HHVM config for Drupal 7 with clean urls working fine.

run.sh

#!/usr/bin/env bash
sudo hhvm --config site1.hhvm.hdf --user www-data --mode daemon -v "Log.Level=Verbose" -v "Log.NoSilencer=on" -v "Log.Header=on"

site1.hhvm.hdf

Server {
  Port = 8001
  SourceRoot = /var/www/site1
  DefaultDocument = index.php
}

Eval {
  Jit = true
}

Log {
  Level = Error
  UseLogFile = true
  File = /var/log/hhvm/error.log
  Access {
    * {
      File = /var/log/hhvm/access.log
      Format = %h %l %u %t \"%r\" %>s %b
    }
  }
}
VirtualHost {
  * {
    Pattern = .*
    ServerVariables {
      PHP_SELF = /index.php
      SCRIPT_NAME = /index.php
    }
    RewriteRules {
      index {
        pattern = ^(.*)$
        to = index.php/$1
        qsa = true
      }
    }
  }
}

StaticFile {
  FilesMatch {
    * {
      pattern = .*\.(dll|exe)
      headers {
        * = Content-Disposition: attachment
      }
    }
  }
  Extensions {
    css = text/css
    gif = image/gif
    html = text/html
    jpe = image/jpeg
    jpeg = image/jpeg
    jpg = image/jpeg
    png = image/png
    tif = image/tiff
    tiff = image/tiff
    txt = text/plain
  }
}