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We are running ArcGIS 10.1 sp1 and have installed 64-bit background geoprocessing. We are also upgrading to FME 2013. I know in the past we have had to install the 32-bit version of FME due to compatibility issues - I think regarding writing to File Geodatabases.

Now that ArcGIS has 64-bit background processing available, am I able to install the 64-bit version of FME? Or do I still need to install the 32-bit version in order to have full compatibility? Does the 64-bit background geoprocessing even have anything to do with the compatibility?

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You can install both the fme 64 and 32 bit. ESRI doesn't have a 64 bit application. You will extend the fme32 with arcgis.
No the 64 bit background processing won't use fme.
I have both installed and use each with extended software.

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