# Publications

### **Papers describing PCJ:**

1. **M. Nowicki, Ł. Górski, P. Bała** [Performance evaluation of Java/PCJ implementation of parallel algorithms on the cloud (extended version)](https://onlinelibrary.wiley.com/doi/full/10.1002/cpe.6536), w: *Concurrency and Computation: Practice and Experience*, *Wiley, 2021,* ISSN: 1532-0626, eISSN: 1532-0634, Art. no. 6536 s. 1-15, [DOI: 10.1002/cpe.6536](https://doi.org/10.1002/cpe.6536)
2. **M. Nowicki, Ł. Górski, P. Bała** [Scalable computing in Java with PCJ Library. Improved collective operations.](https://open.icm.edu.pl/items/5375ddd3-627c-45c7-b8fe-9130fa88a73a)" In: *Proceedings of International Symposium on Grids and Clouds 2021 - Proceedings of Science (ISGC2021)*, 2021, vol. 378, p. 7; [DOI: 10.22323/1.378.0007](https://doi.org/10.22323/1.378.0007)
3. **M. Nowicki, Ł. Górski, P. Bała** [Performance Evaluation of Java/PCJ Implementation of Parallel Algorithms on the Cloud](https://link.springer.com/chapter/10.1007/978-3-030-71593-9_17), In: *Euro-Par 2020: Parallel Processing Workshops. Euro-Par 2020*, Springer, Cham, 2021, ISBN: 978-3-030-71592-2, pp. 213–224
4. **M. Nowicki, Ł. Górski, P. Bała** [PCJ Java library as a solution to integrate HPC, Big Data and Artificial Intelligence workloads](https://journalofbigdata.springeropen.com/articles/10.1186/s40537-021-00454-6), In: *Journal of Big Data*, Springer, 2021, ISSN: 2196-1115, Vol. 8 no. 1, Art no. 62, s. 1-21, [DOI: 10.1186/s40537-021-00454-6](https://doi.org/10.1186/s40537-021-00454-6)
5. **M. Nowicki, Ł. Górski, P. Bała** [PCJ – Java Library for Highly Scalable HPC and Big Data Processing](https://ieeexplore.ieee.org/abstract/document/8514322) 2018 International Conference on High Performance Computing & Simulation (HPCS), pp:12-20 IEEE, 2018
6. **M. Nowicki, Ł. Górski, P. Bała** [Performance evaluation of parallel computing and Big Data processing with Java and PCJ library](https://www.researchgate.net/publication/325533243_Performance_evaluation_of_parallel_computing_and_Big_Data_processing_with_Java_and_PCJ_library) CUG 2018
7. **M. Nowicki, M. Ryczkowska, Ł. Górski, P. Bała** [Big Data analytics in Java with PCJ library - performance comparison with Hadoop](https://link.springer.com/chapter/10.1007/978-3-319-78054-2_30).In: Wyrzykowski R., Dongarra J., Deelman E., Karczewski K. (eds) *Parallel Processing and Applied Mathematics. PPAM 2017.* Lecture Notes in Computer Science, vol 10778. Springer, Cham, pp 318-327 (2018)
8. **M. Nowicki, Ł. Górski, P. Bała** [Evaluation of the parallel performance of the Java and PCJ on the Intel KNL based systems.](https://link.springer.com/chapter/10.1007/978-3-319-78054-2_27) In: Wyrzykowski R., Dongarra J., Deelman E., Karczewski K. (eds) *Parallel Processing and Applied Mathematics. PPAM 2017*. Lecture Notes in Computer Science, vol 10778. Springer, Cham, pp 288-297 (2018)
9. **M. Szynkiewicz, M. Nowicki** [Fault-tolerance mechanisms for the Java parallel codes implemented with the PCJ library.](https://link.springer.com/chapter/10.1007/978-3-319-78054-2_28) In: Wyrzykowski R., Dongarra J., Deelman E., Karczewski K. (eds) *Parallel Processing and Applied Mathematics. PPAM 2017*. Lecture Notes in Computer Science, vol 10778. Springer, Cham, pp 298-307 (2018)
10. **M. Nowicki, Ł. Górski, M. Ryczkowska, P. Bała** [PCJ as a tool for masivelly parallel data processing.](https://www.researchgate.net/publication/320591874_PCJ_as_a_tool_for_massively_parallel_data_processing) In: M. Bubak, M. Turała, K. Wiatr (Eds.) *CGW Workshop'17* ACK Cyfronet AGH 2017, pp 39-40
11. **M. Nowicki, P. Bała** [Programowanie równoległe w języku Java z wykorzystaniem biblioteki PCJ](https://www.researchgate.net/publication/313233416_Programowanie_rownolegle_w_jezyku_Java_z_wykorzystaniem_biblioteki_PCJ) W: Ł. Kuźmiński, J. Doskocz, P. Kardasz (Red.) Innowacje w polskiej nauce w obszarze matematyki i informatyki. Przegląd aktualnej tematyki badawczej Wydawnictwo Nauka i Biznes 2016. pp 130-140
12. **M. Nowicki, P. Bała** [Programowanie równoległe w języku Java z wykorzystaniem biblioteki PCJ](https://www.researchgate.net/publication/309210944_Programowanie_rownolegle_w_jezyku_Java_z_wykorzystaniem_biblioteki_PCJ) W: *Materiały konferencyjne – Innowacyjne Projekty Badawcze*.Dolnośląski Akcelerator Technologii i Innowacji Sp. z o. o. Wrocław 2.09.2016 p. 30
13. **M. Nowicki**, **M. Ryczkowska, Ł. Górski, M. Szynkiewicz, P. Bała** [PCJ - a Java library for heterogenous parallel computing](http://www.wseas.us/e-library/conferences/2016/barcelona/SECEA/SECEA-08.pdf) In: X. Zhuang (Ed.) *Recent Advances in Information Science (Recent Advances in Computer Engineering Series vol 36)* WSEAS Press 2016 pp. 66-72
14. **M. Nowicki**, **Ł. Górski, P. Grabarczyk, P. Bała** [PCJ - Java library for high performance computing in PGAS model](http://ieeexplore.ieee.org/xpl/abstractAuthors.jsp?arnumber=6903687) In: W. W. Smari and V. Zeljkovic (Eds.) *2012 International Conference on High Performance Computing and Simulation (HPCS)* IEEE 2014 pp. 202-209
15. **M. Nowicki**, **P. Bała** [PCJ-new approach for parallel computations in java](https://link.springer.com/chapter/10.1007/978-3-642-36803-5_8) In: P. Manninen, P. Oster (Eds.) *Applied Parallel and Scientific Computing*, LNCS 7782, Springer, Heidelberg (2013) pp. 115-125
16. **M. Nowicki**, **P. Bała** [Parallel computations in Java with PCJ library](http://ieeexplore.ieee.org/xpl/login.jsp?tp=\&arnumber=6266941\&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6266941) In: W. W. Smari and V. Zeljkovic (Eds.) *2012 International Conference on High Performance Computing and Simulation (HPCS)* IEEE 2012 pp. 381-387

### **Papers where PCJ is used to develop parallel applications:**

1. **M. Nowicki, M. Mroczek, D. Mukhedkar, P. Bała, V.N. Pimenoff, L.S. Arroyo Mühr** [HPV-KITE: sequence analysis software for rapid HPV genotype detection](https://academic.oup.com/bib/article/26/2/bbaf155/8109669), *Briefings in Bioinformatics*, Volume 26, Issue 2, March 2025, bbaf155, <https://doi.org/10.1093/bib/bbaf155>
2. **M. Nowicki** [Comparison of sort algorithms in Hadoop and PCJ](https://rdcu.be/caSpO) Journal of Big Data 2020 7:101
3. **J. Posner, L. Reitz, C. Fohry** [Comparison of the HPC and Big Data Java Libraries Spark, PCJ and APGAS](https://sc18.supercomputing.org/proceedings/workshops/workshop_files/ws_pawatm101s2-file2.pdf) Parallel Applications Workshop - Alternatives to MPI, SC'18, Dallas 2018
4. **M. Nowicki, D. Bzhalava, P. Bała** [Massively Parallel Implementation of Sequence Alignment with BLAST Using PCJ Library ](https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0079)*J. Comp. Biology* 25 (8):871-881, 2018
5. **M. Nowicki, D. Bzhalava, P. Bała** [Massively Parallel Sequence Alignment with BLAST through Work Distribution Implemented using PCJ Library](https://link.springer.com/chapter/10.1007/978-3-319-65482-9_36) In: S. Ibrahim, Kim-Kwang R. Choo, Z. Yan, W. Pedrycz (Eds.) *Algorithms and Architectures for Parallel Processing. ICA3PP 2017*. Lecture Notes in Computer Science, vol 10393. Springer, Cham ,2017, pp. 503-512
6. **R. Istrate, P. Barkoutsos, M. Dolfi, P. Staar, C. Bekas**[ Exploring graph analytics with the PCJ toolbox](https://link.springer.com/chapter/10.1007/978-3-319-78054-2_29). In: Wyrzykowski R., Dongarra J., Deelman E., Karczewski K. (eds) *Parallel Processing and Applied Mathematics. PPAM 2017*. Lecture Notes in Computer Science, vol 10778. Springer, Cham, pp 308-317 (2018)
7. **M Ryczkowska, M Nowicki** [Performance comparison of graph BFS implemented in MapReduce and PGAS programming models.](https://link.springer.com/chapter/10.1007/978-3-319-78054-2_31) In: Wyrzykowski R., Dongarra J., Deelman E., Karczewski K. (eds) *Parallel Processing and Applied Mathematics. PPAM 2017*. Lecture Notes in Computer Science, vol 10778. Springer, Cham, pp 328-337 (2018)
8. **M Ryczkowska, M Nowicki, P Bała** [Level-synchronous BFS algorithm implemented in Java using PCJ Library](http://ieeexplore.ieee.org/document/7881411/) In: *2016 International Conference on Computational Science and Computational Intelligence (CSCI)*, Las Vegas, NV, USA}, 2016, pp. 596-601
9. **Ł. Górski, F. Rakowski, P. Bała** [A case study of software load balancing policies implemented with the PGAS programming model](http://ieeexplore.ieee.org/document/7568368/) In: W. W. Smari, V. Zejkovic (Eds) (eds.) *2016 International Conference on High Performance Computing & Simulation (HPCS)*, IEEE 2016, pp. 443 - 448
10. **M Ryczkowska, M Nowicki, P Bala** [The Performance Evaluation of the Java Implementation of Graph500](http://link.springer.com/chapter/10.1007/978-3-319-32152-3_21) In: R. Wyrzykowski et all (eds.) Parallel Processing and Applied Mathematics, Springer 2016 pp. 221-230
11. **Ł Górski, F Rakowski, P Bała** [Parallel Differential Evolution in the PGAS Programming Model Implemented with PCJ Java Library](http://link.springer.com/chapter/10.1007/978-3-319-32149-3_42) In: R. Wyrzykowski et all (eds.) *Parallel Processing and Applied Mathematics*, Springer 2015, pp. 448-458
12. **M Nowicki, M Marchwiany, M Szpindler, P Bała** [On-line Service for Teaching Parallel Programming](http://link.springer.com/chapter/10.1007/978-3-319-27308-2_7) In:*Euro-Par 2015: Parallel Processing Workshops*, Springer 2015, pp. 78-89
13. **M. Ryczkowska** [Evaluating PCJ library for graph problems-Graph500 in PCJ](http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6903800\&tag=1) In: W. W. Smari and V. Zeljkovic (Eds.) 2012 *International Conference on High Performance Computing and Simulation (HPCS)* IEEE 2014 pp. 1005-1007