cytomining / cytominer-vm Goto Github PK

https://github.com/GitCredentialManager/git-credential-manager#ubuntudebian-distributions

• cytominer_ami.json: update ami_name (latest Ubuntu) and related items in builders
• docker.sh: update to latest instructions
• efs.sh: nothing
• init.sh: nothing
• python.sh: specify versions for everything, use cytominer-database on PyPi. Add back Python2
• r.sh: specify versions for everything, figure out how to do that for R packages, use cytominer on CRAN
• s3.sh: update s3fs-fuse installation procedure
• tools.sh: use apt instead of apt-get
• README.md: explain why we use we need to mount S3, and any other FAQs
• all: wrap column to 80
• Figure out why an instance created with this AMI gives *** System restart required *** on launch. Maybe read this hashicorp/packer#4555 (comment)
• See if there is anything to be done here https://github.com/cytomining/cytominer-vm/pull/5/files#r607784533. @bethac07 had followed up with So I added sudo mount -a to the bashrc as well and that makes the bucket auto-mount, so in that sense it's "fixed", but I would be curious to understand how to make it work the way it does in the AMI
• Read this https://serverfault.com/a/261807 and make sure we are consistent with the roles of the three files.

Notes:
@connersk said: Yup used https://github.com/cytomining/cytominer-vm but I had to tweak a few things, the VM runs Ubuntu 14.04 which is no longer supported, so I updated it to Ubuntu 18.04, changed the R and python installations, and used a different means of creating a python 3 virtual environment

I used this recipe to make 2 new AMIs in 2 new accounts, which mostly worked fine, except that the EFS even though it shows that it was rw mounted was not letting me write to it. The fix was to sudo chmod 777 ~/efs once; once I did that, any other new machines made from that AMI no longer had that issue. I tried in the second AMI to switch our current chmod command in efs.sh to sudo chmod 777, but the issue persisted - maybe it needs to be run AFTER the initial mount, though I don't know why? Just wanted to document it here though.

I'm trying to build my vm using cytominer (so i can run CP through AWS) and am running into this error:

(base) mtegtmey@wm255-7d4 cytominer-vm % packer build  -var 'security_group_ids=sg-0ff4f2fd2399826dd' -var 'subnet_id=subnet-012ff95d179048dd8' -var 'vpc_id=vpc-04ed5c99b7ad6cfb8' cytominer_ami.json


amazon-ebs: output will be in this color.

==> amazon-ebs: Prevalidating any provided VPC information
==> amazon-ebs: Prevalidating AMI Name: cytomining/images/hvm-ssd/cytominer-ubuntu-bionic-18.04-amd64-server-1673888019
    amazon-ebs: Found Image ID: ami-08fdec01f5df9998f
==> amazon-ebs: Creating temporary keypair: packer_63c58113-0979-f18d-cda2-595cfe9c4429
==> amazon-ebs: Launching a source AWS instance...
    amazon-ebs: Instance ID: i-0f853212f9d6aa85c
==> amazon-ebs: Waiting for instance (i-0f853212f9d6aa85c) to become ready...
==> amazon-ebs: Using SSH communicator to connect: 100.25.119.37
==> amazon-ebs: Waiting for SSH to become available...
==> amazon-ebs: Timeout waiting for SSH.
==> amazon-ebs: Terminating the source AWS instance...
==> amazon-ebs: Cleaning up any extra volumes...
==> amazon-ebs: No volumes to clean up, skipping
==> amazon-ebs: Deleting temporary keypair...
Build 'amazon-ebs' errored after 5 minutes 52 seconds: Timeout waiting for SSH.

==> Wait completed after 5 minutes 52 seconds

==> Some builds didn't complete successfully and had errors:
--> amazon-ebs: Timeout waiting for SSH.

==> Builds finished but no artifacts were created.
(base) mtegtmey@wm255-7d4 cytominer-vm %

Am pretty unfamiliar with AWS at the moment, but here's a screenshot of my instance from my EC2 console. Maybe my ssh is just taking too long and timing out.

I've updated all of the .sh files to comply with my AWS configuration, any thoughts on how to troubleshoot this? Thanks!

feather
docopts

sudo apt-get install build-essential checkinstall python-setuptools