configs
configs copied to clipboard
Azure: Update to Azure config [WIP]
Additions:
- More Azure specific features included in NF-Core config
Relates to #401
name: Azure about: Add more features to Azure config
Please follow these steps before submitting your PR:
- [x] If your PR is a work in progress, include
[WIP]
in its title - [x] Your PR targets the
master
branch - [ ] You've included links to relevant issues, if any
Steps for adding a new config profile:
- [x] Add your custom config file to the
conf/
directory - [x] Add your documentation file to the
docs/
directory - [x] Add your custom profile to the
nfcore_custom.config
file in the top-level directory - [x] Add your custom profile to the
README.md
file in the top-level directory - [x] Add your profile name to the
profile:
scope in.github/workflows/main.yml
Check if nextflow config runs in repository root
tests can be ignored, it's a bug in NXF
@vsmalladi I haven't had a chance to check this. I'm on leave next week but when I get a chance I will give it a go. If it has everything we need and doesn't break anything we should smash that merge button.
@vsmalladi I'm finding this raises an error with the autoscaling formula. Works fine if autoscalling is turned off. Have you found this?
Caused by:
Status code 400, {
"odata.metadata":"REDACTED/$metadata#Microsoft.Azure.Batch.Protocol.Entities.Container.errors/@Element","code":"AutoScalingFormulaEvaluationError","message":{
"lang":"en-US","value":"The specified auto-scaling formula has evaluation error\nRequestId:e89088e4-6879-4f4c-9d49-f413864b358b\nTime:2022-10-25T15:44:23.3590143Z"
},"values":[
{
"key":"Message","value":"Line 3, Col 25: Argument 1 is invalid"
},{
"key":"Result","value":"$TargetDedicatedNodes=0;$TargetLowPriorityNodes=0;$NodeDeallocationOption=requeue"
}
]
}
@adamrtalbot That is odd. I have not found that issue. Can you see your quota for Dedicated nodes in Dv3 family?
Looks like plenty of nodes. If I turn off autoscaling it's fine. If I add a custom autoscaling formula to the pool it's fine:
pools {
auto {
vmType = params.vm_type
autoScale = true
vmCount = 1
maxVmCount = 12
scaleFormula = '''
$TargetLowPriorityNodes = 1;
$TargetDedicatedNodes = 0;
$NodeDeallocationOption = taskcompletion;
'''
}
}
Is the default autoscaling formula in Nextflow broken?
@adamrtalbot What version of nextflow, and pipeline are you testing.
I can give it a try on my end.
nextflow -version
N E X T F L O W
version 22.04.5 build 5708
created 15-07-2022 16:09 UTC
cite doi:10.1038/nbt.3820
http://nextflow.io
java -version
openjdk version "17.0.4.1" 2022-08-12
OpenJDK Runtime Environment Temurin-17.0.4.1+1 (build 17.0.4.1+1)
OpenJDK 64-Bit Server VM Temurin-17.0.4.1+1 (build 17.0.4.1+1, mixed mode, sharing)
It fails with every pipeline, for example:
nextflow run \
nf-core/sarek \
-profile test \
-c ~/configs/conf/azurebatch.config \
-ansi-log false \
-w az://work/ \
--az_location $AZURE_BATCH_LOCATION \
--batch_name $AZURE_BATCH_ACCOUNT_NAME \
--batch_key $AZURE_BATCH_ACCOUNT_KEY \
--storage_name $AZURE_STORAGE_ACCOUNT_NAME \
--storage_key $AZURE_STORAGE_ACCOUNT_KEY
@adamrtalbot I just tested this config and had no issues running it as is.
N E X T F L O W
version 22.10.0 build 5826
created 13-10-2022 05:44 UTC (00:44 CDT)
cite doi:10.1038/nbt.3820
http://nextflow.io
The scaling is targeting low priority nodes, by default the autoscale would use dedicated nodes. So I wonder if you look at quotas in your batch account under Total dedicated vCPUs
and Dv3 Series
section to see if its 0. If its 0 then I think that would be the issue.
@vsmalladi if you had no issues, shall we just go for it?
@adamrtalbot ya lets merge and see if anyone brings up any issues that we can solve.