The ongoing period of the pandemic makes everybody focused on the matters related to fighting this immense problem posed to the societies worldwide. The governments deal with the threat by publishing regulations which should allow to mitigate the pandemic, walking on thin ice as the decision makers do not always know how to properly respond to the threat in order to save people. Computer-based simulations of e.g. parts of the city or rural area should provide significant help, however, there are some requirements to fulfill. The simulation should be verifiable, supported by the urban research and it should be possible to run it in appropriate scale. Thus in this paper we present an interdisciplinary work of urban researchers and computer scientists, proposing a scalable, HPC-grade model of simulation, which was tested in a real scenario and may be further used to extend our knowledge about epidemic spread and the results of its counteracting methods. The paper shows the relevant state of the art, discusses the micro-scale simulation model, sketches out the elements of its implementation and provides tangible results gathered for a part of the city of Krakow, Poland.