(New page: This is a set of instructions for the steps required to upgrade the software that makes up a Windows installation of The GPM. The components are a MySQL installation, an Apache installati...) |
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*Remember to '''back up all configuration files'''. | *Remember to '''back up all configuration files'''. | ||
- | == Upgrading MySQL 4 to MySQL 5== | + | == MySQL Upgrades == |
+ | === Upgrading MySQL 4 to MySQL 5=== | ||
Note: this set of directions applies to upgrading from MySQL version 4.0.12 to 5.0.67, but should work from any 4.0 to any 5.0 version. The official upgrade guide for MySQL can be found at [http://dev.mysql.com/doc/refman/5.0/en/upgrade.html Upgrading MySQL]. Directions specific to the GPM can be found below. | Note: this set of directions applies to upgrading from MySQL version 4.0.12 to 5.0.67, but should work from any 4.0 to any 5.0 version. The official upgrade guide for MySQL can be found at [http://dev.mysql.com/doc/refman/5.0/en/upgrade.html Upgrading MySQL]. Directions specific to the GPM can be found below. | ||
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###Type: <tt>alter table peptide max_rows=1000000000 avg_row_length=75;</tt> This will take several minutes to complete. | ###Type: <tt>alter table peptide max_rows=1000000000 avg_row_length=75;</tt> This will take several minutes to complete. | ||
#'''The upgrade is now complete.''' | #'''The upgrade is now complete.''' | ||
+ | |||
+ | === Migrating MySQL from 32-bit to 64-bit === | ||
+ | '''Prerequisites, 32-bit installation''': you must have sufficient storage space on your 32-bit installation for roughly five times the space of your current database storage. E.g., if your GPMDB installation takes up 30 gigabytes (GiB) of disk space, you may need up to 150 GiB of storage to create the database dump files. | ||
+ | |||
+ | '''Prerequisites, 64-bit installation''': a bare installation of 64-bit MySQL is preferred, but not required. | ||
+ | The directions below will remove any existing tables/databases from the various databases that make up an installation of GPMDB '''including the usernames and passwords defined in the ''mysql'' database'''. If there is information already existing on your 64-bit MySQL installation in databases that share names with any of the tables in GPMDB, '''back them up before proceeding'''. If the 64-bit installation is pristine and otherwise unused, there is no data to back up, so that step can be skipped. | ||
+ | |||
+ | *On the 32-bit installation: | ||
+ | #Go to a command prompt. | ||
+ | #Navigate to the \bin\ directory of your MySQL installation. | ||
+ | #Type: <tt>mysqldump -u(root-like username) -p --all-databases -f --add-drop-database --add-drop-table --verbose --result-file=c:\path\to\(dump_file_name)</tt>. This may take quite some time to run, depending on the size of your installation. | ||
+ | ##''-u'': the username for the MySQL installation login. | ||
+ | ##''-p'': tells the program to prompt the user for the password for the username defined after the ''-u'' option. | ||
+ | ##''--all-databases'': dumps information for all databases in the installation. | ||
+ | ##''-f'': forces the dump process to continue if there are errors. | ||
+ | ##''--add-drop-database'': adds the 'drop database' command before creating the database, to ensure the table structures remain the same. | ||
+ | ##''--add-drop-table'': adds a 'drop table' command before creating each table, to ensure the numbering of auto_increment fields remains consistent. | ||
+ | ##''--verbose'': this makes the mysqldump program print out status information as it writes out the database information to disk. This is purely as a metric to help you gauge how much time remains in the dump process, and to possibly assist in troubleshooting, should problems arise. It can be left out. | ||
+ | ##''--result-file'': the path and name of the dump file to be created. Without this option specified, the data is printed to the console and would need to be redirected to be written to disk. | ||
+ | #If desired, compress the output before transferring it to the 64-bit installation. | ||
+ | *On the 64-bit installation: | ||
+ | #Ensure you have backed up any existing information in the 64-bit database you do not want to lose, '''such as other mysql users, if any'''. | ||
+ | #Place the (dump_file_name) file you created on the 32-bit installation to some location on the 64-bit installation (e.g., C:\data\(dump_file_name)) and ensure it is uncompressed. | ||
+ | #Go to a command prompt. | ||
+ | #Navigate to the \bin\ directory of your MySQL installation. | ||
+ | #Log into MySQL as a root-like user: type <tt>mysql -u(root-like username) -p</tt> | ||
+ | #At the MySQL prompt, type: <tt>source c:\data\(dump_file_name);</tt> This will start the importation process, which will take quite some time. Once it completes, use the web interface to check to ensure that the data accessible through the 64-bit installation matches what is available through the web interface on the 32-bit installation. |
This is a set of instructions for the steps required to upgrade the software that makes up a Windows installation of The GPM. The components are a MySQL installation, an Apache installation and a Perl installation. While this set of directions is specific to a Windows installation of the software suite, the basic directions should still apply to a UNIX-like environment.
Notes regarding these directions:
Note: this set of directions applies to upgrading from MySQL version 4.0.12 to 5.0.67, but should work from any 4.0 to any 5.0 version. The official upgrade guide for MySQL can be found at Upgrading MySQL. Directions specific to the GPM can be found below.
# sets pointer size to allow tables up to 256 TB (integer between 2 and 7
# for number of bytes to allocate for the row pointer).
myisam_data_pointer_size=6
Prerequisites, 32-bit installation: you must have sufficient storage space on your 32-bit installation for roughly five times the space of your current database storage. E.g., if your GPMDB installation takes up 30 gigabytes (GiB) of disk space, you may need up to 150 GiB of storage to create the database dump files.
Prerequisites, 64-bit installation: a bare installation of 64-bit MySQL is preferred, but not required. The directions below will remove any existing tables/databases from the various databases that make up an installation of GPMDB including the usernames and passwords defined in the mysql database. If there is information already existing on your 64-bit MySQL installation in databases that share names with any of the tables in GPMDB, back them up before proceeding. If the 64-bit installation is pristine and otherwise unused, there is no data to back up, so that step can be skipped.