Parallel computing allow to use several processor (CPU) for one job. The gain is not linear and often saturates around 8 or 16 threads but you can save a lot of time compare to one CPU.
Parallel computing can be available depending on the software and/or the input.
- Some software allow to use several CPU because they were developed for that purpose and some not: See Thread and MPI methods.
- If the input can be split and be processed separally, thus you can cut it in 100 files and launch 100 jobs.
ABiMS provide two environments depending on the software you will use:
- Thread: spread jobs within one node - Common
- MPI: spead jobs across all nodes - Rare
Environnement Thread
It's the more efficient method because all the exchanges of information take place within one hardware host. But the maximum number of CPU < the maximum number of CPU in the node.
The number of slots available across the cluster is 800 slots
qsub
Argument to use in the qsub script:
#$ -pe thread <number_of_cpu>
To book the slots as soon as they are relase -R y
software
To get the parameter within the software, display the help.
The variable $NSLOTS can be used in the program arguments to set the number of CPU according the the SGE setting -pe thread
Examples
- Blast : -a <number_of_cpu> note: it's more efficient to split the input query file
- TCoffee : -n_core <number_of_cpu> note: the default behaviour of TCoffe is to use all the CPU available. So please, set the number of CPU
- Mira : -GE:not=<nombre de coeurs>
Environnement MPI (implémentation avec la bibliothèque openMPI)
This method allow to submit parts of the job across the whole cluster. Thereby, there is more resource available. But this method is not as efficient as the Thread method because the information are exchanged through the network. Those software are also very rare.
The number of slots available across the cluster is 256 slots
Pre-requisites:
- To process jobs across the cluster, it's necessary to set up an authenfication rsa_key for ssh:
[<votre_login>@nz ~]$ cd $HOME/.ssh
[<votre_login>@nz .ssh]$ ssh-keygen -t rsa
[<votre_login>@nz .ssh]$ cat id_rsa.pub >> authorized_keys
- It is mandatory to log at least one time with each node before using the openmpi method (to append $HOME/.ssh/known_hosts). To facilitate this step, you can launch the following command:
[<votre_login>@nz ~]$ all_nodes.sh ls
qsub
Argument to use in the qsub script:
#$ -pe openmpi <number_of_cpu>
To book the slots as soon as they are relase -R y
The software must be launched though mpirun:
mpirun -np <nb core> <full_path_of_the_program> <arg program>
Example of qsub script:
#!/bin/bash
#$ -S /bin/bash
#$ -cwd # Export des variables
#$ -V
#$ -q long.q
#$ -pe openmpi 8
mpirun -np 8 /usr/local/genome2/bin/phyml-mpi -i input.phy --datatype "nt" --model 012345 --bootstrap 10 --search BEST --alpha e -f m --pinv e -o tlr --nclasses 4
The qsub command:
qsub ./phyml-mpi.sh
Software
Example of program which allow mpi:
- clustalw : sequence alignment
- raxmlHPC-MPI : phylogeny
- phyml-mpi : phylogeny
