6.4.1. Copy Output Data and Run script logs to S3 Bucket#

Note

You need permissions to copy to a S3 Bucket.

See also

S3 Access Control

Be sure you enter your access credentials on the parallel cluster by running:

aws configure

Currently, the bucket listed below has ACL turned off

See also

S3 disable ACL

See example of sharing bucket across accounts.

See also

Bucket owner granting cross-account permissions

6.4.2. Copy scripts and logs to /fsx#

The CTM_LOG files don’t contain any information about the compute nodes that the jobs were run on. Note, it is important to keep a record of the NPCOL, NPROW setting and the number of nodes and tasks used as specified in the run script: #SBATCH –nodes=16 #SBATCH –ntasks-per-node=8 It is also important to know what volume was used to read and write the input and output data, so it is recommended to save a copy of the standard out and error logs, and a copy of the run scripts to the OUTPUT directory for each benchmark.

cd /shared/build/openmpi_gcc/CMAQ_v533/CCTM/scripts
cp run*.log /fsx/data/output
cp run*.csh /fsx/data/output

6.4.3. Examine the output files#

Note

The following commands will vary depending on what APPL or domain decomposition was run

cd /fsx/data/output/output_CCTM_v533_gcc_2016_CONUS_16x18pe
ls -lht

output:

total 173G
drwxrwxr-x 2 ubuntu ubuntu 145K Jan  5 23:53 LOGS
-rw-rw-r-- 1 ubuntu ubuntu 3.2G Jan  5 23:53 CCTM_CGRID_v533_gcc_2016_CONUS_16x18pe_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu 2.2G Jan  5 23:52 CCTM_ACONC_v533_gcc_2016_CONUS_16x18pe_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu  78G Jan  5 23:52 CCTM_CONC_v533_gcc_2016_CONUS_16x18pe_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu 348M Jan  5 23:52 CCTM_APMDIAG_v533_gcc_2016_CONUS_16x18pe_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu 1.5G Jan  5 23:52 CCTM_WETDEP1_v533_gcc_2016_CONUS_16x18pe_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu 1.7G Jan  5 23:52 CCTM_DRYDEP_v533_gcc_2016_CONUS_16x18pe_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu 3.6K Jan  5 23:22 CCTM_v533_gcc_2016_CONUS_16x18pe_20151223.cfg
-rw-rw-r-- 1 ubuntu ubuntu 3.2G Jan  5 23:22 CCTM_CGRID_v533_gcc_2016_CONUS_16x18pe_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu 2.2G Jan  5 23:21 CCTM_ACONC_v533_gcc_2016_CONUS_16x18pe_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu  78G Jan  5 23:21 CCTM_CONC_v533_gcc_2016_CONUS_16x18pe_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu 348M Jan  5 23:21 CCTM_APMDIAG_v533_gcc_2016_CONUS_16x18pe_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu 1.5G Jan  5 23:21 CCTM_WETDEP1_v533_gcc_2016_CONUS_16x18pe_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu 1.7G Jan  5 23:21 CCTM_DRYDEP_v533_gcc_2016_CONUS_16x18pe_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu 3.6K Jan  5 22:49 CCTM_v533_gcc_2016_CONUS_16x18pe_20151222.cfg

Check disk space

 du -sh
173G    .

6.4.4. Copy the output to an S3 Bucket#

Examine the example script

cd /shared/pcluster-cmaq/s3_scripts
cat s3_upload.c5n.18xlarge.csh

output:

#!/bin/csh -f
# Script to upload output data to S3 bucket
# NOTE: a new bucket needs to be created to store each set of cluster runs

aws s3 mb s3://c5n-head-c5n.18xlarge-compute-conus-output
aws s3 cp --recursive /fsx/data/output/ s3://c5n-head-c5n.18xlarge-compute-conus-output
aws s3 cp --recursive /fsx/data/POST s3://c5n-head-c5n.18xlarge-compute-conus-output

If you do not have permissions to write to the s3 bucket, you may need to ask the administrator of your account to add S3 Bucket writing permissions.

Run the script to copy all of the CMAQ output and logs to the S3 bucket.

./s3_upload.c5n.18xlarge.csh