merge from master

CHANGELOG.rst

@@ -3,12 +3,18 @@
 Change Log
 ==========
 
-5.3.0
+5.4.0
 =====
 
 * Support for Python 3.12.
 
 
+5.3.0
+=====
+
+* Add config option `disable_metrics_collection`
+
+
 5.2.2
 =====
 

awsf3/aws_run_workflow_generic.sh

@@ -8,10 +8,11 @@ export ACCESS_KEY=
 export SECRET_KEY=
 export REGION=
 export SINGULARITY_OPTION_TO_PASS=
+export DISABLE_METRICS_COLLECTION=false
 export S3_ENCRYPT_KEY_ID=
 
 printHelpAndExit() {
-    echo "Usage: ${0##*/} -i JOBID -l LOGBUCKET -V VERSION -A AWSF_IMAGE [-m SHUTDOWN_MIN] [-p PASSWORD] [-a ACCESS_KEY] [-s SECRET_KEY] [-r REGION] [-g] [-k S3_ENCRYPT_KEY_ID]"
+    echo "Usage: ${0##*/} -i JOBID -l LOGBUCKET -V VERSION -A AWSF_IMAGE [-m SHUTDOWN_MIN] [-p PASSWORD] [-a ACCESS_KEY] [-s SECRET_KEY] [-r REGION] [-g] [-c] [-k S3_ENCRYPT_KEY_ID]"
     echo "-i JOBID : awsem job id (required)"
     echo "-l LOGBUCKET : bucket for sending log file (required)"
     echo "-V TIBANNA_VERSION : tibanna version (used in the run_task lambda that launched this instance)"
@@ -22,10 +23,11 @@ printHelpAndExit() {
     echo "-s SECRET_KEY : secret key for certian s3 bucket access (if not set, use IAM permission only)"
     echo "-r REGION : region for the profile set for certain s3 bucket access (if not set, use IAM permission only)"
     echo "-g : use singularity"
+    echo "-c : Metrics collection is disabled if flag is set"
     echo "-k S3_ENCRYPT_KEY_ID : KMS key to encrypt s3 files with"
     exit "$1"
 }
-while getopts "i:m:l:p:a:s:r:gV:A:k:" opt; do
+while getopts "i:m:l:p:a:s:r:gcV:A:k:" opt; do
     case $opt in
         i) export JOBID=$OPTARG;;
         l) export LOGBUCKET=$OPTARG;;  # bucket for sending log file
@@ -37,6 +39,7 @@ while getopts "i:m:l:p:a:s:r:gV:A:k:" opt; do
         s) export SECRET_KEY=$OPTARG;;  # secret key for certian s3 bucket access
         r) export REGION=$OPTARG;;  # region for the profile set for certian s3 bucket access
         g) export SINGULARITY_OPTION_TO_PASS=-g;;  # use singularity
+        c) export DISABLE_METRICS_COLLECTION=true;;  # disable metrics collection
         k) export S3_ENCRYPT_KEY_ID=$OPTARG;;  # KMS key ID to encrypt s3 files with
         h) printHelpAndExit 0;;
         [?]) printHelpAndExit 1;;
@@ -176,24 +179,29 @@ exl mkdir -p $LOCAL_OUTDIR
 mv $LOGFILE1 $LOGFILE2
 export LOGFILE=$LOGFILE2
 
-
 exl echo
-exl echo "## Installing and activating Cloudwatch agent to collect metrics"
 cwd0=$(pwd)
 cd ~
 
-ARCHITECTURE="$(dpkg --print-architecture)"
-CW_AGENT_LINK="https://s3.amazonaws.com/amazoncloudwatch-agent/ubuntu/${ARCHITECTURE}/latest/amazon-cloudwatch-agent.deb"
-apt install -y wget
-exl echo "Loading Cloudwatch Agent from ${CW_AGENT_LINK}"
-wget "${CW_AGENT_LINK}"
-sudo dpkg -i -E ./amazon-cloudwatch-agent.deb
-# If we want to collect new metrics, the following file has to be modified
-exl echo "## Using CW Agent config: https://raw.githubusercontent.com/4dn-dcic/tibanna/master/awsf3/cloudwatch_agent_config.json"
-wget https://raw.githubusercontent.com/4dn-dcic/tibanna/master/awsf3/cloudwatch_agent_config.json
-mv ./cloudwatch_agent_config.json /opt/aws/amazon-cloudwatch-agent/bin/config.json
-# This starts the agent with the downloaded configuration file
-sudo /opt/aws/amazon-cloudwatch-agent/bin/amazon-cloudwatch-agent-ctl -a fetch-config -m ec2 -s -c file:/opt/aws/amazon-cloudwatch-agent/bin/config.json
+if [ "$DISABLE_METRICS_COLLECTION" = false ] ; then
+  exl echo "## Installing and activating Cloudwatch agent to collect metrics"
+  ARCHITECTURE="$(dpkg --print-architecture)"
+  CW_AGENT_LINK="https://s3.amazonaws.com/amazoncloudwatch-agent/ubuntu/${ARCHITECTURE}/latest/amazon-cloudwatch-agent.deb"
+  apt install -y wget
+  exl echo "Loading Cloudwatch Agent from ${CW_AGENT_LINK}"
+  wget "${CW_AGENT_LINK}"
+  sudo dpkg -i -E ./amazon-cloudwatch-agent.deb
+  # If we want to collect new metrics, the following file has to be modified
+  exl echo "## Using CW Agent config: https://raw.githubusercontent.com/4dn-dcic/tibanna/master/awsf3/cloudwatch_agent_config.json"
+  wget https://raw.githubusercontent.com/4dn-dcic/tibanna/master/awsf3/cloudwatch_agent_config.json
+  mv ./cloudwatch_agent_config.json /opt/aws/amazon-cloudwatch-agent/bin/config.json
+  # This starts the agent with the downloaded configuration file
+  sudo /opt/aws/amazon-cloudwatch-agent/bin/amazon-cloudwatch-agent-ctl -a fetch-config -m ec2 -s -c file:/opt/aws/amazon-cloudwatch-agent/bin/config.json
+else
+  exl echo "## Metrics collection is disabled"
+fi
+
+
 
 # Set up cronjob to monitor AWS spot instance termination notice.
 # Works only in deployed Tibanna version >=1.6.0 since the ec2 needed more permissions to call `aws ec2 describe-spot-instance-requests`

docs/execution_json.rst

@@ -572,6 +572,10 @@ The ``config`` field describes execution configuration.
     - type of EBS (e.g. ``gp3``, ``gp2``, ``io1``, ``io2``)
     - optional (default: gp3 (version >= ``1.0.0``) or gp2 (version < ``1.0.0``))
 
+:disable_metrics_collection:
+    - <true|false>, default: false
+    - If true, the cloudwatch agent is not installed on the EC2 and CPU/memory/storage won't be collected and send to AWS CloudWatch. Disabling metrics collection can reduce CloudWatch associated costs.
+
 :cloudwatch_dashboard:
     - **This option is now depricated.**
     - if true, Memory Used, Disk Used, CPU Utilization Cloudwatch metrics are collected into a single Cloudwatch Dashboard page. (default ``false``)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "tibanna"
-version = "5.3.0"
+version = "5.4.0"
 description = "Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud."
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"

tibanna/ec2_utils.py

@@ -325,6 +325,8 @@ def fill_default(self):
             self.mem_as_is = False
         if not hasattr(self, 'ebs_size_as_is'):  # if false, add 5GB overhead
             self.ebs_size_as_is = False
+        if not hasattr(self, 'disable_metrics_collection'): 
+            self.disable_metrics_collection = False
         if not hasattr(self, 'ami_id'):
             self.ami_id = "" # will be assigned instance architecture specific later
         if not hasattr(self, 'ami_per_region'):
@@ -741,6 +743,8 @@ def create_userdata(self, profile=None):
         str += " -l $LOGBUCKET"
         str += " -V {version}".format(version=__version__)
         str += " -A {awsf_image}".format(awsf_image=cfg.awsf_image)
+        if cfg.disable_metrics_collection:
+            str += " -c"
         if cfg.kms_key_id:
             str += " -k %s" % cfg.kms_key_id
         if cfg.password:

tibanna/lambdas/requirements.txt

@@ -1,4 +1,4 @@
 Benchmark-4dn>=0.5.24
 boto3>=1.9.0
 botocore>=1.12.1
-tomlkit>=0.11.0
+tomlkit>=0.11.0,<1.0.0