bscpkgs/garlic/doc/ug.mm

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.\" .COVER
.\" .TL
.\" Garlic: User guide
.\" .AF "Barcelona Supercomputing Center"
.\" .AU "Rodrigo Arias Mallo"
.\" .COVEND
.H 1 "Overview"
.P
The garlic framework is designed to fulfill all the requirements of an
experimenter in all the steps up to publication. The experience gained
while using it suggests that we move along three stages despicted in the
following diagram:
.DS CB
.S 9p 10p
.PS 5
linewid=1;
right
box "Source" "code"
arrow "Development" above
box "Program"
arrow "Experiment" above
box "Results"
arrow "Data" "exploration"
box "Figures"
.PE
.S P P
.DE
In the development phase the experimenter changes the source code in
order to introduce new features or fix bugs. Once the program is
considered functional, the next phase is the experimentation, where
several experiment configurations are tested to evaluate the program. It
is common that some problems are spotted during this phase, which lead
the experimenter to go back to the development phase and change the
source code.
.P
Finally, when the experiment is considered completed, the
experimenter moves to the next phase, which envolves the exploration of
the data generated by the experiment. During this phase, it is common to
generate results in the form of plots or tables which provide a clear
insight in those quantities of interest. It is also common that after
looking at the figures, some changes in the experiment configuration
need to be introduced (or even in the source code of the program).
.P
Therefore, the experimenter may move forward and backwards along three
phases several times. The garlic framework provides support for all the
three stages (with different degrees of madurity).
.H 1 "Development (work in progress)"
.P
During the development phase, a functional program is produced by
modifying its source code. This process is generally cyclic: the
developer needs to compile, debug and correct mistakes. We want to
minimize the delay times, so the programs can be executed as soon as
needed, but under a controlled environment so that the same behavior
occurs during the experimentation phase.
.P
In particular, we want that several experimenters can reproduce the
the same development environment so they can debug each other programs
when reporting bugs. Therefore, the environment must be carefully
controlled to avoid non-reproducible scenarios.
.\" ===================================================================
.H 2 "Getting the development tools"
.P
To create a development
environment, first copy or download the sources of your program (not the
dependencies) in a new directory placed in the target machine
(MareNostrum\~4).
.P
The default environment contains packages commonly used to develop
programs, listed in the \fIgarlic/index.nix\fP file:
.\" FIXME: Unify garlic.unsafeDevelop in garlic.develop, so we can
.\" specify the packages directly
.DS I
.VERBON
develop = let 
  packages = with self; [
    coreutils htop procps-ng vim which strace
    tmux gdb kakoune universal-ctags bashInteractive
    glibcLocales ncurses git screen curl
    # Add more nixpkgs packages here...
  ] ++ with bsc; [
    slurm clangOmpss2 icc mcxx perf
    # Add more bsc packages here...
  ];
  ...
.VERBOFF
.DE
If you need additional packages, add them to the list, so that they
become available in the environment. Those may include any dependency
required to build your program.
.P
Then use the build machine (xeon07) to build the
.I garlic.develop
derivation:
.DS I
.VERBON
build% nix-build -A garlic.develop
\&...
build% grep ln result
ln -fs /gpfs/projects/.../bin/stage1 .nix-develop
.VERBOFF
.DE
Copy the \fIln\fP command and run it in the target machine
(MareNostrum\~4), in the new directory used for your program
development. The link will be created as a hidden file named
\fI.nix-develop\fP and will be used to remember your environment.
Several environments can be stored using this method, with different
packages in different directories. You will need to rebuild the
.I garlic.develop
derivation and update the
.I .nix-develop
link after the package list changes to update the environment. Once the
environment link is created, there is no need to repeat this steps again.
.P
Before entering the environment, you will need to access the required
resources for your progam, which may include several compute nodes.
.\" ===================================================================
.H 2 "Allocating resources for development"
.P
Our target machine (MareNostrum 4) provides an interactive shell, that
can be requested with the number of computational resources required for
development. To do so, connect to the login node and allocate an
interactive session:
.DS I
.VERBON
% ssh mn1
login% salloc ...
target%
.VERBOFF
.DE
This operation may take some minutes to complete depending on the load
of the cluster. But once the session is ready, any subsequent execution
of programs will be immediate.
.\" ===================================================================
.H 2 "Accessing the developement environment"
.P
The utility program \fInix-develop\fP has been designed to access the
development environment of the current directory, by looking for the
\fI.nix-develop\fP file. It creates a namespace where the required
packages are installed and ready to be used. Now you can access the
newly created environment by running:
.DS I
.VERBON
target% nix-develop
develop%
.VERBOFF
.DE
The spawned shell contains all the packages pre-defined in the
\fIgarlic.develop\fP derivation, and can now be accessed by typing the
name of the commands.
.DS I
.VERBON
develop% which gcc
/nix/store/azayfhqyg9...s8aqfmy-gcc-wrapper-9.3.0/bin/gcc
develop% which gdb
/nix/store/1c833b2y8j...pnjn2nv9d46zv44dk-gdb-9.2/bin/gdb
.VERBOFF
.DE
If you need additional packages, you can add them in the
\fIgarlic/index.nix\fP file as mentioned previously. To keep the
same current resources, so you don't need to wait again for the
resources to be allocated, exit only from the development shell:
.DS I
.VERBON
develop% exit
target%
.VERBOFF
.DE
Then update the
.I .nix-develop
link and enter into the new develop environment:
.DS I
.VERBON
target% nix-develop
develop%
.VERBOFF
.DE
.\" ===================================================================
.H 2 "Execution"
The allocated shell can only execute tasks in the current node, which
may be enough for some tests. To do so, you can directly run your
program as:
.DS I
.VERBON
develop$ ./program
.VERBOFF
.DE
If you need to run a multi-node program, typically using MPI
communications, then you can do so by using srun. Notice that you need
to allocate several nodes when calling salloc previously. The srun
command will execute the given program \fBoutside\fP the development
environment if executed as-is. So we re-enter the develop environment by
calling nix-develop as a wrapper of the program:
.\" FIXME: wrap srun to reenter the develop environment by its own
.DS I
.VERBON
develop$ srun nix-develop ./program
.VERBOFF
.DE
.H 2 "Debugging"
The debugger can be used to directly execute the program if is executed
in only one node by using:
.DS I
.VERBON
develop$ gdb ./program
.VERBOFF
.DE
Or it can be attached to an already running program by using its PID.
You will need to first connect to the node running it (say target2), and
run gdb inside the nix-develop environment. Use
.I squeue
to see the compute nodes running your program: 
.DS I
.VERBON
login$ ssh target2
target2$ cd project-develop
target2$ nix-develop
develop$ gdb -p $pid
.VERBOFF
.DE
You can repeat this step to control the execution of programs running in
different nodes simultaneously.
.P
In those cases where the program crashes before being able to attach the
debugger, enable the generation of core dumps:
.DS I
.VERBON
develop$ ulimit -c unlimited
.VERBOFF
.DE
And rerun the program, which will generate a core file that can be
opened by gdb and contains the state of the memory when the crash
happened. Beware that the core dump file can be very large, depending on
the memory used by your program at the crash.
.\" ===================================================================
.H 1 "Experimentation"
The experimentation phase begins with a functional program which is the
object of study. The experimenter then designs an experiment aimed at
measuring some properties of the program. The experiment is then
executed and the results are stored for further analysis.
.H 2 "Writing the experiment configuration"
.P
The term experiment is quite overloaded in this document. We are going
to see how to write the recipe that describes the execution pipeline of
an experiment.
.P
Within the garlic benchmark, experiments are typically sorted by a
hierarchy depending on which application they belong. Take a look at the
\fCgarlic/exp\fP directory and you will find some folders and .nix
files.
.P
Each of those recipes files describe a function that returns a
derivation, which, once built will result in the first stage script of
the execution pipeline.
.P
The first part of states the name of the attributes required as the
input of the function. Typically some packages, common tools and options:
.DS I
.VERBON
{
  stdenv
, stdexp
, bsc
, targetMachine
, stages
, garlicTools
}:
.VERBOFF
.DE
.P
Notice the \fCtargetMachine\fP argument, which provides information
about the machine in which the experiment will run. You should write
your experiment in such a way that runs in multiple clusters.
.DS I
.VERBON
varConf = {
  blocks = [ 1 2 4 ];
  nodes = [ 1 ];
};
.VERBOFF
.DE
.P
The \fCvarConf\fP is the attribute set that allows you to vary some
factors in the experiment.
.DS I
.VERBON
genConf = var: fix (self: targetMachine.config // {
  expName = "example";
  unitName = self.expName + "-b" + toString self.blocks;
  blocks = var.blocks;
  nodes = var.nodes;
  cpusPerTask = 1;
  tasksPerNode = self.hw.socketsPerNode;
});
.VERBOFF
.DE
.P
The \fCgenConf\fP function is the central part of the description of the
experiment. Takes as input \fBone\fP configuration from the cartesian
product of
.I varConfig
and returns the complete configuration. In our case, it will be
called 3 times, with the following inputs at each time:
.DS I
.VERBON
{ blocks = 1; nodes = 1; }
{ blocks = 2; nodes = 1; }
{ blocks = 4; nodes = 1; }
.VERBOFF
.DE
.P
The return value can be inspected by calling the function in the
interactive nix repl:
.DS I
.VERBON
nix-repl> genConf { blocks = 2; nodes = 1; }
{
  blocks = 2;
  cpusPerTask = 1;
  expName = "example";
  hw = { ... };
  march = "skylake-avx512";
  mtune = "skylake-avx512";
  name = "mn4";
  nixPrefix = "/gpfs/projects/bsc15/nix";
  nodes = 1;
  sshHost = "mn1";
  tasksPerNode = 2;
  unitName = "example-b2";
}
.VERBOFF
.DE
.P
Some configuration parameters were added by
.I targetMachine.config ,
such as the
.I nixPrefix ,
.I sshHost
or the
.I hw
attribute set, which are specific for the cluster they experiment is
going to run. Also, the
.I unitName
got assigned the proper name based on the number of blocks, but the
number of tasks per node were assigned based on the hardware description
of the target machine.
.P
By following this rule, the experiments can easily be ported to machines
with other hardware characteristics, and we only need to define the
hardware details once. Then all the experiments will be updated based on
those details.
.H 2 "First steps"
.P
The complete results generally take a long time to be finished, so it is
advisable to design the experiments iteratively, in order to quickly
obtain some feedback. Some recommendations:
.BL
.LI
Start with one unit only.
.LI
Set the number of runs low (say 5) but more than one.
.LI
Use a small problem size, so the execution time is low.
.LI
Set the time limit low, so deadlocks are caught early.
.LE
.P
As soon as the first runs are complete, examine the results and test
that everything looks good. You would likely want to check:
.BL
.LI
The resources where assigned as intended (nodes and CPU affinity).
.LI
No errors or warnings: look at stderr and stdout logs.
.LI
If a deadlock happens, it will run out of the time limit.
.LE
.P
As you gain confidence over that the execution went as planned, begin
increasing the problem size, the number of runs, the time limit and
lastly the number of units. The rationale is that each unit that is
shared among experiments gets assigned the same hash. Therefore, you can
iteratively add more units to an experiment, and if they are already
executed (and the results were generated) is reused.
.SK
.H 1 "Annex A: Branch name diagram"
.DS CB
.S -2
.PS 4.6/25.4
copy "gitbranch.pic"
.PE
.S P
.DE
.TC