Submitting installations as Slurm jobs¶
EasyBuild can submit jobs to different backends including Slurm to install software, to distribute the often time-consuming installation of a set of software applications and the dependencies they require to a cluster.
This is done via the --job command line option.
It is important to be aware of some details before you start using this, which we'll cover here.
Configuration¶
The EasyBuild configuration that is active at the time that eb --job is used
will be passed down into the submitted job automatically, via command line options to the eb
command that is run in the job script.
This includes not only command line options used next to --job, but also configuration settings
that are specified via an EasyBuild configuration file or through
$EASYBUILD_* environment variables.
This implies that any EasyBuild configuration files or $EASYBUILD_* environment variables
that are in place in the job environment are most likely irrelevant, since configuration settings
they specify they will most likely be overruled by the corresponding command line options.
Using eb --job¶
Job backend¶
The default job backend in EasyBuild v4.x is GC3Pie.
To let EasyBuild submit jobs to Slurm instead, you should set the job-backend configuration setting
to Slurm, for example by setting the corresponding environment variable:
export EASYBUILD_JOB_BACKEND='Slurm'
Job resources¶
To submit an installation as a job, simply use eb --job:
eb example.eb --job
By default, EasyBuild will submit single-core jobs requesting for 24 hours of walltime.
You can tweak the requested resources via the job-cores and job-max-walltime configuration options.
For example:
# submit job to install example, using 5 cores and 2 hours of max. walltime
eb example.eb --job --job-cores 5 --job-max-walltime 2
Note that not all job-* configuration settings apply to all job backends,
see the EasyBuild documentation for more details.
Controlling Slurm submission options¶
When using Slurm as a job backend, EasyBuild will automatically generate job scripts which
use the eb command to perform a single installation. These scripts will be submitted
using the sbatch command.
EasyBuild currently doesn't provide away to customize the Slurm submission options,
for example to submit to a particular partition, or to use a particular account,
build you can set the corresponding $SBATCH_* environment variables prior to running eb --job.
For example, to specify a particular account that should be used for the jobs submitted by EasyBuild
(equivalent with using the -A or --account command line option for sbatch):
export SBATCH_ACCOUNT='example_project'
Or to submit to a particular Slurm partition (equivalent with the -p or --partition option for sbatch):
export SBATCH_PARTITION='example_partition'
For more information about supported $SBATCH_* environment variables,
see the Slurm documentation.
Combining --job and --robot¶
If one or more dependencies are still missing for the software you want to install,
you can combine --job and --robot to get EasyBuild to submit a separate job
for each of the installations. These jobs will not --robot, they will each only
perform a single installation.
Dependencies between jobs will be "registered" at submission time, so Slurm will put jobs on hold until the jobs that install the required (build) dependencies have completed successfully, and cancel jobs if the job to install a dependency failed for some reason.
Attention points¶
There are a couple of important things to keep an eye on when submitting installations as jobs...
Differences on cluster workernodes¶
Sometimes the resources available on the login nodes and cluster workernodes are slightly different, and you may need to take this into account in your EasyBuild configuration.
For example, plenty of disk space may be available in the /tmp temporary filesystem on a login node,
while the workernodes require you to use a different location for temporary files and directories.
As a result, you may need to slightly change your EasyBuild configuration when submitting installations
as jobs, to avoid that they fail almost instantly due to a lack of disk space.
Keep in mind that the active EasyBuild configuration is passed down into the submitted jobs, so any configuration that is present on the workernodes may not have any effect.
For example, if you commonly use /tmp/$USER for build directories on a login node,
you may need to tweak that when submitting jobs to use a different location:
# EasByuild is configured to use /tmp/$USER on the login node
login01 $ eb --show-config | grep buildpath
buildpath (E) = /tmp/example
# use /localdisk/$USER for build directories when submitting installations as jobs
login01 $ eb --job --buildpath /localdisk/$USER example.eb --robot
Temporary log files and build directories¶
The temporary log file that EasyBuild creates is most likely going to end up on the local disk
of the workernode on which the job was started (by default in $TMPDIR or /tmp).
If an installation fails, the job will finish and temporary files will likely be cleaned up instantly,
which may leave you wondering about the actual cause of the failing installation...
To remedy this, there are a couple of EasyBuild configuration options you can use:
-
You can use
--tmp-logdirto specify a different location where EasyBuild should store temporary log files, for example:$ eb --job example.eb --tmp-logdir $HOME/eb_tmplogs -
If you prefer having the entire log file stored in the Slurm job output files, you can use
--logtostdoutwhen submitting the jobs. This will result in extensive logging to your terminal window when submitting the jobs, but it will also make EasyBuild log tostdoutwhen the installation is running in the job, and hence the log messages will be captured in the job output files.
The same remark applies to build directories: they should be on a local filesystem (to avoid problems that often occur when building software on a parallel filesystem like GPFS or Lustre), which will probably be cleaned up automatically when a job fails. Here it is less easy to provide general advice on how to deal with this, but one thing you can consider is retrying the installation in an interactive job, so you can inspect the build directory after the installation fails.
Lock files¶
EasyBuild creates locks to prevent that the same installation is started multiple times on different system to the same installation directory.
If an installation fails or gets interrupted, EasyBuild cleans up those locks automatically.
However, if a Slurm job that is using EasyBuild to install software gets cancelled (because it
ran out of walltime, tried to consume too much memory, through an scancel command, etc.),
EasyBuild will not get the chance to clean up the lock file.
If this occurs you will need to either clean up the lock file (which is located in the software/.locks
subdirectory of installpath) manually, or re-submit the job with eb --job --ignore-locks.
Example¶
As an example, we will let EasyBuild submit jobs to install AUGUSTUS with the foss/2020b toolchain.
Configuration¶
Before using --job, let's make sure that EasyBuild is properly configured:
# use $HOME/easybuild for software, modules, sources, etc.
export EASYBUILD_PREFIX=$HOME/easybuild
# use ramdisk for build directories
export EASYBUILD_BUILDPATH=/dev/shm/$USER
# use Slurm as job backend
export EASYBUILD_JOB_BACKEND=Slurm
In addition, add the path to the centrally installed software to $MODULEPATH via module use:
module use /easybuild/modules/all
Load the EasyBuild module:
module load EasyBuild
Let's assume that we also need to inform Slurm that jobs should be submitted into a particular account:
export SBATCH_ACCOUNT=example_project
This will be picked up by the sbatch commands that EasyBuild will run to submit the software installation jobs.
Submitting jobs to install AUGUSTUS¶
Now we can let EasyBuild submit jobs for AUGUSTUS.
Let's first check what is still missing:
$ eb AUGUSTUS-3.4.0-foss-2020b.eb --missing
...
11 out of 61 required modules missing:
* HTSlib/1.11-GCC-10.2.0 (HTSlib-1.11-GCC-10.2.0.eb)
* lpsolve/5.5.2.11-GCC-10.2.0 (lpsolve-5.5.2.11-GCC-10.2.0.eb)
* Boost/1.74.0-GCC-10.2.0 (Boost-1.74.0-GCC-10.2.0.eb)
* GSL/2.6-GCC-10.2.0 (GSL-2.6-GCC-10.2.0.eb)
* SAMtools/1.11-GCC-10.2.0 (SAMtools-1.11-GCC-10.2.0.eb)
* BCFtools/1.11-GCC-10.2.0 (BCFtools-1.11-GCC-10.2.0.eb)
* METIS/5.1.0-GCCcore-10.2.0 (METIS-5.1.0-GCCcore-10.2.0.eb)
* BamTools/2.5.1-GCC-10.2.0 (BamTools-2.5.1-GCC-10.2.0.eb)
* MPFR/4.1.0-GCCcore-10.2.0 (MPFR-4.1.0-GCCcore-10.2.0.eb)
* SuiteSparse/5.8.1-foss-2020b-METIS-5.1.0 (SuiteSparse-5.8.1-foss-2020b-METIS-5.1.0.eb)
* AUGUSTUS/3.4.0-foss-2020b (AUGUSTUS-3.4.0-foss-2020b.eb)
Several dependencies are not installed yet, so we will need to use --robot to ensure that
EasyBuild also submits jobs to install these first.
To speed up the installations a bit, we will request 10 cores for each submitted job (via --job-cores).
That should be sufficient to let each installation finish in (well) under 1 hour,
so we only request 1 hour of walltime per job (via --job-max-walltime).
In order to have some meaningful job output files, we also enable trace mode (via --trace).
$ eb AUGUSTUS-3.4.0-foss-2020b.eb --job --job-cores 10 --job-max-walltime 1 --robot --trace
...
== resolving dependencies ...
...
== List of submitted jobs (11): Boost-1.74.0-GCC-10.2.0 (Boost/1.74.0-GCC-10.2.0): 1000011; GSL-2.6-GCC-10.2.0 (GSL/2.6-GCC-10.2.0): 1000004; SAMtools-1.11-GCC-10.2.0 (SAMtools/1.11-GCC-10.2.0): 1000005; HTSlib-1.11-GCC-10.2.0 (HTSlib/1.11-GCC-10.2.0): 1000006; BCFtools-1.11-GCC-10.2.0 (BCFtools/1.11-GCC-10.2.0): 1000001; lpsolve-5.5.2.11-GCC-10.2.0 (lpsolve/5.5.2.11-GCC-10.2.0): 1000007; BamTools-2.5.1-GCC-10.2.0 (BamTools/2.5.1-GCC-10.2.0): 1000008; METIS-5.1.0-GCCcore-10.2.0 (METIS/5.1.0-GCCcore-10.2.0): 1000009; MPFR-4.1.0-GCCcore-10.2.0 (MPFR/4.1.0-GCCcore-10.2.0): 1000010; SuiteSparse-5.8.1-foss-2020b-METIS-5.1.0 (SuiteSparse/5.8.1-foss-2020b-METIS-5.1.0): 1000002; AUGUSTUS-3.4.0-foss-2020b (AUGUSTUS/3.4.0-foss-2020b): 1000003
== Submitted parallel build jobs, exiting now
Inspecting the submitted jobs¶
Once EasyBuild has submitted the jobs, we can inspect them via Slurm's squeue command:
$ squeue -u $USER -la
JOBID PARTITION NAME USER STATE TIME TIME_LIMI NODES NODELIST(REASON)
1000001 small BCFtools user123 PENDING 0:00 2:00:00 1 (Dependency)
1000002 small SuiteSpa user123 PENDING 0:00 2:00:00 1 (Dependency)
1000003 small AUGUSTUS user123 PENDING 0:00 2:00:00 1 (Dependency)
1000004 small GSL-2.6- user123 RUNNING 0:21 2:00:00 1 node003
1000005 small SAMtools user123 RUNNING 0:21 2:00:00 1 node007
1000006 small HTSlib-1 user123 RUNNING 0:21 2:00:00 1 node007
1000007 small lpsolve- user123 RUNNING 0:21 2:00:00 1 node011
1000008 small BamTools user123 RUNNING 0:21 2:00:00 1 node011
1000009 small METIS-5. user123 RUNNING 0:21 2:00:00 1 node013
1000010 small MPFR-4.1 user123 RUNNING 0:21 2:00:00 1 node029
1000011 small Boost-1. user123 RUNNING 0:24 2:00:00 1 node029
Note that 3 jobs can not be started yet, because those installations require on one or more missing dependencies. As soon as the jobs for those dependencies (successfully) complete, these jobs will be able to start.
Final result¶
After about 20 minutes, AUGUSTUS and all missing dependencies should be installed:
$ ls -lrt $HOME/easybuild/modules/all/*/*.lua | tail -11
-rw-rw----. 1 example example 1634 Mar 29 10:13 /users/example/easybuild/modules/all/HTSlib/1.11-GCC-10.2.0.lua
-rw-rw----. 1 example example 1792 Mar 29 10:13 /users/example/easybuild/modules/all/SAMtools/1.11-GCC-10.2.0.lua
-rw-rw----. 1 example example 1147 Mar 29 10:13 /users/example/easybuild/modules/all/BamTools/2.5.1-GCC-10.2.0.lua
-rw-rw----. 1 example example 957 Mar 29 10:13 /users/example/easybuild/modules/all/lpsolve/5.5.2.11-GCC-10.2.0.lua
-rw-rw----. 1 example example 1549 Mar 29 10:13 /users/example/easybuild/modules/all/METIS/5.1.0-GCCcore-10.2.0.lua
-rw-rw----. 1 example example 1525 Mar 29 10:14 /users/example/easybuild/modules/all/GSL/2.6-GCC-10.2.0.lua
-rw-rw----. 1 example example 1221 Mar 29 10:15 /users/example/easybuild/modules/all/MPFR/4.1.0-GCCcore-10.2.0.lua
-rw-rw----. 1 example example 1678 Mar 29 10:15 /users/example/easybuild/modules/all/BCFtools/1.11-GCC-10.2.0.lua
-rw-rw----. 1 example example 1292 Mar 29 10:21 /users/example/easybuild/modules/all/Boost/1.74.0-GCC-10.2.0.lua
-rw-rw----. 1 example example 1365 Mar 29 10:28 /users/example/easybuild/modules/all/SuiteSparse/5.8.1-foss-2020b-METIS-5.1.0.lua
-rw-rw----. 1 example example 2233 Mar 29 10:30 /users/example/easybuild/modules/all/AUGUSTUS/3.4.0-foss-2020b.lua
$ module use $HOME/easybuild/modules/all
$ module avail AUGUSTUS
-------- /users/hkenneth/easybuild/modules/all --------
AUGUSTUS/3.4.0-foss-2020b