A simple pbs queue management framework for multiple supercomputers
Cloudmesh PBS provides an easy mechanism to interface with queuing systems. It is based on cloudmesh version 2 that uses separate packages instead of one big cloudmesh package. The packages are named cloudmesh_*, where * is a placeholder for the package names.
The advantage of cloudmesh_pbs is that it can start pbs jobs on remote machines while using some simple templates. These jobs are entered in a local database and their status on the remote machines can be monitored. At this time we provide a simple API, but will soon add also a command interface as well as a secure rest interface.
The easiest way to install cloudmesh PBS is with pip. We recommend that you do it in a virtual environment. Once you have created and activated a virtualenv you can install cloudmesh_pbs with the following commands:
pip install cmd3 pip install cloudmesh_base pip install cloudmesh_database (not yet needed in this release) pip install cloudmesh_pbs
The source code can be found at:
When dealing with remote services we often need to customize interfaces and access. Instead of completely reinventing a specification file, we are leveraging first the ssh config file for the remote login to the servers that allow us to execute pbs commands. Second we have defined a simple yaml file that allows us to set up some service specific items. At this time it supports the specification of jobs submitted through various supercomputers that are either managed individually through queues, through groups of queues that are managed for multiple machines in a single management node.
We assume that you have set up all machine in ssh config that you like to access with a simple keyword. For example you like to access the machine cluster.example.com. We also assume you have the username albert on that machine. In this case we assume you have set up a simple ssh config such as:
Host cluster Hostname cluster.example.com User albert
Naturally once you place your public key in the authorized_hosts files on the cluster, you will be able to log into the machine with:
Naturally, you can try commands such as:
ssh cluster uname -a
You should be able to also verify if you can execute the command qstat with:
ssh cluster qstat
If this all works you can specify a yaml file for cloudmesh_pbs. We have included a sample yaml file in the etc directory of the source code that you can modify accordingly. If we use the example you will have:
meta: yaml_version: 2.1 kind: pbs cloudmesh: pbs: cluster: manager: cluster scripts: ~/qsub/india queues: - batch - long
This file is places in the directory ~/.cloudmesh
The important part of the file is in the cloudmesh - pbs portion. Here the name of the machine that we used in .ssh/config is used, e.g. cluster. The manager is specified to also be the machine cluster. This is the machine on which the qsub and qstat commands are executed for this machine. If the management node is different it can be specified here. The scripts attribute specifies where the pbs scripts are placed on the remote machine before they are submitted. To add specific queues you simply can include them as a list in the queues attribute
queue management will be enhanced
The API to interface with the queues is straight forward and documented in more details here:
A simple example will show you how to submit a job and check upon its status. First we define a default host:
host = "india"
Next we declare the pbs instance that we use to interact with the various systems. Upon creation it reads the ssh config file and the cloudmesh yaml file:
pbs = PBS(deploy=True) Next we find the manager of the host that we use to copy and to initiate the pbs commands on:: manager = pbs.manager(host)
let us create on that host the directory ~/scripts/test:
Now we need to create a pbs job script. For this we use a template that we have in the etc directory:
script_template = pbs.read_script("etc/job.pbs")
the template contains the ability to replace the script with some real commands. Let us use the uname command:
script = """ uname -a """
Also we want to give the job a unique id. For that we maintain in pbs an internal variable that will be increased every time we submit a job. We do it here with the incr command:
pbs.jobid_incr() jobname = "job-" + pbs.jobid_get() job_script = pbs.create_script(jobname, script, script_template)
Let us now submit the job to the given host:
r = pbs.qsub(jobname, host, script, template=script_template)
it will return the information of the job. Optionally one can define an output format (see the API) such as a dict or a yaml representation. To optain the PBS variable list as a dict we can use:
d = pbs.variable_list(r)
Status of the job
The status of a job can be obtained with:
r = jobstatus(self, host, jobid)
It will not only include the status, but also the environment variables the job is executed in.
Termination of the Job
Listing of all jobs
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