The MQSeries adapter gives you great flexibility in configuring your hardware. There are at least three main patterns of use:
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BizTalk Server, the adapter, and MQSeries Server for Windows on the same computer.
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BizTalk Server and the adapter on one computer, and MQSeries Server for Windows (including the MQSAgent) on a second computer, which connects to one or more additional computers that are running MQSeries Server.
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Multiple BizTalk Server installations in a group and the adapter, and MQSeries Server (including MQSAgent) on a separate computer.
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The BizTalk Server 2006 version of the MQSeries adapter and the BizTalk Server 2004 version of the MQSeries adapter can work with the same remote MQSeries Server on Windows. This is possible because the MQSAgent (MQSAgent2) COM+ application used with BizTalk Server 2006 can coexist with the MQSAgent COM+ application used with BizTalk Server 2004.
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The MQSAgent COM+ application is not supported running on a 64-bit version of Windows Server. A BizTalk Server-based computer that is running on a 64-bit version of Windows Server can communicate with a remote 32-bit computer that has the MQSAgent installed.
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The adapter functions correctly if you cluster MQSeries Server and the MQSeries Queue Managers.
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The MQSAgent COM+ application should not be clustered in this case. Instead, both nodes of the cluster should have the MQSAgent COM+ application installed and configured. In this scenario, if the MQSAgent COM+ application stops, the next call from the client will restart it.
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Other Resources
Using the MQSeries Adapter