forked from rarias/bscpkgs
255 lines
8.7 KiB
Plaintext
255 lines
8.7 KiB
Plaintext
.TL
|
|
Garlic: the execution pipeline
|
|
.AU
|
|
Rodrigo Arias Mallo
|
|
.AI
|
|
Barcelona Supercomputing Center
|
|
.AB
|
|
.LP
|
|
This document covers the execution of experiments in the Garlic
|
|
benchmark, which are performed under strict conditions. The several
|
|
stages of the execution are documented so the experimenter can have a
|
|
global overview of how the benchmark runs under the hood.
|
|
The results of the experiment are stored in a known path to be used in
|
|
posterior processing steps.
|
|
.AE
|
|
.\"#####################################################################
|
|
.nr GROWPS 3
|
|
.nr PSINCR 1.5p
|
|
.\".nr PD 0.5m
|
|
.nr PI 2m
|
|
\".2C
|
|
.\"#####################################################################
|
|
.NH 1
|
|
Introduction
|
|
.LP
|
|
Every experiment in the Garlic
|
|
benchmark is controlled by a single
|
|
.I nix
|
|
file placed in the
|
|
.CW garlic/exp
|
|
subdirectory.
|
|
Experiments are formed by several
|
|
.I "experimental units"
|
|
or simply
|
|
.I units .
|
|
A unit is the result of each unique configuration of the experiment
|
|
(typically involves the cartesian product of all factors) and
|
|
consists of several shell scripts executed sequentially to setup the
|
|
.I "execution environment" ,
|
|
which finally launch the actual program being analyzed.
|
|
The scripts that prepare the environment and the program itself are
|
|
called the
|
|
.I stages
|
|
of the execution and altogether form the
|
|
.I "execution pipeline"
|
|
or simply the
|
|
.I pipeline .
|
|
The experimenter must know with very good details all the stages
|
|
involved in the pipeline, as they have a large impact on the execution.
|
|
.PP
|
|
Additionally, the execution time is impacted by the target machine in
|
|
which the experiments run. The software used for the benchmark is
|
|
carefully configured and tuned for the hardware used in the execution;
|
|
in particular, the experiments are designed to run in MareNostrum 4
|
|
cluster with the SLURM workload manager and the Omni-Path
|
|
interconnection network. In the future we plan to add
|
|
support for other clusters in order to execute the experiments in other
|
|
machines.
|
|
.\"#####################################################################
|
|
.NH 1
|
|
Isolation
|
|
.LP
|
|
The benchmark is designed so that both the compilation of every software
|
|
package and the execution of the experiment is performed under strict
|
|
conditions. We can ensure that two executions of the same experiment are
|
|
actually running the same program in the same software environment.
|
|
.PP
|
|
All the software used by an experiment is included in the
|
|
.I "nix store"
|
|
which is, by convention, located at the
|
|
.CW /nix
|
|
directory. Unfortunately, it is common for libraries to try to load
|
|
software from other paths like
|
|
.CW /usr
|
|
or
|
|
.CW /lib .
|
|
It is also common that configuration files are loaded from
|
|
.CW /etc
|
|
and from the home directory of the user that runs the experiment.
|
|
Additionally, some environment variables are recognized by the libraries
|
|
used in the experiment, which change their behavior. As we cannot
|
|
control the software and configuration files in those directories, we
|
|
couldn't guarantee that the execution behaves as intended.
|
|
.PP
|
|
In order to avoid this problem, we create a
|
|
.I sandbox
|
|
where only the files in the nix store are available (with some other
|
|
exceptions). Therefore, even if the libraries try to access any path
|
|
outside the nix store, they will find that the files are not there
|
|
anymore. Additionally, the environment variables are cleared before
|
|
entering the environment (with some exceptions as well).
|
|
.\"#####################################################################
|
|
.NH 1
|
|
Execution pipeline
|
|
.LP
|
|
Several predefined stages form the
|
|
.I standard
|
|
execution pipeline and are defined in the
|
|
.I stdPipeline
|
|
array. The standard pipeline prepares the resources and the environment
|
|
to run a program (usually in parallel) in the compute nodes. It is
|
|
divided in two main parts:
|
|
connecting to the target machine to submit a job and executing the job.
|
|
Finally, the complete execution pipeline ends by running the actual
|
|
program, which is not part of the standard pipeline, as should be
|
|
defined differently for each program.
|
|
.NH 2
|
|
Job submission
|
|
.LP
|
|
Some stages are involved in the job submission: the
|
|
.I trebuchet
|
|
stage connects via
|
|
.I ssh
|
|
to the target machine and executes the next stage there. Once in the
|
|
target machine, the
|
|
.I runexp
|
|
stage computes the output path to store the experiment results, using
|
|
the user in the target machine and changes the working directory there.
|
|
In MareNostrum 4 the output path is at
|
|
.CW /gpfs/projects/bsc15/garlic/$user/out .
|
|
Then the
|
|
.I isolate
|
|
stage is executed to enter the sandbox and the
|
|
.I experiment
|
|
stage begins, which creates a directory to store the experiment output,
|
|
and launches several
|
|
.I unit
|
|
stages.
|
|
.PP
|
|
Each unit executes a
|
|
.I sbatch
|
|
stage which runs the
|
|
.I sbatch(1)
|
|
program with a job script that simply calls the next stage. The
|
|
sbatch program internally reads the
|
|
.CW /etc/slurm/slurm.conf
|
|
file from outside the sandbox, so we must explicitly allow this file to
|
|
be available, as well as the
|
|
.I munge
|
|
socket used for authentication by the SLURM daemon. Once the jobs are
|
|
submitted to SLURM, the experiment stage ends and the trebuchet finishes
|
|
the execution. The jobs will be queued for execution without any other
|
|
intervention from the user.
|
|
.PP
|
|
The rationale behind running sbatch from the sandbox is because the
|
|
options provided in environment variables override the options from the
|
|
job script. Therefore, we avoid this problem by running sbatch from the
|
|
sandbox, where the interfering environment variables are removed. The
|
|
sbatch program is also provided in the
|
|
.I "nix store" ,
|
|
with a version compatible with the SLURM daemon running in the target
|
|
machine.
|
|
.NH 2
|
|
Job execution
|
|
.LP
|
|
Once an unit job has been selected for execution, SLURM
|
|
allocates the resources (usually several nodes) and then selects one of
|
|
the nodes to run the job script: it is not executed in parallel yet.
|
|
The job script runs from a child process forked from on of the SLURM
|
|
daemon processes, which are outside the sandbox. Therefore, we first run the
|
|
.I isolate
|
|
stage
|
|
to enter the sandbox again.
|
|
.PP
|
|
The next stage is called
|
|
.I control
|
|
and determines if enough data has been generated by the experiment unit
|
|
or if it should continue repeating the execution. At the current time,
|
|
it is only implemented as a simple loop that runs the next stage a fixed
|
|
amount of times (by default, it is repeated 30 times).
|
|
.PP
|
|
The following stage is
|
|
.I srun
|
|
which launches several copies of the next stage to run in
|
|
parallel (when using more than one task). Runs one copy per task,
|
|
effectively creating one process per task. The CPUs affinity is
|
|
configured by the parameter
|
|
.I --cpu-bind
|
|
and is important to set it correctly (see more details in the
|
|
.I srun(1)
|
|
manual). Appending the
|
|
.I verbose
|
|
value to the cpu bind option causes srun to print the assigned affinity
|
|
of each task, which is very valuable when examining the execution log.
|
|
.PP
|
|
The mechanism by which srun executes multiple processes is the same used
|
|
by sbatch, it forks from a SLURM daemon running in the computing nodes.
|
|
Therefore, the execution begins outside the sandbox. The next stage is
|
|
.I isolate
|
|
which enters again the sandbox in every task. All remaining stages are
|
|
running now in parallel.
|
|
.\" ###################################################################
|
|
.NH 2
|
|
The program
|
|
.LP
|
|
At this point in the execution, the standard pipeline has been
|
|
completely executed, and we are ready to run the actual program that is
|
|
the matter of the experiment. Usually, programs require some arguments
|
|
to be passed in the command line. The
|
|
.I exec
|
|
stage sets the arguments (and optionally some environment variables) and
|
|
executes the last stage, the
|
|
.I program .
|
|
.PP
|
|
The experimenters are required to define these last stages, as they
|
|
define the specific way in which the program must be executed.
|
|
Additional stages may be included before or after the program run, so
|
|
they can perform additional steps.
|
|
.\" ###################################################################
|
|
.NH 2
|
|
Stage overview
|
|
.LP
|
|
The complete execution pipeline using the standard pipeline is shown in
|
|
the Table 1. Some properties are also reflected about the execution
|
|
stages.
|
|
.KF
|
|
.TS
|
|
center;
|
|
lB cB cB cB cB cB
|
|
l c c c c c.
|
|
_
|
|
Stage Target Safe Copies User Std
|
|
_
|
|
trebuchet xeon no no yes yes
|
|
runexp login no no yes yes
|
|
isolate login no no no yes
|
|
experiment login yes no no yes
|
|
unit login yes no no yes
|
|
sbatch login yes no no yes
|
|
_
|
|
isolate comp no no no yes
|
|
control comp yes no no yes
|
|
srun comp yes no no yes
|
|
isolate comp no yes no yes
|
|
_
|
|
exec comp yes yes no no
|
|
program comp yes yes no no
|
|
_
|
|
.TE
|
|
.QS
|
|
.B "Table 1" :
|
|
The stages of a complete execution pipeline. The
|
|
.B target
|
|
column determines where the stage is running,
|
|
.B safe
|
|
states if the stage begins the execution inside the sandbox,
|
|
.B user
|
|
if it can be executed directly by the user,
|
|
.B copies
|
|
if there are several instances running in parallel and
|
|
.B std
|
|
if is part of the standard execution pipeline.
|
|
.QE
|
|
.KE
|