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Incorrect FIFO alignment

Question asked by mater.michael on Mar 27, 2016
I am running the LSM6DS3 in continuous FIFO mode capturing gyro and acc data. While collecting data I periodically pole to see if the water mark is met (96 words), and if so read out half of them (leaving some in the FIFO). Every once in a while (seeming randomly) the data seems to be misaligned, meaning all the data for one "sample" of 6 words is shifted. I get acc_Z in acc_Y and acc_Y in gyro_Z. The next read the data seems to be back to where it should be. How do I ensure the FIFO alignment during FIFO reads?
I am running at 800Hz, no decimation, Acc and Gyro data, reading via SPI at full speed.