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cytomining / profiling-handbook

Image-based Profiling Handbook
https://cytomining.github.io/profiling-handbook/
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Mounting AWS Volumes in Config #28

Closed gwaybio closed 2 years ago

gwaybio commented 5 years ago

Introduction

It took me a bit of troubleshooting to mount a volume as described in step 1.1. I eventually did get it to work, but the steps I used were not listed. It is possible (and even likely) that I am doing something slightly wrong that makes the instructions a bit off, but I thought it would be useful to document here:

Troubleshooting

The error I initially received upon login after SSH'ing into the instance was:

mount.nfs4: failed to resolve server name or service not known

I had initially thought this was because of improper region settings so I double checked these. They looked ok to me, so I looked into why I was getting this error on login.

I saw this line in the .bashrc

sudo mount -t nfs4 -o nfsvers=4.1,rsize=1048576,wsize=1048576,hard,timeo=600,retrans=2 us-east-1a.fs-3609f37f.efs.us-east-1.amazonaws.com:/ ~/efs

(I also tried swapping us-east-1a with us-east-1b to no effect)

However, the volume on the AWS gui still looked like it was assigned to the correct instance.

So, after adding my credentials in an aws configure command, I successfully mounted the volume after following these steps. It worked! 🎉

Recommendation

So, not sure to what extent this solution is specific to me (maybe I configured something slightly wrong) or if it belongs in the actual handbook. Either way I thought it was useful to document.

gwaybio commented 5 years ago

Ah, I now see a similar set of instructions at the bottom of the page in step 1.1 that describes a similar procedure!

shntnu commented 5 years ago

Thanks for documenting all this!

sudo mount -t nfs4 -o nfsvers=4.1,rsize=1048576,wsize=1048576,hard,timeo=600,retrans=2 us-east-1a.fs-3609f37f.efs.us-east-1.amazonaws.com:/ ~/efs

^ that line is for mounting the network file system ("EFS") whereas you want to mound a local disk ("EBS")

You've figured out how to mount an EBS, and indeed, I think you need to have created the EBS in the same region (and maybe same availability zone (AZ)?) to be able to mount.

@gwaygenomics If you can confirm that, please edit this following line appropriately (i.e. say that it should be in the same region and AZ): https://github.com/cytomining/profiling-handbook/blob/c2b577fa17cf51abfdc957b246d3e4992c2e7549/01-config.Rmd#L96

shntnu commented 5 years ago

So the above is regarding EBS, but did your EFS mount ok? i.e. when you so ls ~/efs/, do you see anything? @gwaygenomics

gwaybio commented 5 years ago

Hmm, still new to this - didn't realize the distinction between EBS and EFS! Indeed, the project structure is there with ls ~/efs/

gwaybio commented 5 years ago

I still do get an error upon login though:

mount.nfs4: Failed to resolve server us-east-1a.fs-3609f37f.efs.us-east-1.amazonaws.com: Name or service not known

Maybe this is safe to ignore?