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MSMQ can use an installable file system for its base directory. For this, the base directory must point to any directory on this file system. Because the installable file system may not initialize late in the boot cycle, MSMQ service will wait on a directory to become available for a period of time (in seconds) specified in "FSMaxTimeout" DWORD registry value.
If you put MSMQ storage on the installable file system, it is your responsibility to ensure that file system is available (that is, the network does not disconnect, the flash card is not removed, and so on) when MSMQ is started. It is possible to move the MSMQ storage from one file system (or one directory to another) by stopping MSMQ, changing base directory ("BaseDir") value in registry, and copying the contents of storage to the new place.
Note that MSMQ is a very storage-intensive application, so a slow file system may significantly degrade the performance.
MSMQ can have its storage located on flash or compact flash card, just as on any other installable file systems. This ensures that messages are not lost if the system suffers total power loss (or locks up so that it requires cold boot). However, while the internal file system is transactional and fault tolerant, the flash card uses a simple file allocation table (FAT) file system, which does not support these features.
Also, the flash card should not be removed from the system when MSMQ is operational. Doing so may lead to message loss and file corruption. Always stop MSMQ before removing the flash card.