TYPO3 Core

Did you try running the script with full path? Running the script local is not supported by CLI.

Wrong:
./cli_dispatch.phpsh lowlevel_refindex -c

Right:
/path/to/your/typo3/cli_dispatch.phpsh lowlevel_refindex -c

Additionally you can try using another php to compile this script.
Example:
/usr/bin/php5 /path/to/your/typo3/cli_dispatch.phpsh lowlevel_refindex -c

Fatal errors are never expected behaviors. And maybe something is wrong, can be fixed or a warning can be given out.

Thats why I will let it stay open.

I have some big databases where even memory_limit=1024M is not enough. So this should be fixed. The error occurs too when updating the index (-e).

I tried the patch for TYPO3 4.5 and it did not help (maybe there is less memory used but its not enough).

From the programming logic it really seems to be a bug that the class creates a new instance of itself for each record instead of calling the method in its own instance (but since it is using properties to keep track ($this->word_strings etc) maybe this is necessary (and thus the patch is not good).

I'm using TYPO3 6.2.11 and still have the memory issue.

The main reason in my eyes is that all rows of a table are fetched at once (exec_SELECTgetRows) and then analysed, instead of only fetching one row after another.

Also, table sys_log is analyzed, which is huge in older instances -> see #66338.

Patch set 2 for branch master of project Packages/TYPO3.CMS has been pushed to the review server.
It is available at http://review.typo3.org/38573

Patch set 3 for branch master of project Packages/TYPO3.CMS has been pushed to the review server.
It is available at http://review.typo3.org/38573

Patch set 4 for branch master of project Packages/TYPO3.CMS has been pushed to the review server.
It is available at http://review.typo3.org/38573

Patch set 1 for branch TYPO3_6-2 of project Packages/TYPO3.CMS has been pushed to the review server.
It is available at http://review.typo3.org/38587