====== Use cases ======
===== OpenMPI + affinity =====

We saw that the Linux kernel seems to be incapable of using correctly all the CPUs from the cpusets.

Indeed, reserving 2 out of 8 cores on a node and running a code that uses 2
process, these 2 process where not well assigned to each cpu.
We had to give the CPU MAP to OpenMPI to do cpu_affinity:

<code bash>
 i=0 ; oarprint core -P host,cpuset -F "% slot=%" | while read line ; do echo "rank $i=$line"; ((i++)); done > affinity.txt

 [user@node12 tmp]$ mpirun -np 8 --mca btl openib,self -v -display-allocation -display-map  --machinefile $OAR_NODEFILE -rf affinity.txt /home/user/espresso-4.0.4/PW/pw.x < BeO_100.inp
</code>

===== NUMA topology optimization =====
In this use case, we've got a numa host (an Altix 450) having a "squared" topology: nodes are interconnected by routers like in this view:

{{:wiki:lfi_topology.png?nolink&300|}}
In yellow, "routers", in magenta, "nodes" (2 dual-core processors per node)

Routers interconnect IRUS (chassis) on which the nodes are plugged (4 or 5 nodes per IRU). 

What we want is that for jobs that can enter into 2 IRUS or less, minimize the distance between the resources (ie use IRUS that have only one router interconnexion between them). The topology may be siplified as follows:

{{:wiki:lfi_topology_square.png?nolink&300|}}

The idea is to use moldable jobs and an admission rule that converts automatically the user requests to a moldable job. This job uses 2 resource properties: **numa_x** and **numa_y** that may be analogue to the square coordinates. What we want in fact, is the job that ends the soonest between a job running on an X or on a Y coordinate (we only want vertical or horizontal placed jobs).

The numa_x and numa_y properties are set up this way (pnode is a property corresponding to physical nodes):

{|border="1"
!pnode
!iru
!numa_x
!numa_y
|-
|itanium1
|1
|0
|1
|-
|itanium2
|1
|0
|1
|-
|itanium3
|1
|0
|1
|-
|itanium4
|1
|0
|1
|-
|itanium5
|2
|1
|1
|-
|itanium6
|2
|1
|1
|-
|itanium7
|2
|1
|1
|-
|itanium8
|2
|1
|1
|-
|itanium9
|2
|1
|1
|-
|itanium10
|3
|0
|0
|-
|itanium11
|3
|0
|0
|-
|itanium12
|3
|0
|0
|-
|itanium13
|3
|0
|0
|-
|itanium14
|3
|0
|0
|-
|itanium15
|4
|1
|0
|-
|itanium16
|4
|1
|0
|-
|itanium17
|4
|1
|0
|-
|itanium18
|4
|1
|0
|}

For example, the following requested ressources:
<code>
 -l /core=16
</code>
will result into:
<code>
 -l /numa_x=1/pnode=4/cpu=2/core=2 -l /numa_y=1/pnode=4/cpu=2/core=2
</code>

Here is the admission rule making that optimization:

<code bash>
 # Title : Numa optimization
 # Description : Creates a moldable job to take into account the "squared" topology of an Altix 450
 my $n_core_per_cpus=2;
 my $n_cpu_per_pnode=2;
 if (grep(/^itanium$/, @{$type_list}) && (grep(/^manual$/, @{$type_list}) == "") && $#$ref_resource_list == 0){
   print "[ADMINSSION RULE] Optimizing for numa architecture (use \\"-t manual\\" to disable)";
   my $resources_def=$ref_resource_list->[0];
   my $core=0;
   my $cpu=0;
   my $pnode=0;
   foreach my $r (@{$resources_def->[0]}) {
     foreach my $resource (@{$r->{resources}}) {
       if ($resource->{resource} eq "core") {$core=$resource->{value};}
       if ($resource->{resource} eq "cpu") {$cpu=$resource->{value};}
       if ($resource->{resource} eq "pnode") {$pnode=$resource->{value};}
     }
   }
   # Now, calculate the number of total cores
   my $n_cores=0;
   if ($pnode == 0 && $cpu != 0 && $core == 0) {
     $n_cores = $cpu*$n_core_per_cpus;
   }
   elsif ($pnode != 0 && $cpu == 0 && $core == 0) {
     $n_cores = $pnode*$n_cpu_per_pnode*$n_core_per_cpus;
   }
   elsif ($pnode != 0 && $cpu == 0 && $core != 0) {
     $n_cores = $pnode*$core;
   }
   elsif ($pnode == 0 && $cpu != 0 && $core != 0) {
     $n_cores = $cpu*$core;
   }
   elsif ($pnode == 0 && $cpu == 0 && $core != 0) {
     $n_cores = $core;
   }
   else { $n_cores = $pnode*$cpu*$core; }
   print "[ADMINSSION RULE] You requested $n_cores cores\";
   if ($n_cores > 32) {
     print "[ADMISSION RULE] Big job (>32 cores), no optimization is possible";
   }else{
     print "[ADMISSION RULE] Optimization produces: /numa_x=1/$pnode/$cpu/$core
                                         /numa_y=1/$pnode/$cpu/$core";
 
     my @newarray=eval(Dumper(@{$ref_resource_list}->[0]));
     push (@{$ref_resource_list},@newarray);
     unshift(@{%{@{@{@{$ref_resource_list}->[0]}->[0]}->[0]}->{resources}},{'resource' => 'numa_x','value' => '1'});
     unshift(@{%{@{@{@{$ref_resource_list}->[1]}->[0]}->[0]}->{resources}},{'resource' => 'numa_y','value' => '1'});
   }
 }
</code>

====== Users tips ======
===== oarsh completion =====
//Tip based on an idea from Jerome Reybert//

In order to complete nodes names in a oarsh command, add these lines in your .bashrc

<code bash>
function _oarsh_complete_() {
  if [ -n "$OAR_NODEFILE" -a "$COMP_CWORD" -eq 1 ]; then
    local word=${comp_words[comp_cword]}
    local list=$(cat $OAR_NODEFILE | uniq | tr '\n' ' ')
    COMPREPLY=($(compgen -W "$list" -- "${word}"))
  fi
}
complete -o default -F _oarsh_complete_ oarsh
</code>

Then try oarsh <TAB>
===== OAR aware shell prompt for Interactive jobs =====
If you want to have a bash prompt with your job id and the remaining walltime then you can add in your ~/.bashrc:

<code bash>
if [ "$PS1" ]; then
    __oar_ps1_remaining_time(){
        if [ -n "$OAR_JOB_WALLTIME_SECONDS" -a -n "$OAR_NODE_FILE" -a -r "$OAR_NODE_FILE" ]; then
            DATE_NOW=$(date +%s)
            DATE_JOB_START=$(stat -c %Y $OAR_NODE_FILE)
            DATE_TMP=$OAR_JOB_WALLTIME_SECONDS
            ((DATE_TMP = (DATE_TMP - DATE_NOW + DATE_JOB_START) / 60))
            echo -n "$DATE_TMP"
        fi
    }
    PS1='[\u@\h|\W]$([ -n "$OAR_NODE_FILE" ] && echo -n "(\[\e[1;32m\]$OAR_JOB_ID\[\e[0m\]-->\[\e[1;34m\]$(__oar_ps1_remaining_time)mn\[\e[0m\])")\$ '
    if [ -n "$OAR_NODE_FILE" ]; then
        echo "[OAR] OAR_JOB_ID=$OAR_JOB_ID"
        echo "[OAR] Your nodes are:"
        sort $OAR_NODE_FILE | uniq -c | awk '{printf("      %s*%d", $2, $1)}END{printf("\n")}' | sed -e 's/,$//'
    fi
fi
</code>


Then the prompt inside an Interactive job will be like:

<code bash>
  [capitn@node006~](3101-->29mn)$
</code>

===== Many small jobs grouping =====
Many small jobs of a few seconds may be painful for the OAR system. OAR may spend more time scheduling, allocating and launching than the actual computation time for each job.

Gabriel Moreau developed a script that may be useful when you have a large set of small jobs. It groups you jobs into a unique bigger OAR job:
  * http://servforge.legi.grenoble-inp.fr/pub/soft-trokata/oarutils/oar-parexec.html
You can download it from this page:
  * http://servforge.legi.grenoble-inp.fr/projects/soft-trokata/wiki/SoftWare/OarUtils

For a more generic approach you can use Cigri, a grid middleware running onto OAR cluster(s) that is able to automatically group parametric jobs. Cigri is currently in a re-writing process and a new public release is planned for the end of 2012.

Please contact Bruno.Bzeznik@imag.fr for more informations.

===== Overcoming quoting issues n oarsub commands =====
One may get a bit of a weird behavior when trying to submit a series of jobs through a bash script. For instance:
<code bash>
#!/bin/bash

for d in ../test/*/ ; do
    CMD="oarsub -p \"cputype='xeon'\" -l /nodes=1,walltime=04:00:00 -S \"./myscript.sh $d/in $d/out\""
    echo $CMD
    $CMD
done
</code>
This does not work, due to quoting issues.

A solution is to use a bash arrays to define the command, as follows:
<code bash>
#!/bin/bash

for d in ../test/*/ ; do
    declare -a CMD
    CMD=(oarsub -p "cputype='xeon'" -l /nodes=1,walltime=04:00:00 -S "./myscript.sh $d/in $d/out")
    "${CMD[@]}"
done
</code>
This works.
===== Environment variables through oarsh =====

  * http://servforge.legi.grenoble-inp.fr/pub/soft-trokata/oarutils/oar-envsh.html
  * http://servforge.legi.grenoble-inp.fr/projects/soft-trokata/wiki/SoftWare/OarUtils