WRF on the Cloud

Ramboll Modeling on the Cloud Contract Results

WRF on AWS: LADCO User's Guide

Last Update: 16May2019 How to configure/optimize AWS for running WRF.

Summary

• AWS pcluster v2.1.0 instance using ALinux
• WRFv3.9.1 compiled with netCDF4 (compression)
• PGI compiler 2018 with OpenMPI v3.1.3
• NetCDF C 4.6.2, Fortran 4.2
• Spot instances with sc1 cold storage volumes

The AWS Parallel Cluster package is a way to build a computing cluster such that there is constantly running master node that is used to launch jobs on compute nodes. The compute nodes are only started when a job is initiated. The compute nodes will shut down after a default 10 minutes of idle use (you can change the idle time through the pcluster config file). This system lets you choose different instance types for the master and compute nodes. We chose an inexpensive master instance (c4.large @ 2 CPU 3.75 Gb RAM) and compute optimized compute instances (c4.4xlarge @ 16 CPU 30 Gb RAM). We attached a 10 Tb EBS volume (sc1 Cold HDD) for storage.

For the workflow, we run an operational script system that downloads MADIS obs, runs WPS, REAL, and WRF. It also runs a script to replace the NOAA SST with GLSEA SST. The simulation is run as multiple 32 CPU 5.5 day simulations at the same time.

After WRF completes, we run MCIP and WRFCAMx, and ingest the results into AMET. We archive the wrfout, MCIP, and WRFCAMx data to S3 Glacier.

Notes

• No success with MPICH (v3.2.1) on AWS ALinux. Tried with GCC (7.2.1), PGI (2018), and Intel (xe 2019) compilers; also tried WRFV4.0 and nothing worked with MPICH. WRF compiles, but it was unstable and crashed consistently with segfaults after a seemingly random number of output timesteps
• Stable WRF is created with OpenMPI; ultimately settled on PGI 2018 and OpenMPI v3.1.3
• Prototyping and testing done with EC2 ondemand m5a.* instance (see ondemand pcluster config below) and gp2 EBS volumes
• Production done with EC2 spot c4* instances (see spot pcluster config below) and sc1 volumes

AWS Configuration

Packages/software installed:

• PGI 2018
• GCC and Gfortran 7.2.1
• NetCDF C 4.6.2, Fortran 4.2
• HDF5 1.10.1
• JASPER 1.900.2
• ZLIB 1.2.11
• R 3.4.1
• OpenMPI 3.1.3
• yum -y install screen dstat htop strace perf pdsh ImageMagick

Misc Notes

Adding ssh users to a pcluster instance

AWS documentation for adding users with OpenLDAP

The post-install command in the pcluster configuration file should invoke the settings in the post_install_users.sh script described above. Alternatively, if you already have an instance running you can run the script as sudo to invoke the settings:

  > sudo ./post_install_users.sh

After running the script you need to use the add-key.sh and add-user.sh script described in the above link.

 #Usage (using zac as an example)
 > sudo ./add-user.sh zac {####., e.g, 2001}
 > sudo ./add-key.sh zac ladco.key
 #Add users to /etc/passwd file
 > sudo getent passwd zac
 > sudo vi /etc/passwd
 #Change ladco to primary group
 > sudo usermod zac -g ladco

Using AWS S3 for offline storage

Data are moved off of the compute servers to the AWS Simple Storage Solution for intermediate to long-term storage. The AWS CLI is used to access/manage the data on S3.

View the S3 commands, with an example for the copy (cp) command

 > aws s3 help
 > aws s3 cp help

List the S3 buckets

 > aws s3 ls
 2019-02-06 21:18:09 ladco-wrf
 > aws s3 ls ladco-wrf/
 PRE 24Apr2019/
 PRE 24Jan2019/
 PRE LADCO_2016_WRFv39_APLX/
 PRE LADCO_2016_WRFv39_YNT/
 PRE LADCO_2016_WRFv39_YNT_GFS/
 PRE LADCO_2016_WRFv39_YNT_NAM/
 PRE aws-reports/

Copy a file from one of the s3 buckets to a location on the compute server

 aws s3 cp s3://ladco-wrf/LADCO_2016_WRFv39_YNT_GFS/wrfout_d01_2016-06-10_00:00:00 /data2/wrf3.9.1/LADCO_2016_WRFv39_YNT_GFS/

Add New Volume to Running Instance

From the AWS Console

• Go to Volumes
• Create a new Volume
• Under the Actions menu, select Attach Volume
• Select the Instance to which attach the new volume

From the AWS Instance

• Check that the volume is available

lsblk

• Confirm that the volume is empty (assuming the volume is attached as /dev/xvdf)

sudo file -s /dev/xvdf

If this command returns the following, it confirms that it is empty.

/dev/xvdf: data

• Format the volume to an ext4 filesystem

sudo mkfs -t ext4 /dev/xvdf

• Create a new directory and mount the volume

sudo mkdir /newdata
sudo mount /dev/xvdf /newdata

Copy output files from EC2 volume to S2 Glacier

#!/bin/csh -f

set PROJECT = LADCO_2016_WRFv39_YNT_GFS
set NEW_YN = Y 

if ( $NEW_YN == Y ) then
   # Create a new storage vault
   aws glacier create-vault --vault-name $PROJECT --account-id -

   # Add tags to describe vault (10 tags max)
   aws glacier add-tags-to-vault --account-id - --vault-name $PROJECT --tags model="WRFv3.9.1",simyear=2016,stdate=20160610,endate=20160619,awsinst=ec2-ondemand,desc="LADCO YNT GFS Test Run"
endif

# Upload files to the storage vault
set datadir = /data/wrf3.9.1/${PROJECT}/output_full/wrf_out/2016
cd $datadir
foreach f ( *wrfout* )
   echo "Copying $f"
   aws glacier upload-archive --account-id - --vault-name $PROJECT --body $f
end

# Remove files on ec2 after the files are all uploaded
# rm -f $datadir/*wrfout*