click on one task for the hello
when open task dialog click in the execution logs tab
then donwload the 1) task stdout, 2) task stderr, 3) task log and upload them here
thanks for your help, Paolo! I followed your instructions and downloaded
task-1.command.out.txt which had Bonjour world! inside, task-1.command.err.txt was empty and when tried to download task-1.command.log.txt got Unable to download file: .command.log message on the website. I've also checked a corresponding work directory here: /fusion/s3/my-bucket/scratch/5DQRTBKJsIIay1/bf/71c55281bdbbb44ead372c5acf3746 and it was empty.
let's followup tmorrow
Hi Paolo, thanks! I've used this policy - https://github.com/seqeralabs/nf-tower-aws/blob/4aa2b6f913928cdf5ac9a270022b80d306d56b18/forge/forge-policy.json#L59, which only mentions
s3:get and s3:list. Is that the correct one?
though, looks like I completely missed this section... https://help.tower.nf/compute-envs/aws-batch/#access-to-s3-buckets
Ok, let me try
I ended up creating a user group (it has larger character limit on policies), I've added both https://github.com/seqeralabs/nf-tower-aws/blob/master/forge/forge-policy.json (compute) and https://github.com/seqeralabs/nf-tower-aws/blob/master/launch/s3-bucket-write.json (s3 access) policies to that group. Then I added my tower user to that group. Then I reran the Hello world pipeline, but it's still the same, the pipeline finishes without problems, but there are no
.command.* files in the work directories. Am I missing anything?
👆 I wonder if it has anything to do with this: https://github.com/seqeralabs/nf-tower/issues/327#issuecomment-956339788
I wonder could I deploy nf-tower in my local PC, and discard the SMTP auth to login?
if it is OK, any guide / link to the deploy? Thanks
if it is OK, any guide / link to the deploy? Thanks
What is the main tactics to handle spot instance restart (after it was terminated by AWS)? It looks like there is no exit code when this happens... Shall I just set
maxRetries to some reasonable value for all of the processes by default? (At the moment my maxRetries depends on the exit code, but as there is not exit code provided by AWS, it should be applied to any reason)
process.errorStrategy = 'retry'
process.maxRetries = 5 // or more
Hello to the NextFlow Community! What is the best way to trouble shoot an issue with trying to launch a nf workflow from tower using AWS Batch. My workflow worked great until recently when I tried to rerun it. There is likely an issue on the AWS side with my Jobs stuck in runnable status. I have exhausted all of my resources and looked at every option to resolve this issue from AWS, stack-overflow, etc. All my environments are healthy and functional. I have migrated to nf Tower thinking this would bypass or resolve my issues but they still persist. I don't know if this is the correct place to post this but I am desperate for help now. Thank you in advance!
Hello @kkerns85 , in my experience troubleshooting this kind of problem is "part art, part science" given the number of inter-connecting factors. We'd be happy to assist if you open an issue at https://github.com/seqeralabs/nf-tower/issues and can provide more details on your setup.
One initial suggestion I have for you is to check the underlying ECS clusters once your Jobs become Runnable - are Worker instances able to join the cluster(s), or does the membership count remain at 0?
One initial suggestion I have for you is to check the underlying ECS clusters once your Jobs become Runnable - are Worker instances able to join the cluster(s), or does the membership count remain at 0?
4 replies
Regarding nf-core pipelines, see the docs here: https://nf-co.re/developers/adding_pipelines (basically, join slack and tell us about it in the
#new-pipelines channel)
1 reply
Hi all - we're launching NF Tower actions programmatically. Our workflow runs often share identical parameters for the initial processes, but differ in the parameters used at later ones. Is there a way to always use the
-resume option in NF Tower, so that the outputs from these initial processes can be reused? Thanks!
21 replies
Hi all, I'm attempting to build HISAT2 indices for a large genome as part of the nf-core rnaseq pipeline. This is a high-memory, long running type of job since it's a big genome. It's a non-reference organisms, so I can't download these indices. I used tower to set up my compute environment on AWS batch with mainly default parameters. This particular job is getting stuck in the "submitted" state, and based on conversation with the slack channel, we're thinking this may be a scheduler / resource issue. Has anyone else run into something similar and know how to address it?
2 replies
I cant see launchpad and workspace , if I deployed it on local system.. http://localhost8000 .How to setup this on local?
The open source version is not the same as the version that runs at https://tower.nf - it's possible that it doesn't have these features
Which are the api's supported here - http://localhost:8080 ? I can see only GET api's like http://localhost:8080/service-info?token, http://localhost:8080/workflow/list?token
Has anyone come across (or documented) a breakdown of what capabilities are available between hosted, community and enterprise deployments of nextflow tower? Thank you! https://help.tower.nf/getting-started/deployments/
Off the top of my head I think that the hosted / enterprise editions can launch pipelines, have organisational structures with multi-user access and roles, workspaces for organising runs and credentials and so on. The community edition is basically just for monitoring runs that you launch yourself, and you can't really share those runs with anyone.
3 replies
(this is pretty much what those docs say too, just a little more verbose)
And a bunch of other stuff that I haven't mentioned probably.
Hi all, I'm testing Tower to see the capabilities of the tool and it's truly awesome. One doubt that I've is, is it possible to describe the same detail level for the nextflow CLI the compute environments? I mean, using Tower, I can define some parameters for example to create an Slurm cluster: login hostname, login port, etc. How these parameters could be used on a CLI Nextflow pipeline? Using executors? Thanks in advance!
for example, nextlow does not need to be aware of slurm login host, therefore there isn't such option
thanks for the answer @pditommaso , and how can we approach something similar without using Tower? for example, having a central node with Nextflow to deploy processes or pipelines against remote Slurm clusters? Maybe a wrapper or a custom script?
21 replies
Many many thanks for your answers again @ewels , and of course, congratule always the great work of the devs on the Nextflow/Tower tools because are truly awesome without doubts
Hi there, thanks for the great tool.
I’ve noticed lately that the jobs remain in the blue running state, even though they have been cancelled and are not running anymore. Failed jobs and successfully completed jobs are accurately reflected, however. For reference, I am running all my jobs on SLURM. I was wondering if there is maybe something I am doing wrong on my part or if there is any parameter I should change to fix this? I noticed this happening about a month ago. Thanks!
including the workflow id, and the nextflow logs
@pditommaso an "open in new tab" button would be nice :eyes: :sweat_smile: