I am considering trying out an external GPU to run a project on, but wondered if it can run a different project than the existing GPU

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Certainly can. You can either let BOINC allocate tasks by itself, or you can use the <exclude_gpu> configuration option to restrict its freedom of action - I use that to restrict the more demanding projects to use the faster GPU only.

At least for me it works only in theory, I have two GPUs in my machine and I tried the following cc_config, BOINC did indeed excluded as asked but it only downloaded in pairs, when the first WU finished it insisted that no work is needed until the 2nd finished and then it will load another pair.

<cc_config>
<options>
<allow_multiple_clients>1</allow_multiple_clients>
<allow_remote_gui_rpc>1</allow_remote_gui_rpc>
<use_all_gpus>1</use_all_gpus>
<exclude_gpu>
<url>http://www.primegrid.com/</url>
<device_num>1</device_num>
<app>genefer15</app>
</exclude_gpu>
<exclude_gpu>
<url>http://www.primegrid.com/</url>
<device_num>0</device_num>
<app>genefer16</app>
</exclude_gpu>
</options>
</cc_config>