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@tfoote: we were partiioning the bags based on size inside a single run.

What fixed above issue was NOT to record /rosout and /diagnostics topics. Instead we recorded /rosout_agg and /diagnostics_agg. Since we had around 30 nodes in the system with all of them publishing on /rosout there were apparently just too many connections. Not sure if it makes fully sense but we hadn't had this issue ever after.