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The software is telling you that it is trying to use the indicated com port to communicate with the clock and it cannot.
Something or some other program is already using it. Sometimes Windows erroneously reports this error even though you have every other program closed and are not using the com port in question. If your software crashed when trying to communicate with the clock earlier in the day, it could be stuck believing the connection to the clock is still active.
To fix the error, either close out of the program completely and then try it again in 3-5 minutes or reboot the computer. Rebooting usually does the trick if exiting the program and trying again does not.
If that does not work, another option is to disable the com port in question and reenable it in Device Manager. If you are using Windows XP, for example, you would:
Open Control Panel.
Select Device Manager.
Scroll down to “Ports”.
Right click on Communication Port COM1.
Within the right-click menu, click "Disable".
Perform the PC's restart that Windows will require to put the change into effect.
After restarting , follow steps above to get back to “COM1”.
Within the right-click menu, click "Enable".
The COM port should be released at this point and you may try to poll your Smart Clock as usual.