This is a module factored out of legacy code to provide common bash utilities to Atlas scripts.
This package can be installed via Bioconda:
conda install -c ebi-gene-expression-group atlas-bash-util
Any of the bash functions from generic_routines.sh can be accessed via the atlas-bash-utils accessor script, like:
> atlas-bash-util capitalize_first_letter foo
Foo
This package also contains functions to facilitate submissions to our LSF compute cluster, principally this is for interactive waiting for jobs to run and checking of errors.
Usage:
atlas-lsf -h
Usage: ./atlas-lsf [ -c <command string> ] \
[ -w <working directory, default current working directory> ] \
[ -m <memory in MB or in the format <size>[units], defaults to cluster default. Different units can be specified using the suffix [K|M|G|T]> ] \
[ -p <number of cores, defaults to cluster default> ] \
[ -j <job name, defaults to cluster default> ] \
[ -g <job group name, defaults to cluster default> ] \
[ -l <log prefix, no logs written by default> ] \
[ -e <clean up log files after monitored run? Defaults to no> ] \
[ -m <monitor submitted job? Defaults to yes> ] \
[ -f <poll frequency in seconds if job is monitored. Defaults to 10.> ] \
[ -q <lsf queue, defaults to cluster default ]
[ -v <name of the conda environment in which to run the job> ]
Examples:
Submit a job but don't keep track of it:
> atlas-lsf -c "sleep 10" -f 2 -n no
Job submission succeeded, received job ID 5308898
Submit and monitor a job, see that it completes without error:
> atlas-lsf -c "sleep 10" -f 2 -s status
Job submission succeeded, received job ID 5308537
Starting status is PEND...
Status is now RUN.....
Status is now DONE
> echo $?
0
Submit and monitor a job and see that it fails:
> atlas-lsf -c "sleep 10; exit 5" -f 2 -s status
Job submission succeeded, received job ID 5308510
Starting status is PEND...
Status is now RUN.....
Status is now EXIT
Command "sleep 10; exit 5" failed, status EXIT
> echo $?
1
View STDOUT and STDERR of the job as it runs (this is the default style):
> ./atlas-lsf -c "echo ONE;sleep 5;echo TWO;echo ERROR 1>&2;sleep 5;echo THREE;echo BOO! 1>&2;" -l $(pwd)/foo -f 2 -s std_out_err
Job submission succeeded, received job ID 5316059
Monitor style: std_out_err
==> /path/to/foo.err <==
==> /path/to/foo.out <==
==> /path/to/foo.err <==
ERROR
==> /path/to/foo.out <==
ONE
TWO
==> /path/to/foo.err <==
BOO!
==> /path/to/foo.out <==
THREE
------------------------------------------------------------
Sender: LSF System <lsf@foo-cluster-47-01>
Subject: Job 5316059: <echo ONE;sleep 5;echo TWO;echo ERROR 1>&2;sleep 5;echo THREE;echo BOO! 1>&2> in cluster <cluster> Done
Job <echo ONE;sleep 5;echo TWO;echo ERROR 1>&2;sleep 5;echo THREE;echo BOO! 1>&2> was submitted from host <foo-cluster-08-04> by user <user> in cluster <cluster> at Thu Dec 2 17:36:28 2021
Job was executed on host(s) <foo-cluster-47-01>, in queue <standard>, as user <user> in cluster <cluster> at Thu Dec 2 17:36:29 2021
</homes/user> was used as the home directory.
</path/to> was used as the working directory.
Started at Thu Dec 2 17:36:29 2021
Terminated at Thu Dec 2 17:36:40 2021
Results reported at Thu Dec 2 17:36:40 2021
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
echo ONE;sleep 5;echo TWO;echo ERROR 1>&2;sleep 5;echo THREE;echo BOO! 1>&2;
------------------------------------------------------------
Successfully completed.
Resource usage summary:
CPU time : 0.04 sec.
Max Memory : 6 MB
Average Memory : 6.00 MB
Total Requested Memory : -
Delta Memory : -
Max Swap : -
Max Processes : 3
Max Threads : 4
Run time : 10 sec.
Turnaround time : 12 sec.
The output (if any) is above this job summary.
PS:
Read file </path/to/foo.err> for stderr output of this job.
Submit a job that should run in a conda environment:
> atlas-lsf -v myenv -c "echo $CONDA_PREFIX > myenv.txt" -f 2 -n no
Job submission succeeded, received job ID 2711148
>cat myenv.txt
/hps/software/users/GTL/user/miniconda3/envs/myenv
This package also contains functions to facilitate submissions to our SLURM compute cluster, principally this is for interactive waiting for jobs to run and checking of errors.
Usage:
./slurm/atlas-slurm -h
Usage: ./slurm/atlas-slurm [ -c <command string, mandatory field> ] \
[ -w <working directory, mandatory field> ] \
[ -m <memory in MB or in the format <size>[units], defaults to cluster default. Different units can be specified using the suffix [K|M|G|T]> ] \
[ -p <number of cores, defaults to cluster default> ] \
[ -j <job name, defaults to cluster default> ] \
[ -g <job group name, defaults to cluster default> ] \
[ -l <log prefix, no logs written by default> ] \
[ -e <clean up log files after monitored run? Defaults to no> ] \
[ -n <monitor submitted job? Defaults to yes> ] \
[ -o <with -l, print standard output content? Defaults to no> ] \
[ -s <monitor style: 'status' for job status updates on polling, 'std_out_err' to report ongoing content of logs (where used). Defaults to std_out_err> ] \
[ -f <poll frequency in seconds if job is monitored. Defaults to 10.> ] \
[ -q <slurm queue, defaults to cluster default> ] \
[ -u <suppress logging output? Default: no> ] \
[ -v <name of the conda environment in which to run the job> ]
Here, command (-c) and working directory (-w) are mandatory field for atlas-slurm. Specifying memory (-m) is advised, if memory is not specified with -m flag (e.g. -m 1G), it will use 4000Mb by default. If queue/partition is not specified it will use production by default.
Here, CPU-time is a mandatory field for SLURM submission. It will allocate maximum allowed time for the partition/queue by default.
Examples:
Submit and monitor a job, see that it completes without error:
> slurm/atlas-slurm -c "sleep 10" -f 2 -s status -m 2000 -w "/tmp"