Common Errors and Warnings

bash

script.sh: line N: VARIABLE: unbound variable
The variable VARIABLE in script.sh is undefined when called at line N. Bash will report this as an error when set -u is defined in a script. If it is acceptable for VARIABLE to be undefined, rewrite the variable as ${VARIABLE:-}. That will replace the undefined variable with the empty string, suppressing the warning.

checkjob

job is deferred. Reason: NoResources (cannot create reservation for job 'N' (intital reservation attempt)
This is a fairly generic error. The number N is the job identifier. This error often means that the job requested more resources than are physically possibly on the given queue. Read all the output of checkjob carefully for more information about the job and why it might have failed to start. Refer to Resource Limits and Scheduling Policies for information on cluster limits.

qsub

qsub: Job exceeds queue resource limits MSG=cannot satisfy queue max walltime requirement
The job violated one or more of torque's resource requirements. in this case, MSG= indicates the job requested a walltime larger than the 30-day limit.
qsub: Job rejected by all possible destinations
This is an uncommon error. If you encounter this error, please let us know and include the script and command line that caused this error.
Warning: submit script is using /bin/sh. This is not recommended. Continuing regardless
The submit script is written to use /bin/sh as the interpreter instead of /bin/bash. This is not recommended as there are minor differences between the two that can cause problems with the job. This is only a warning: the job was submitted successfully. This warning is specific to the halcyon cluster.
Warning: Requested interpreter (${INTERPRETER}) does not exist or is not executable. Cowardly refusing to submit job
The scheduler had a problem finding or executing the interpreter requested and cancelled the job. The variable ${INTERPRETER} will be replaced with the detected interpreter. This is often caused by a mistake on the #! line at the top of the file. This can also occur if the script file uses DOS line endings. The command vi -c "set ff=unix" -c "wq" script.sh will convert a file to UNIX line endings. This warning is specific to the halcyon cluster.
Warning: submit script does not specify an interpreter using #! at the top of the file. This is a Bad Idea(tm). This script may or may not be run by your default shell (${SHELL}?). Continuing regardless
Either the script is missing the #! line or it is not at the top of the file. Empirical evidence has shown that the script will be executed with the user's login shell which is bash by default but a script should not rely upon this behavior. The variable ${SHELL} will be replaced with the contents of the shell variable of the same name which is usually the user's login shell. This is only a warning: the job was submitted successfully. This warning is specific to the halcyon cluster.