12.1. Copy Output Data and Run script logs to S3 Bucket

Note, you will need permissions to copy to a S3 Bucket. see S3 Access Control

Currently, the bucket listed below has ACL turned off see S3 disable ACL

See example of sharing bucket across accounts. see Bucket owner granting cross-account permissions

12.1.1. Copy scripts and logs to /shared

The CTM_LOG files do not 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 /shared/data/output
cp run*.csh /shared/data/output

12.1.2. Examine the output files

cd /shared/data/output/output_CCTM_v533_gcc_2016_CONUS_16x18pe_full
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_full_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu 2.2G Jan  5 23:52 CCTM_ACONC_v533_gcc_2016_CONUS_16x18pe_full_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu  78G Jan  5 23:52 CCTM_CONC_v533_gcc_2016_CONUS_16x18pe_full_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu 348M Jan  5 23:52 CCTM_APMDIAG_v533_gcc_2016_CONUS_16x18pe_full_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu 1.5G Jan  5 23:52 CCTM_WETDEP1_v533_gcc_2016_CONUS_16x18pe_full_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu 1.7G Jan  5 23:52 CCTM_DRYDEP_v533_gcc_2016_CONUS_16x18pe_full_20151223.nc
-rw-rw-r-- 1 ubuntu ubuntu 3.6K Jan  5 23:22 CCTM_v533_gcc_2016_CONUS_16x18pe_full_20151223.cfg
-rw-rw-r-- 1 ubuntu ubuntu 3.2G Jan  5 23:22 CCTM_CGRID_v533_gcc_2016_CONUS_16x18pe_full_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu 2.2G Jan  5 23:21 CCTM_ACONC_v533_gcc_2016_CONUS_16x18pe_full_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu  78G Jan  5 23:21 CCTM_CONC_v533_gcc_2016_CONUS_16x18pe_full_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu 348M Jan  5 23:21 CCTM_APMDIAG_v533_gcc_2016_CONUS_16x18pe_full_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu 1.5G Jan  5 23:21 CCTM_WETDEP1_v533_gcc_2016_CONUS_16x18pe_full_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu 1.7G Jan  5 23:21 CCTM_DRYDEP_v533_gcc_2016_CONUS_16x18pe_full_20151222.nc
-rw-rw-r-- 1 ubuntu ubuntu 3.6K Jan  5 22:49 CCTM_v533_gcc_2016_CONUS_16x18pe_full_20151222.cfg

Check disk space

 du -sh
173G    .

12.1.3. Copy the output to an S3 Bucket

Examine the example script

cd s3_scripts
cat s3_upload.HBv3-120.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

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

aws s3 mb s3://hbv3-120-compute-conus-output
aws s3 cp --recursive /shared/data/output/ s3://hbv3-120-compute-conus-output/
aws s3 cp --recursive /shared/data/POST s3://hbv3-120-compute-conus-output/

If you do not have permissions to write to the s3 bucket listed above, you will need to edit the script to specify the s3 bucket that you have permissions to write to. In addition, edit the script to include a new date stamp, then run the script to copy all of the CMAQ output and logs to the S3 bucket.

./s3_upload.HBv3-120.csh