, the model will write 3 separate output files at the first timestep (0hrs), 3hrs and 9hrs and then no more regardless of how long the model runs for.

How to change the output variables and post-processing

The namelist NAMFPC is the main namelist for the post-processing. Variables in this list can be sensitive to changes as many combinations are possible but not all work.

Model level output

To control model level output the following namelist variables (in NAMFPC) are used:

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bgColor	#f0f0ff
title	Tasks - Change model output

Using the information above, try:

Adjusting the output frequency of the model.
Changing the list of model levels used for output and the output variables.

At the end of the session

Note
Do not forget to close your interactive ppn session on the HPCF using the exit command.

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Versions Compared

Old Version 39

New Version Current

Key

Introduction

In this tutorial...

What you will do:

At the end of this tutorial, you will:

Connecting to the ECMWF HPC Facilities

OpenIFS directories

OpenIFS directories

OpenIFS T21 test forecasts

OpenIFS T21 test forecasts

Single process test

Model output

Parallel runs

Mixed mode: OpenMP/MPI

Acceptance testing

How to control model output

How to control output frequency

Namelist : `NAMCT0`

Examples

Regular output at fixed timesteps

Non-regular output

How to change the output variables and post-processing

Model level output

At the end of the session

Space shortcuts

Page tree

Page History

Versions Compared

Old Version 39

New Version Current

Key

Introduction

In this tutorial...

What you will do:

At the end of this tutorial, you will:

Connecting to the ECMWF HPC Facilities

OpenIFS directories

OpenIFS directories

OpenIFS T21 test forecasts

OpenIFS T21 test forecasts

Single process test

Model output

Parallel runs

Mixed mode: OpenMP/MPI

Acceptance testing

How to control model output

How to control output frequency

Namelist : NAMCT0

Examples

Regular output at fixed timesteps

Non-regular output

How to change the output variables and post-processing

Model level output

At the end of the session

Namelist : `NAMCT0`