Troubleshooting
Common SSH Issues¶
Here are some of the most common issues users face when using SSH.
Keys¶
The following clusters use SSH keys: Atomate, Farm, Franklin, HPC1, HPC2, Impact, Peloton.
If you connect to one of these and are asked for a password (as distinct from a passphrase for your key),
your key is not being recognized. This is usually because of permissions or an unexpected filename.
SSH expects your key to be one of a specific set of names. Unless you have specified something other than
the default, this is probably going to be $HOME/.ssh/id_rsa.
If you specified a different name when generating your key, you can specify it like this:
If you kept the default value, your permissions should be set so that only you can read and write the key (-rw------- or 600).
To ensure this is the case, you can do the following:
On HPC2, your public key is kept in $HOME/.ssh/authorized_keys. Please make sure to not remove your key from this file.
Doing so will cause you will lose access.
If you are trying to use a key to access LSSC0 or any of the Genome Center login nodes, SSH keys will not work, but there is another method.
To enable logins without a password, you will need to enable GSSAPI, which
some systems enable by default. If not enabled, add the following to your
$HOME/.ssh/config file (create it if it doesn't exist):
GSSAPIAuthentication yes
GSSAPIDelegateCredentials yes
The -K command line switch to ssh does the same thing on a one-time
basis.
Once you have GSSAPI enabled, you can get a Kerberos ticket using
SSH will use that ticket while it's valid.
Common Slurm Scheduler Issues¶
These are the most common issues with job scheduling using Slurm.
Using a non-default account¶
If you have access to more than one Slurm account and wish to use an account other than your default,
use the -A or --account flag.
e.g. If your default account is in foogrp and you wish to use bargrp:
No default account¶
Newer slurm accounts have no default specified, and in this case you might get error message like:
sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified
You will need to specify the account explicitly as explained above. You can find out how to view your Slurm account information in the resources section.