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Hi, You can debug the problem by something like rostopic echo /rgbdslam/batch_clouds/header, which will show you which/how many clouds rgbdslam sends out.

What hardware are you using? The communication between rgbdslam and octomap server is known to be brittle on slow machines and when the data needs to be transfered between machines.

Which version of RGBDSLAM are you using? The hydro version on github lets you save the octomap without the octomap_server by using the octomap library directly.