Bosco 1.1 Release

In the last few months, I have outlined the new features of Bosco 1.1.

• Mutli-Cluster Support
• Multi-OS Support
• Single Port Usage
• SSH File Transfer

I am happy to announce that today we are releasing Bosco 1.1.  The official Release notes are available on the OSG Twiki.  It includes all of the features given above.  Try it out!

BOSCO v1.1 Features: Multi-Cluster Support

This is the forth in the in the series of features in the 1.1 release of BOSCO.  The previous posts have focused on SSH File Transfer, Single Port Usage, and Multi-OS Support.  All of these features are new in the 1.1 release.  But now I want to talk about a feature that was in the previous 1.0 release, but is important enough to discuss again, Multi-Cluster Support.  This feature is very technically challenging, so I will start with why you care about Multi-Cluster in BOSCO.

Why do you care about Multi-Cluster?

On a typical campus, the each department may have it's own cluster for their use.  Physics may have a cluster, Computer Science has one, and Chemistry may have another.  Or a computing center may have multiple clusters reflecting multiple generations of hardware.  In either of these cases, users have to pick which cluster to submit jobs to, rather than submitting to which ever has the most free cores.

You don't care what cluster you run on.  You don't care how to submit jobs to the PBS Chemistry cluster or the SGE Computer Science cluster.  In addition, who wants to learn two different cluster submission methods.  You only care about finishing your research.

BOSCO can unify the clusters by overlaying each cluster with an on demand Condor cluster.  That way, you only learn the Condor submission method.  The Condor job you submit to BOSCO will then be run at whichever cluster has the first free cores for you to run on.

What Is Multi-Cluster?

In BOSCO, Multi-Cluster is the feature that allows for submission to multiple clusters with a single submit file.  A user can submit a regular file, such as:

universe = vanilla
output = stdout.out
error = stderr.err
Executable = /bin/echo
arguments = hello
log = job.log
should_transfer_files = YES
when_to_transfer_output = ON_EXIT
queue 1

When the job is submitted, BOSCO will submit glideins to each of the clusters that are configured in BOSCO.  The glideins will start on the worker nodes of the remote clusters and join the local pool at the submission host, creating an on-demand Condor pool.  The jobs will then run on the remote worker nodes through the glideins.  This may be best illustrated by a picture I made for my thesis:

Overview of the BOSCO job submission to a PBS cluster

In the diagram, first BOSCO will submit the glidein to the PBS cluster.  Second, PBS will schedule and start the glidein on a worker node.  Finally, the glidein will report to the BOSCO submit host and will start running user jobs.

The Multi-Cluster feature will continue to be a integral part of the BOSCO.

The Beta release of BOSCO is due out next week (fingers crossed!).  Be watching this blog, and the BOSCO website for more news.

BOSCO v1.1 Features: Multi-OS Support

This is part 3 of my ongoing series describing new features in BOSCO v1.1.  Part 1 covered file transfer over SSH, Part 2 covered single port usage.  This post will cover the Multi-OS Support in BOSCO.

What is it?

The Multi-OS feature is intended to allow users to submit to clusters that may not be the same operating system as the submit host.  This is especially useful when users are running a submit host on their personal computer that is running Debian, while the supercomputer in the next building is running Red Hat 6, a common occurrence.

The Multi-OS components follow a basic process in order to operate:

1. Detect the remote operating system with the findplatform script.
2. Download (from the cloud?) the appropriate bosco version for the platform.
3. Transfer the files needed on the remote cluster.  This includes grabbing the libraries and binaries for the campus factory's glideins.  The glidein creation takes the most time of this process as it needs to compress the libraries and binaries before transferring.
4. When BOSCO detects jobs idle on the submit host, it will start glideins appropriate for the platform to service the jobs.

The Multi-OS support required modification of the cluster addition and adding both a findplatform script and a glidein_creation script.  

Why do I care?

It is becoming increasingly common that what users run on their machines and what is run on supercomputers are different.  When this is true, it is difficult to install software from one onto the other.  The Multi-OS feature will greatly simplify the installation of BOSCO on clusters.

Our goal with the Multi-OS support is that the users may not know it is even working.  The users just say: "I want to run on this cluster", and BOSCO makes it happen.  No matter what operating system is running on the remote cluster.

One of my tests simulated a possible user scenario   I was running a updated RHEL 6 machine which I installed BOSCO.  I wanted to submit jobs to a RHEL 5 cluster located in our datacenter.  If I simply copied over the bosco install from the RHEL 6 submit host, none of the binaries would work.  But instead, I used the bosco_cluster -a to add the RHEL 5 cluster, and jobs ran seamlessly from the RHEL 6 machine to the RHEL 5.  

The Multi-OS support is available in the latest alphas available on the bosco download page.

BOSCO v1.1 Features: Single Port Usage

Welcome to part 2 of my ongoing series of v1.1 features for BOSCO.  Part 1 was on SSH File Transfer.

This time, I'll talk about a new feature that we didn't planned on implementing at first, using only a single port for all communication.  After a small investigation, it was discovered that using a single port is very simple, and with no interruption to other components.  I talked briefly about it in a previous post.

What is it?

In 1.0 of BOSCO, the submit host needed a lot of ports open for connections originating from the remote clusters.  This was caused by 2 mechanisms:

1. File transfer from the BOSCO submit host to the cluster login node before issuing the local submit call (qsub, condor_submit...).  This opens ports on the submit host because the cluster would call out to the submit host to initiate transfers.
2. Connections for control, status, and workflow management between the cluster worker nodes and BOSCO submit host.  This is the Campus Factory, which gives BOSCO the traditional Condor look and feel.

In order for BOSCO to function, the submit host needs a large swath of ports in order to operate correctly.  Also, as you scale, you will need even more ports open.

The file transfers from the submit host to the login node are now being transferred using SSH, see my previous post.

With the new feature of single port usage, all control, status, and workflow management connections are routed through HTCondor's share_port_daemon on port 11000 (which is hardcoded, but I picked at random).

Why should I care?

Limiting BOSCO to using only 1 incoming port is very useful for users on systems not managed by them.  The node will only need 1 port open in order to run BOSCO, 11000.  If the system has a firewall, you only have to request port 11000 be opened, rather than huge swaths.  If you manage the system, then you will be happy that only 1 port needs to be opened in order to allow BOSCO submissions.

Administrators will like this feature as it is more in line with other applications that they may run.  For example, httpd only requires 1 port, 80.  Now BOSCO is in the same realm, only requiring 1 port, 11000.

BOSCO v1.1 Features: SSH File Transfer

I am hoping to write about a few of the new features of BOSCO 1.1 before it comes out in December or January.  This is part 1 of that series:

BOSCO v1.1 Feature: SSH File Transfer

What is it?

SSH File Transfer feature improves the method of staging input and output files to the remote cluster.  In 1.0, files are transferred by starting a daemon on the remote cluster that connects back to the submit host over a random port.  This required a lot of open ports on the submit host.  

The new SSH File Transfer will limit the number of ports required on the submit host.  BOSCO will now transfer files over a port that is forwarded over the SSH connection that BOSCO maintains with the remote cluster.  The transfers are inherently secure as they are over the SSH connection, as well as they are authenticated by the Condor daemons on either end of the connection (remote cluster and submit host).   

This fits into the BOSCO team's goal of lowering the amount of ports used by Condor.  Our eventual goal is using the Shared Port Daemon to limit the required ports to 1 for BOSCO on the submit host.

Why should I care?

This will greatly reduce the number of ports required if you are only using the universe=grid method of submitting jobs.  In fact, it will reduce the open ports on the submit host to 0.  That means no more configuring firewalls for BOSCO (no campus factory support, see below).  Additionally, there is no new configuration required for this feature, it 'just works' (famous last words?)

The Campus Factory, which adds features such as fault tolerant Condor file transfer and transparent multi-cluster support, still requires multiple open ports in the firewall.  Additional effort will be required to change the Campus Factory configuration and daemons to support the single port.  I hope that a single port will be all that is needed for v1.2.  

What's Next

Over the next couple weeks, I hope to write more about upcoming features such as:

• Multi-Platform support (ie cluster and submit host are different platforms)
• Mac OSX Support
• Improved Multi-User support

The Island Grid: Puerto Rico

In the last post, I discussed my trip to Puerto Rico.  Now that my trip is over, and I am back in Lincoln, I would like to share some of the successes of the trip.  I had a great time exploring old San Juan.  I have pictures as well.

Presenting the Holland Computing Center grid

Creating a new User

But on a more relevant note, the Campus Grid in Puerto Rico gained a new user while I was there.  I always feel that computing infrastructure is best built by user's demand.  That has certainly been the case at HCC, where we run between 95%+ utilization on our HPC clusters.  I met with Steve Massey to find how the Island Grid can help him.

Steve Massey is a bio-informatician at the University of Puerto Rico -- Rio Pedres.  His work is an ideal fit for High Throughput Computing.  His processing follows the model of using the same executable against many, many protein pdb files.  We talked for a while on Tuesday, both before and after the power was cut to the UPR campus, about how we can enable this work onto the UPR campus grid, flocking to UNL, and finally to the OSG.  While I was in PR, I worked with Steve to run one of his workflows on the OSG.

I'm not going to pretend to know what is really happening with the workflow, but it takes as input a set of DNA sequences that where pre-calculated (I believe somewhat random) and a pdb file, and calculates the robustness using an external application, Scwrl4.  The output is a robustness file that lists the robustness for the protein with the DNA sequences.

I was able to run this workflow on the OSG using Nebraska's GlideinWMS interface.  I created a submit.sh script that wrote out a simple Condor submit script, and wrapper.sh, that configured the environment on the worker node.  Both of the scripts are available on github.  Together, these two components create the workflow.

There is still work to be done.  The executable that Steve wrote does not properly detect the length of the strand of the amino acid, and therefore is not able to properly calculate robustness and/or send to Scwrl4.

Also, there is another workflow that Steve would like to run.  I hope to continue to work with him to enable these workflows.

Onto the Grid!

In addition to talking to Steve about creating workflows, I also discussed how to integrate his small cluster into the Island Grid in Puerto Rico.  The primary difficulty with adding his cluster is the university's very restrictive firewall.  Therefore, we will be unable to run a central submission host on his cluster, and flocking is out.  But, I believe between Jose and myself, we have a solution.  Either he can run BOSCO and submit through SSH to Steve's SGE cluster, or install Condor worker nodes on Steve's cluster to report to the primary campus cluster, nanobio.

I also talked with a Computer Science researcher to discuss putting his Mac Mini cluster on the Grid.  He is running Linux on the Mac Mini's, therefore it would be a good fit for the grid.  The frontend node to the Mac Mini cluster is not running linux, therefore BOSCO will not work as it needs a consistent platform on the frontend node and the worker nodes.  Instead we will have to install Condor worker nodes on the nodes themselves in order to access the Mac Mini's.

Conclusions

I believe that Puerto Rico has a lot to benefit from creating an Island (Campus) Grid.  They also have a very energetic administrator, Jose, who can spearhead the implementation, with close collaboration with myself and the campus grids team.

Building a Campus Grid on a Island

Hello everyone from San Juan, Puerto Rico.

Hanging Out

I joined my advisor, David, to the Track 2 external advisory board meeting.  My goals while here are:

• Work with Steve Massey to enable his workflow to run on the UPR campus grid.
• Enable HPCf to flock with other local Condor clusters (Steve's and CS's).
• Continue to work with HPCf to enable gratia accounting on their resources.
• Enable HPCf to Nebraska flocking.