Remote job submission

Introduction and disclaimer

A group from Universitat Pompeu Fabra has developed RBoinc, system for remote job submission and monitoring. This system allows scientists to submit jobs (or groups of jobs) from a convenient command-line interface.

In the following, we will use the scientist term to denote the individual who submits and administers the workunits on their workstation through the RBoinc 'client tools'. RBoinc client tools are not to be confused with BOINC clients (i.e. the slaves of the distributed computing architecture); for utmost clarity, we shall prefer the term scientist and scientist workstation to indicate the user of the RBoinc client and their machine.

Warning: this system has been used only by its developers. It will take some work to get it working on other projects.

• For details please see the paper T. Giorgino, M. J. Harvey and G. De Fabritiis, ​Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations, Comp. Phys. Commun. 181, 1402 (2010). http://boinc.berkeley.edu/rboinc.pdf pdf
• Powerpoint slides describing the system are here.
• Client instructions are at ​http://www.multiscalelab.org/utilities/RemoteBoincPublic

(c) 2011 Universitat Pompeu Fabra. Author: Toni Giorgino (at gmail).

Architecture

RBoinc is composed by the following main components

1. Client scripts, which are used by the scientists to submit and retrieve jobs. They are boinc_retrieve and boinc_submit.
2. Server cgis, used to handle files and interfacing with the rest of Boinc. They are called boinc_retrieve_server, boinc_submit_server
3. Various (optional) monitoring scripts, which generate nightly reports, statistics, and the like.

The software should be fairly self-explanatory, but installation may be tricky. The system is in boinc/rboinc/. Here's a general overview

• You will need an apache web server on the Boinc server (either the existing one, or a separate process). This instance will serve
  • the RBOINC cgi-scripts, e.g. at ​http://YOURSERVER:8383/rboinc_cgi
  • a scratch area for temporary file exchage, exposed via WEBDAV, e.g. at ​http://YOURSERVER:8383/DAV
• Wus naming is important and enforced like this: NNN-UUU_GGG-XX-YY-RNDzzzz where
  • NN is the name of the workunit (sub-group)
  • UU is the submitter id
  • GGG is the group
  • XX is the current step in the chain
  • YY is the total n. of steps
  • zzzz is a random number (not needed,actually)
• WUs are kept in a "workflow_directory", a subdir of the project dir, as per slide 22 of the Powerpoint. Inside each dir a "process" bash file is created, which is executed by the assimilator with the name of the assimilated WU as its argument. It will create_work the next step for execution.
• File storage is optimized through hardlinking and pooling. (Network transfers are not yet)
• Warning: authentication is not done yet (do secure the RBoinc port by firewall rules)

Both client and server are composed of Perl scripts (respectively command-line and cgi-bin). The XML::Simple module is used for (un-) xml-ing data structures over the network.

Client components

Installation

Client Perl scripts need be unpacked to some client-visible installation directory. Make sure your Perl installation fulfulls the dependencies (use cpan or your distribution's package manager if not).

Usage

Instructions on using the client scripts are temporarily hosted at ​http://www.multiscalelab.org/utilities/RemoteBoinc .

For details on the chaining mechanism, please see the paper T. Giorgino, M. J. Harvey and G. De Fabritiis, Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations, Comp. Phys. Commun. 181, 1402 (2010). http://boinc.berkeley.edu/rboinc.pdf pdf.

Server-side components

Installation

Overview of the steps to install the RBoinc server components are:

• Setup or adapt an instance of the apache web server on the boinc server (or change the boinc one) to serve the rboinc cgi and DAV paths. See the apache.conf example file provided with the distribution. We shall assume that apache will serve at ​http://YOUR_SERVER:8383/rboinc_cgi
• Copy the rboinc server scripts in the cgi directory, and edit the configuration file to suit your site setup.
• You may want to revise the process script. It is invoked every time a WU is complete, to perform the submission of the next chain step.
• Customize the WU and result template files, as directed below. This will RBoinc-enable Boinc applications of your choice.
• If desired, install the SQL stored procedures (monitoring components).

Security considerations

Servers and scientist's workstation should be on the same intranet and the RBoinc server ports should be firewalled. RBoinc is not meant to be exposed to the Internet. It should be however easy to modify the software to implement the two following protection mechanisms:

• Generic access control, i.e. only allowing authorized users to upload files to the DAV server. This is achieved by setting an access list to the WebDAV directory, with one entry per user. The rboinc clients should then use HTTP-based authentication to gain access to it.
• Scientist isolation. Currently, scientists can use the "-user" parameter to impersonate each other and work on a shared project. If this is not desired, the client should send a per-user authentication token (ideally the usual BOINC authenticator), and the rboinc server should check this against the requested group.

Annotating the WU template files

First, workunit template files should be marked as RBoinc-enabled at the top. This is achieved prepending the following tag to the relevant workunit template:

<rboinc application="md"
        description="Standard ACEMD run with optional DCD and PLUMED"/>

The above line marks the template as RBoinc-enabled and thus scientist-visible as an application. The application attribute will be the user-visible name of the application (which may or may not coincide with BOINC application names). The scientist will identify this template through the -app command line switch on the boinc_submit operation.

Additionally, input files in the workunit template are augmented with RBoinc-related settings. In the WU template, each file_ref element should have a child rboinc element as follows:

   <file_ref>
        <file_number>3</file_number>
        <open_name>input.vel</open_name>
        <copy_file/>
        <rboinc parameter_name="vel_file"
                parameter_description="Binary velocities"
                [ optional="true" ]
                [ immutable="true" ]
                [ encode="true" ]
                />
    </file_ref>

The parameter_name attribute is the command line parameter that will be required by the boinc_submit command for that file. The argument passed by the scientist on the command line to that parameter will be interpreted as a local file, transferred to the BOINC server, and associated to the given BOINC-handled file (in this case, number 3, with BOINC open name "input.vel").

The parameter_description is a descriptive text returned by the command line client when the scientist requests help for the attributes supported by the given application.

The optional optional flag specifies whether supplying the given file upon submission is mandatory or not. If not, it will be replaced by a (server-supplied) default file.

Likewise, the optional immutable flag specifies that the given file will be replaced by a server-supplied default file, and the submitter has no chance to override it.

Finally, if encode is true, the file is subject to a (server-defined) encoding before being sent. The server will store both the original and the encoded version (suffixed with _enc).

Annotating the result template files

Results template files are annotated with RBoinc-specific tags which identify which results should be transferred back to the scientist's workstation. The same tags can be used to build output-input chains, i.e. to automatically submit new workunits as continuations of successfully-completed ones.

The syntax for the results template is as follows:

<file_info>
    <name><OUTFILE_0/></name>
    <generated_locally/>
    <upload_when_present/>
    <max_nbytes>100000000</max_nbytes>
    <url><UPLOAD_URL/></url>
    <gzip_when_done/>
    <rboinc aliases=".vel .vel.gz" 
          [ chain="3" ]  />
</file_info>

The optional chain attribute indicates that, upon successful WU completion, that output file should be used as a third input file for the next step in the chain.

Upon retrieval, files have BOINC-assigned outfile names ending by '_1', '_2', and so on. The aliases attribute contains a space-separated list of extensions which serves two purposes:

• automatic renaming: retrieved files will receive the extension listed as a first element;
• avoiding duplicate retrievals: they are considered when deciding whether a file has been already downloaded (equivalence classes). For example, with the alias above, a result file called xx_1 will NOT be retrieved if one of the following files is present in the download directory: xx_1.vel, xx_1.vel.gz.

Frequently asked questions

Portability and server coexistence

Is your application directly compatible with Windows?

The client scripts are likely portable with minor changes (just install a good Perl interpreter and the required modules).

Is it possible to use your commands with different BOINC projects?

Normally a RBoinc server is tied to the corresponding Boinc server (but it can talk to any of its applications). The RBoinc clients can talk to multiple servers using different URLs (-url option).

I was thinking of having several Boinc projects to assign easily each of them to a specific group of users. Should I be installing multiple servers with their own URLs?

Yes - that will be the most flexible solution (e.g. you wil be able to perform maintenance on each of them separately, make firewall rules, etc). Alternatively, you can create several applications on the same server, if you prefer.

Server and installation

What is the relationship between RBoinc and the assimilator?

This important point should be clarified:

1. a client ("volunteer") computes and returns a WU, which is validated as usual
2. results are stored in "workflow_results/GROUPNAME" (something like name-USER_GROUPNAME-2-10-RND1234-...)
3. the WU is assimilated: the assimilator should execute the process script in the workflow_results/GROUPNAME
4. process creates a WU corresponding the next step of the chain (if necessary)
5. repeat from 1

The retrieve operation is completely independent of the above process: a retrieve can be requested at any time, and it will download any results stored in workflow_results/GROUPNAME.

What is ENCODE_EXECUTABLE ?

It's an optional script to pre-process files before submission, e.g. for a server-side sanity check, or reformatting, etc.

What is ETC_DIR => "$cgi/etc" ? Do I have to copy files included in server/etc ? Which ones will be used ?

Most notably, the files which are supplied as defaults (if any), e.g. those marked as <rboinc immutable="true"/> or <rboinc optional="true"/> in the template.

What is "process.sh"? Is it a daemon? What if server is restarted ?

process is created automatically by the boinc_submit_server in each GROUP directory. (It's at the end of the server submission script.) It's invoked in two cases:

1. as the last step of the submission, when everything has been set up. It will create_work and exit.
2. it will be invoked by the assimilator. if chaining is required, it will create_work for the next "chain step" (depending on the one which just ended successfully) and exit.

Therefore its execution is short and usually triggered by a daemon; stopping/restarting boinc will not affect it.

Job submission

Given that RBoinc takes care of uploading the files, will it be important to ensure that input files for different WUs have different names, so they don't conflict?

The scientist can use and reuse whatever names and contents he likes. The only thing that matters is the file content at the moment of submission. The RBoinc server will generate internal unique names (which are hidden from the user).

Will files with identical names conflict when they end up in the download directory?

No, they will be handled correctly: file names are made unique internally (in fact, equal to the file's MD5), even though the submitter used the same name for different contents. (It's fairly common e.g. for 1000 WUs to have in common at least one of the inputs).

Will there be a problem if a user send simultaneously 1000 jobs by a script?

It's perfectly fine (common indeed).

Retrieve

How does the manual retrieve operation affect workunits once a job has been performed?

Retrieve will free up space taken on the server by the results of the completed WUs. Currently running, scheduled, and future WUs will be otherwise unaffected (e.g., step1 may depend on step0 through the chaining mechanism).

Note, however, that a boinc_retrieve -stop ... command will stop the chaining machinery, ie. the generation of new WUs. This is a stop operation, which should not be confused with a retrieve.

And what about the results if you don't perform a "retrieve"?

The results are kept on the server until the issuing scientist retrieves them. (In fact, they may fill up the server if forgotten.)

The scientist may request the output at any time. Is it also possible to retrieve automatically the output in a predefined folder when a job is performed?

Yes, scientists may request the outputs of successfully-completed WUs at any time (even if they are part of a still-ongoing chain of WUs). Automatic retrieval on the issuing scientist's machine is conveniently done via cron jobs.

(Many thanks to Boris Dayma).