MATLAB® Distributed Computing Server™ Installation Guide R2012a
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Contents Product Installation 1 Cluster Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2 Installing Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . On the Cluster Nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . On the Client Nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4 1-4 1-4 ..........................
Configuring Parallel Computing Products for HPC Server 3 Configure Cluster for Microsoft Windows HPC Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2 Configure Client Computer for HPC Server 2008 . . . . . 3-3 Validate Installation Using Microsoft Windows HPC Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Step 1: Define a Cluster Profile . . . . . . . . . . . . . . . . . . . . . .
Configuring Parallel Computing Products for a Generic Scheduler 5 Interfacing with Generic Schedulers . . . . . . . . . . . . . . . . Support Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Submission Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2 5-2 5-2 Configure Generic Scheduler on Windows Cluster . . . . Without Delegation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Using Passwordless Delegation . . . . . . . . . . . . . .
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1 Product Installation • “Cluster Description” on page 1-2 • “Installing Products” on page 1-4 • “Configuring Your Cluster” on page 1-5 For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
1 Product Installation Cluster Description To set up a cluster, you first install MATLAB® Distributed Computing Server™ (MDCS) on a node called the head node. You can also install the license manager on the head node. After performing this installation, you can then optionally install MDCS on the individual cluster nodes, called worker nodes. You do not need to install the license manager on worker nodes. This figure shows the installations that you perform on your MDCS cluster nodes.
Cluster Description MDCS Cluster Client Node PCT Product Installations on Client Nodes For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
1 Product Installation Installing Products On the Cluster Nodes Install the MathWorks products on your cluster as a network installation according to the instructions found at http://www.mathworks.com/help/base/install/ These instructions include steps for installing, licensing, and activating your installation. You can install in a central location, or individually on each cluster node. Note MathWorks highly recommends installing all MathWorks products on the cluster.
Configuring Your Cluster Configuring Your Cluster When the cluster and client installations are complete, you can proceed to configure the products for the job scheduler of your choice.
1 1-6 Product Installation For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
2 Configuring Parallel Computing Products for an MJS • “Configure Cluster to Use a MATLAB Job Scheduler (MJS)” on page 2-2 • “Configure Windows Firewalls on Client” on page 2-22 • “Validate Installation with MJS” on page 2-23 For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
2 Configuring Parallel Computing Products for an MJS Configure Cluster to Use a MATLAB Job Scheduler (MJS) The mdce service must be running on all machines being used for MATLAB job schedulers (MJS) or workers. This service manages the MJS and worker processes. One of the major tasks of the mdce service is to recover the MJS and worker sessions after a system crash, so that jobs and tasks are not lost as a result of such accidents. The following figure shows the processes that run on your cluster nodes.
Configure Cluster to Use a MATLAB® Job Scheduler (MJS) Note If you do not have a Windows cluster, or if you have already installed a previous version of MATLAB Distributed Computing Server on your Windows cluster, you can skip this step and proceed to Step 2. Configure Windows Firewalls If you are using Windows® firewalls on your cluster nodes, 1 Log in as a user with administrator privileges. 2 Execute the following in a DOS command window. matlabroot\toolbox\distcomp\bin\addMatlabToWindowsFirewall.
2 Configuring Parallel Computing Products for an MJS set MDCEUSER=mydomain\myusername 3 Provide the user password by setting the MDCEPASS parameter: set MDCEPASS=password 4 Save the file. Proceed to the next step. Step 2: Stop mdce Services of Old Installation If you have an older version of MATLAB Distributed Computing Server running on your cluster nodes, you should stop the mdce services before starting the services of the new installation.
Configure Cluster to Use a MATLAB® Job Scheduler (MJS) mdce uninstall -clean Note Using the -clean flag permanently removes all existing job data. Be sure this data is no longer needed before removing it. 4 Repeat the instructions of this step on all worker nodes. Stop mdce on UNIX 1 Log in as root. (If you cannot log in as root, you must alter the following parameters in the matlabroot/toolbox/distcomp/bin/mdce_def.
2 Configuring Parallel Computing Products for an MJS Using Admin Center GUI Note To use Admin Center, you must run it on a computer that has direct network connectivity to all the nodes of your cluster. If you cannot run Admin Center on such a computer, follow the instructions in “Using the Command-Line Interface (Windows)” on page 2-13 or “Using the Command-Line Interface (UNIX)” on page 2-16. Identify Hosts and Start the mdce Service.
Configure Cluster to Use a MATLAB® Job Scheduler (MJS) 2 Click Add or Find. The Add or Find Hosts dialog box opens. 3 Select Enter Hostnames, then list your hosts in the text box. You can use short host names, fully qualified domain names, or individual IP addresses. The following figure shows an example using host names node1, node2, node3, and node4. In your case, use your own host names. For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
2 Configuring Parallel Computing Products for an MJS Keep the check to start mdce service. 4 Click OK to open the Start mdce service dialog box. Proceed through the steps clicking Next and checking the settings at each step. For most settings, the default is appropriate. 2-8 For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
Configure Cluster to Use a MATLAB® Job Scheduler (MJS) It might take a moment for Admin Center to communicate with all the nodes, start the services, and acquire the status of all of them. When Admin Center completes the update, the listing should look something like the following figure. 5 At this point, you should test the connectivity between the nodes. This assures that your cluster can perform the necessary communications for running other MCDS processes.
2 Configuring Parallel Computing Products for an MJS If any of the connectivity tests fail, double-click the icon that indicates a failure to get information about that specific test; or use the Log tab to get all test results. With this information, you can refer to the troubleshooting section of the MATLAB Distributed Computing Server System Administrator’s Guide. If you need further help, contact the MathWorks install support team. . 7 If your tests pass, click Close to return to the Admin Center GUI.
Configure Cluster to Use a MATLAB® Job Scheduler (MJS) Start the MJS. 1 To start an MJS (job manager), click Start in the MJS module. (This is one of several ways to open the New MJS dialog box.) In the New MJS dialog box, specify a name and host for your MJS. This example shows an MJS called MyMJS to run on host node1. 2 Click OK to start the MJS and return to the Admin Center GUI. Start the Workers. 1 To start workers, click Start in the Workers module.
2 Configuring Parallel Computing Products for an MJS 5 Click OK to start the workers and return to the Admin Center dialog box. It might take a moment for Admin Center to initialize all the workers and acquire their status. When all the workers are started, Admin Center looks something like the following figure. If your workers are all idle and connected, your cluster is ready for use. 2-12 For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
Configure Cluster to Use a MATLAB® Job Scheduler (MJS) If you encounter any problems or failures, contact the MathWorks install support team. For more information about Admin Center functionality, such as stopping processes or saving sessions, see the “Admin Center” chapter in the MATLAB Distributed Computing Server System Administrator’s Guide. Using the Command-Line Interface (Windows) Start the mdce Service. You must install the mdce service on all nodes (head node and worker nodes).
2 Configuring Parallel Computing Products for an MJS Command Window, and select Run as Administrator. This option is available only if you are running User Account Control (UAC).
Configure Cluster to Use a MATLAB® Job Scheduler (MJS) Start the MJS. To start the MATLAB job scheduler (MJS), enter the following commands in a DOS command window. You do not have to be at the machine on which the MJS runs, as long as you have access to the MDCS installation.
2 Configuring Parallel Computing Products for an MJS 2 Start the workers on each node, using the text for that identifies the name of the MJS you want this worker registered with.
Configure Cluster to Use a MATLAB® Job Scheduler (MJS) protocol, platform (such as in a mixed environment), or other information, see the help for remotemdce by typing ./remotemdce -help Start the MJS. To start the MATLAB job scheduler (MJS), enter the following commands. You do not have to be at the machine on which the MJS runs, as long as you have access to the MDCS installation.
2 Configuring Parallel Computing Products for an MJS cd matlabroot/toolbox/distcomp/bin 2 Start the workers on each node, using the text for that identifies the name of the MJS you want this worker registered with. Enter this text on a single line: ./startworker -jobmanagerhost -jobmanager -remotehost -v To run more than one worker session on the same machine, give each worker a unique name with the -name option: ./startworker ... -name .
Configure Cluster to Use a MATLAB® Job Scheduler (MJS) ln -s matlabroot/toolbox/distcomp/bin/mdce /etc/mdce 2 Create the following link to the boot script file: ln -s matlabroot/toolbox/distcomp/bin/mdce /etc/init.d/mdce 3 Set the boot script file permissions: chmod 555 /etc/init.d/mdce 4 Look in /etc/inittab for the default run level. Create a link in the rc folder associated with that run level. For example, if the run level is 5, execute these commands: cd /etc/rc5.d; ln -s ../init.
2 Configuring Parallel Computing Products for an MJS Red Hat Platform (non-Fedora) On each cluster node, register the mdce service as a known service and configure it to start automatically at system boot time by following these steps: 1 Create the following link, if it does not already exist: ln -s matlabroot/toolbox/distcomp/bin/mdce /etc/mdce 2 Create the following link to the boot script file: ln -s matlabroot/toolbox/distcomp/bin/mdce /etc/init.
Configure Cluster to Use a MATLAB® Job Scheduler (MJS) sudo cp ./util/com.mathworks.mdce.plist /Library/LaunchDaemons 4 Start mdce and observe that it starts inside launchd: sudo ./mdce start The command output should read: Starting the MATLAB Distributed Computing Server using launchctl. For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
2 Configuring Parallel Computing Products for an MJS Configure Windows Firewalls on Client If you are using Windows firewalls on your client node, 1 Log in as a user with administrative privileges. 2 Execute the following in a DOS command window. matlabroot\toolbox\distcomp\bin\addMatlabToWindowsFirewall.bat This command adds MATLAB as an allowed program. If you are using other firewalls, you must configure them for similar accommodation.
Validate Installation with MJS Validate Installation with MJS This procedure verifies that your parallel computing products are installed and configured correctly. Step 1: Verify the Cluster Connection To verify the network connection from the client computer to the MJS computer, follow these instructions. Note In these instructions, matlabroot refers to the folder where MATLAB is installed on the client computer. Do not confuse this with the MDCS cluster computers.
2 Configuring Parallel Computing Products for an MJS 3 With the new profile selected in the list, click Rename and edit the profile name to be MJStest. Press Enter. 4 In the Properties tab, provide settings for the following fields: a Set the Description field to For testing installation with MJS. b Set the Host field to the name of the host on which your MJS is running. Depending on your network, this might be only a host name, or it might have to be a fully qualified domain name.
Validate Installation with MJS 3 Click Validate. The Validation Results tab shows the output. The following figure shows the results of a profile that passed all validation tests. Note If your validation does not pass, contact the MathWorks install support team. If your validation passed, you now have a valid profile that you can use in other parallel applications.
2 2-26 Configuring Parallel Computing Products for an MJS For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
3 Configuring Parallel Computing Products for HPC Server • “Configure Cluster for Microsoft Windows HPC Server” on page 3-2 • “Configure Client Computer for HPC Server 2008” on page 3-3 • “Validate Installation Using Microsoft Windows HPC Server” on page 3-4 For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
3 Configuring Parallel Computing Products for HPC Server Configure Cluster for Microsoft Windows HPC Server Note You must have the 64-bit version of MATLAB Distributed Computing Server installed on your cluster to use it with HPC Server. 32-bit MDCS does not support HPC Server. Follow these instruction to configure your MDCS installation to work with Windows HPC Server or Compute Cluster Server (CCS). In the following instructions, matlabroot refers to the MATLAB installation location.
Configure Client Computer for HPC Server 2008 Configure Client Computer for HPC Server 2008 This configuring applies to all versions of HPC Server 2008, including HPC Server 2008 R2. Note If using HPC Server 2008 in a network share installation, the network share location must be in the “Intranet” zone. You might need to adjust the Internet Options for your cluster nodes and add the network share location to the list of Intranet sites.
3 Configuring Parallel Computing Products for HPC Server Validate Installation Using Microsoft Windows HPC Server This procedure verifies that your parallel computing products are installed and configured correctly for using Microsoft® Windows HPC Server or Compute Cluster Server (CCS). Step 1: Define a Cluster Profile In this step you define a cluster profile to use in subsequent steps. 1 Start the Cluster Profile Manager from the MATLAB desktop by selecting Parallel > Manage Profiles.
Validate Installation Using Microsoft® Windows® HPC Server e Set the ClusterMatlabRoot to the installation location of the MATLAB to be executed by the worker machines, as determined in Chapter 1 of the installation instructions. f Set the ClusterVersion field to HPCServer2008 or CCS. g If you want to test SOA job submissions on an HPC Server 2008 cluster, set UseSOAJobSubmission to true. Otherwise leave the setting Use default or false.
3 Configuring Parallel Computing Products for HPC Server 2 Select your cluster profile in the listing. 3 Click Validate. The Validation Results tab shows the output. The following figure shows the results of a profile that passed all validation tests. Note If your validation does not pass, contact the MathWorks install support team. If your validation passed, you now have a valid profile that you can use in other parallel applications.
4 Configuring Parallel Computing Products for Supported Third-Party Schedulers (PBS Pro, Platform LSF, TORQUE) • “Configure Platform LSF Scheduler on Windows Cluster” on page 4-2 • “Configure Windows Firewalls on Client” on page 4-5 • “Validate Installation Using an LSF, PBS Pro, or TORQUE Scheduler” on page 4-6 Note You must use the generic scheduler interface for any of the following: • Any third-party schedule not listed above (e.g., Sun Grid Engine, GridMP, etc.
4 Configuring Parallel Computing Products for Supported Third-Party Schedulers (PBS Pro, Platform LSF, TORQUE) Configure Platform LSF Scheduler on Windows Cluster If your cluster is already set up to use mpiexec and smpd, you can use Parallel Computing Toolbox™ software with your existing configuration if you are using a compatible MPI implementation library (as defined in matlabroot\toolbox\distcomp\mpi\mpiLibConf.m).
Configure Platform LSF Scheduler on Windows Cluster matlabroot\bin\win32\smpd -install or matlabroot\bin\win64\smpd -install This command installs the service and starts it. As long as the service remains installed, it will start each time the node boots. 3 If this is a worker machine and you did not run the installer on it to install MDCS software (for example, if you are running MDCS software from a shared installation), execute the following command in a DOS command window. matlabroot\bin\matlab.
4 Configuring Parallel Computing Products for Supported Third-Party Schedulers (PBS Pro, Platform LSF, TORQUE) Using Passwordless Delegation 1 Log in as a user with administrator privileges. 2 Start smpd by typing in a DOS command window one of the following, as appropriate: matlabroot\bin\win32\smpd -register_spn or matlabroot\bin\win64\smpd -register_spn This command installs the service and starts it. As long as the service remains installed, it will start each time the node boots.
Configure Windows Firewalls on Client Configure Windows Firewalls on Client If you are using Windows firewalls on your cluster nodes, 1 Log in as a user with administrative privileges. 2 Execute the following in a DOS command window. matlabroot\toolbox\distcomp\bin\addMatlabToWindowsFirewall.bat This command adds MATLAB as an allowed program. If you are using other firewalls, you must configure them for similar accommodation.
4 Configuring Parallel Computing Products for Supported Third-Party Schedulers (PBS Pro, Platform LSF, TORQUE) Validate Installation Using an LSF, PBS Pro, or TORQUE Scheduler This procedure verifies that the parallel computing products are installed and configured correctly on your cluster. Step 1: Define a Cluster Profile In this step you define a cluster profile to use in subsequent steps. 1 Start the Cluster Profile Manager from the MATLAB desktop by selecting Parallel > Manage Profiles.
Validate Installation Using an LSF, PBS Pro, or TORQUE Scheduler The dialog box should look something like this, or slightly different for PBS Pro® or TORQUE schedulers. 5 Click Done to save your cluster profile. Step 2: Validate the Cluster Profile In this step you verify your cluster profile, and thereby your installation. 1 If it is not already open, start the Cluster Profile Manager from the MATLAB desktop by selecting Parallel > Manage Cluster Profiles. 2 Select your cluster profile in the listing.
4 Configuring Parallel Computing Products for Supported Third-Party Schedulers (PBS Pro, Platform LSF, TORQUE) Note If your validation does not pass, contact the MathWorks install support team. If your validation passed, you now have a valid profile that you can use in other parallel applications. You can make any modifications to your profile appropriate for your applications, such as NumWorkersRange, AttachedFiles, AdditionalPaths, etc.
5 Configuring Parallel Computing Products for a Generic Scheduler Note You must use the generic scheduler interface for any of the following: • Any third-party schedule not listed in previous chapters (e.g., Sun Grid Engine, GridMP, etc.) • PBS other than PBS Pro • A nonshared file system when the client cannot directly submit to the scheduler (e.g., TORQUE on Windows) This chapter includes the following sections.
5 Configuring Parallel Computing Products for a Generic Scheduler Interfacing with Generic Schedulers In this section...
Interfacing with Generic Schedulers submit directly to the cluster (for example, if the scheduler’s client utilities are not installed). • Nonshared — When there is not a shared file system between client and cluster machines. Before using the support scripts, decide which submission mode describes your particular network setup. For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
5 Configuring Parallel Computing Products for a Generic Scheduler Configure Generic Scheduler on Windows Cluster If your cluster is already set up to use mpiexec and smpd, you can use Parallel Computing Toolbox™ software with your existing configuration if you are using a compatible MPI implementation library (as defined in matlabroot\toolbox\distcomp\mpi\mpiLibConf.m).
Configure Generic Scheduler on Windows Cluster matlabroot\bin\win32\smpd -install or matlabroot\bin\win64\smpd -install This command installs the service and starts it. As long as the service remains installed, it will start each time the node boots. 3 If this is a worker machine and you did not run the installer on it to install MDCS software (for example, if you are running MDCS software from a shared installation), execute the following command in a DOS command window. matlabroot\bin\matlab.
5 Configuring Parallel Computing Products for a Generic Scheduler Using Passwordless Delegation 1 Log in as a user with administrator privileges. 2 Start smpd by typing in a DOS command window one of the following, as appropriate: matlabroot\bin\win32\smpd -register_spn or matlabroot\bin\win64\smpd -register_spn This command installs the service and starts it. As long as the service remains installed, it will start each time the node boots.
Configure Sun Grid Engine on Linux Cluster Configure Sun Grid Engine on Linux Cluster To run parallel jobs with MATLAB Distributed Computing Server and Sun™ Grid Engine (SGE), you need to establish a “matlab” parallel environment for SGE. The “matlab” parallel environment described in these instructions is based on the “MPI” example shipped with SGE. To use this parallel environment, you must use the matlabpe.
5 Configuring Parallel Computing Products for a Generic Scheduler qconf -mq all.q This will bring up a text editor for you to make changes: search for the line pe_list, and add matlab. 5 Ensure you can submit a trivial job to the PE: $ echo "hostname" | qsub -pe matlab 1 6 Use qstat to check that the job runs correctly, and check that the output file contains the name of the host that ran the job. The default filename for the output file is ~/STDIN.o###, where ### is the SGE job number.
Configure Windows Firewalls on Client Configure Windows Firewalls on Client If you are using Windows firewalls on your cluster nodes, 1 Log in as a user with administrative privileges. 2 Execute the following in a DOS command window. matlabroot\toolbox\distcomp\bin\addMatlabToWindowsFirewall.bat This command adds MATLAB as an allowed program. If you are using other firewalls, you must configure them to for accommodation. For help, contact the MathWorks install support team at 508-647-7000 or http://www.
5 Configuring Parallel Computing Products for a Generic Scheduler Validate Installation Using a Generic Scheduler Testing the installation of the parallel computing products with a generic scheduler requires familiarity with your network configuration, with your scheduler interface, and with the generic scheduler interface of Parallel Computing Toolbox software. Note The remainder of this chapter illustrates only the case of using LSF in a nonshared file system.
Validate Installation Using a Generic Scheduler Users Desktop Cluster MATLAB worker MATLAB client Run command (ssh) r/w Local drive (Local job data location, e.g., C:\Temp\joblocation) Submit job (qsub/bsub) Login node Scheduler cluster-hostname Copy (sFTP) MATLAB worker MATLAB worker r/w Shared drive (Cluster job data location, e.g.
5 Configuring Parallel Computing Products for a Generic Scheduler Step 1: Set Up Windows Client Host On the Client Host 1 You need the necessary scripts on the path of the MATLAB client. You can do this by copying them to a folder already on the path.
Validate Installation Using a Generic Scheduler e Set IndependentSubmitFcn with the following text: {@independentSubmitFcn, 'cluster-host-name', '/network/share/joblocation'} where cluster-host-name is the name of the cluster host from which the job will be submitted to the scheduler; and, /network/share/joblocation is the location on the cluster where the scheduler can access job data. This must be accessible from all cluster nodes.
5 Configuring Parallel Computing Products for a Generic Scheduler Step 3: Validate Cluster Profile In this step you validate your cluster profile, and thereby your installation. 5-14 For help, contact the MathWorks install support team at 508-647-7000 or http://www.mathworks.
Validate Installation Using a Generic Scheduler 1 If it is not already open, start the Cluster Profile Manager from the MATLAB desktop by selecting Parallel > Manage Cluster Profiles. 2 Select your cluster profile in the listing. 3 Click Validate. The Validation Results tab shows the output. The following figure shows the results of a profile that passed all validation tests. Note If your validation fails any stage, contact the MathWorks install support team.
