How do you know the cache isn't being cleared? I had a similar problem today, but I was relying on the "curr_items" count in Memcached to test it, which isn't an accurate test.
I set up a Magento shell, which called:
Mage::app()->getCacheInstance()->flush();
This is the method that the "Flush Cache Storage" button calls in the Magento admin. I wanted to check that Memcached was really getting cleared.
I connected to Memcached using telnet, and monitored the "curr_items" count before and after clearing the cache. It barely changed (usually just dropped by one item).
Then I found this: http://www.couchbase.com/issues/browse/MB-2258
It says that the "curr_items" count doesn't drop, even when a (brutal) flush_all is executed directly on the Memcached server. The count only drops the next time someone tries to access a key which no longer exists.
True enough, that's what happened. My cache was being cleared as desired, but only when I refreshed a few pages for the first time, did the count drop (and then rise again, on subsequent requests).
I observed the same results when I ran flush_all from the telnet connection. The count remained unchanged, until I tried to access one of the former keys, at which point the count dropped by one.
Sometimes the cache location (like "/tmp/") or service (like Memcache) is shared with other applications. "Flush Magento Cache" removes only those entries that Magento reliably tracks as it's own. "Flush Cache Storage" clears everything but might affect other applications if they're using it.
Normally the location is "var/cache/" in Magento's folder so is not shared after all. It is safe to use either button. Sometimes (rarely) entries are not clearly tagged or Magento loses track of them and only the second button has an effect on them. I tend to use the second button when I'm having difficulty tracking down the cause of a problem.
Best Answer
Yes you can flush cache storage using Admin panel by clicking button "Flush Cache Storage" which you can find under:
from command line you can try command below :
Also disabling your log size and merging js/css files could also help ( if not already changed)
However i would recommend to fix your innod size issue first, for that you would need to change your hosting plan may be , because innod size can't be increased once created.
If you keep clearing cache, you would face slowness of website and impact on site performance too. Secondly, you can't keep clearing cache all times.
clearing cache is avoiding the issue not fixing the issue to fix the issue you need to increase innod size.