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Configuration: Linux Centos 6, NGINX, Mysql

We are trying to use MAGMI a common tool for mass importing of data in Mysql based on webbrowser. I run in an issue. As a try to import more than a small quantity 2000-2500 records the MAGMI simply doesn't import the remaining records and the UI seems to freeze. It happens randomly and almost around 450 but some times after 600 seconds after the import run.

No errors seems to appear in the frontend and even the LOGs on the webserver do not show nothing suspicious.

I'm lost. What can I do ? What is the ideal configuration of mysql for Magmi to work good ? I don't want to use the Magmi CLI because I need non expert people to be able to handle with MAGMI. And divide the CSV in many chunks is for me not a solution too.

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