Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Updating and upgrading to Mascot Server 2.5

This page describes how to update your Mascot Server to version 2.5, upgrade your Mascot licence to use additional processors, and migrate a Mascot installation to new hardware. For the correct procedure, please choose from the options, below. If none of these apply, email support@matrixscience.com for more specific advice. In all cases, additional information can be found in the Installation & Setup Manual on the Mascot 2.5 program disk (manual.pdf).

If updating and upgrading:

Towards the end of the installation, you will be asked to register your Mascot 2.5 product key to obtain a licence file. This product key can be found on a sticker on the CD case or may have been sent by email. A licence file will be returned by email, and must be saved to mascot/config/licdb. Important: If you want to make a trial installation, do not register using your permanent Mascot 2.5 product key. Email support@matrixscience.com to request a 14 day temporary licence key

  1. Updating Mascot Server to version 2.5 on the current hardware
  2. Upgrading Mascot Server to use additional processors on the current hardware
  3. Migrating to new hardware, optionally including an update to version 2.5 and/or an upgrade to use additional processors
  4. Upgrading Mascot Server to use additional processors while converting to a cluster but keeping the current hardware as the master node
  5. Upgrading a Mascot Server cluster to use the processors on additional search nodes
  1. Updating Mascot Server to version 2.5 on the current hardware

     

    Linux:

    1. The update procedure is described in Chapter 2 of the Installation & Setup Manual
    2. If updating Perl, do this before updating Mascot. Perl 5.18 is recommended, Perl 5.8, 5.10, 5.12, 5.14, and 5.16 are also supported. An installer for ActivePerl 5.18 is included on the program disk.
    3. You might wish to make a backup of the existing files before they are overwritten. All configuration files in the config directory apart from mascot.dat and the security settings will be overwritten by new files. All results files and sequence databases apart from SwissProt will be retained. The installation script will update mascot.dat by adding new options, but will retain all existing sequence database configuration settings and other options.

    Windows:

    1. Do not uninstall the old version of Mascot. Just run the 32-bit or 64-bit setup as described in Chapter 3 of the Installation & Setup Manual
    2. If updating Perl, do this before updating Mascot. Perl 5.16 is recommended, Perl 5.10, 5.12 and 5.14 are also supported. An installer for ActivePerl 5.16 is included on the program disk. You cannot perform single-step updates for ActivePerl. You must uninstall the old version before installing the new one. As a precaution, it is also worth deleting the Perl application directory after the uninstall step and re-booting.
    3. If any files from the previous version of Mascot have been modified, they will be moved to a folder under the main Mascot folder called _install_backup.

  2. Upgrading Mascot Server to use additional processors on the current hardware

     

    Mascot Server on a single PC (SMP):

    1. Register the new product key (Database Status; Licence Info; Register a new product key). A licence file will be returned by email. Save this to mascot/config/licdb
    2. Go to the Database Status page and verify that the number of processors shows the correct, new value.
    3. The number of threads displayed for each active database should be -1, which means this setting is auto-determined. If the number of threads for a database has been specified as a fixed number, you may or may not wish to change this in view of having more processors available (Configuration Editor; Database Manager).

    Mascot Server Cluster:

    1. If you need to add new search nodes, you are in the wrong section. Refer to Upgrading Mascot Server cluster to use the processors on additional search nodes
    2. Register the new product key (Database Status; Licence Info; Register a new product key). A licence file will be returned by email. Save this to mascot/config/licdb
    3. In the cluster section of mascot.dat, the number of processors in SubClusterSet 0 should be set to -1 (automatic). If it is a fixed number, you will need to change this to -1 or to the new number of processors.
    4. Re-start the Mascot Service (Windows) or kill and re-start ms-monitor.exe (Linux).
    5. Go to the Database Status page and verify that the number of processors shows the new, correct value.

  3. Migrating to new hardware, optionally including an update to version 2.5 and/or an upgrade to use additional processors

     

    To migrate to new hardware without any update or upgrade, contact support@matrixscience.com to request a new product key, in advance.

    If you do not wish to transfer your old searches, skip steps 4 – 6

    1. Install Mascot on the new system by following the instructions in Chapter 2 (Linux) or Chapter 3 (Windows) of the Installation & Setup Manual
    2. If updating from Mascot 2.3 or earlier, towards the end of the installation, before trying to register your 2.5 product key, copy your old licence file to the Mascot config directory on the new server (this is a small text file called mascot.license in the Mascot config directory on the old server).
    3. Ensure everything is working correctly. Run a couple of test searches from a web browser on a different PC and make sure you can view the result reports.
    4. Copy all your search result files from the old system. That is, all the "daily" directories, such as 20120630, in mascot/data. Do not copy mascot/data/test or mascot/data/cache. Do not copy across the files in mascot/data itself.
    5. Copy over mascot/data/mascot.job, replacing the file on the new system (this file contains the last job number).
    6. Copy over the search log (mascot/logs/searches.log), replacing the file on the new system. Check you can open old search results using the links in the search log.
    7. If Mascot security was enabled on the old system, copy across mascot/config/security_options.xml, group.xml, and user.xml. Other files in mascot/config that you may have modified are enzymes, taxonomy, quantitation.xml, and fragmentation_rules. Best to use diff (Linux) or fc (Windows) to compare the old and new versions before copying any old configuration files to the new system.
    8. The sequence database migration procedure is described on this page
    9. Mascot must then be deleted or uninstalled from the old system.

  4. Upgrading Mascot Server to use additional processors while converting to a cluster but keeping the current hardware as the master node

     

    Linux:

    1. If you are also updating to version 2.5, follow Updating Mascot Server to version 2.5 on the current hardware. Make sure you choose to configure as a cluster at step 4 of the installation script.
      OR
      If already on version 2.5, register the new product key (Database Status; Licence Info; Register a new product key). A licence file will be returned by email. Save this to mascot/config/licdb
    2. Kill ms-monitor.exe.
    3. If already on version 2.5, edit the cluster section of mascot.dat to enable cluster mode. In the cluster section of mascot.dat, the number of processors in SubClusterSet 0 should be set to -1 (automatic). If it is a fixed number, you will need to change this to -1 or to the new number of processors.
    4. Create a nodelist.txt file as described in Chapter 11 of the Installation & Setup Manual (page 174).
    5. The operating system on each search node must be configured exactly as described in Chapter 11. For example, it must be possible for the master node to communicate with each search node using ssh with key based authentication.
    6. Start ms-monitor.exe.

    Windows:

    1. If you are also updating to version 2.5, follow Updating Mascot Server to version 2.5 on the current hardware. Make sure you choose to configure as a cluster when that stage of the setup Wizard is reached.
      OR
      If already on version 2.5, register the new product key (Database Status; Licence Info; Register a new product key). A licence file will be returned by email. Save this to mascot/config/licdb
    2. If already on version 2.5, re-run setup, choose Change, and choose to configure as a cluster when that stage of the setup Wizard is reached.
    3. The operating system on each search node must be configured exactly as described in Chapter 11 of the Installation & Setup Manual.

  5. Upgrading a Mascot Server cluster to use the processors on additional search nodes

     

    1. If you are also updating to version 2.5, follow Updating Mascot Server to version 2.5 on the current hardware.
      OR
      If already on version 2.5, register the new product key (Database Status; Licence Info; Register a new product key). A licence file will be returned by email. Save this to mascot/config/licdb
    2. Stop the Mascot Service (Windows) or kill ms-monitor.exe (Linux).
    3. In the cluster section of mascot.dat, the number of processors in SubClusterSet 0 should be set to -1 (automatic). If it is a fixed number, you will need to change this to -1 or the to new number of processors.
    4. Edit mascot/config/nodelist.txt to add new definitions for additional search nodes by analogy with existing definitions.
    5. The operating system on each new search node must be configured exactly as described in Chapter 11 of the Installation & Setup Manual.
    6. Start the Mascot Service (Windows) or start ms-monitor.exe (Linux).