University of Jyväskylä High-Performance Computing Master's Thesis Guide: Chemistry, Physics, Computer Science and Vasara

Start with the three-branch HPC thesis map

The University of Jyväskylä High-Performance Computing programme is one Master of Science degree, but thesis planning must begin by identifying the student’s specialisation. Chemistry, Physics and Computer Science use three different research-course packages. Chemistry uses KEMS903 Thesis Seminar, KEMS9550 Master’s Thesis and KEMS901 Maturity Exam. Physics uses FYSS9489 Master’s Seminar, FYSS9490 MSc Thesis and FYSS9495 Maturity Test. Computer Science uses TIES501 Master’s thesis seminar, TIES502 Master’s Thesis and TIES503 Maturity Test (MSc).

Do not merge these into one generic HPC thesis route. The programme shares computing coursework, but the thesis administration, seminar structure, maturity course and some methodological expectations depend on the specialisation.

Programme identity and current curriculum

The current Study Guide object is HPCMP2024. It awards a Master of Science, contains 120+ ECTS and is taught in English. Responsibility is shared by the Faculty of Mathematics and Science and the Faculty of Information Technology, with coordination across the Departments of Physics and Chemistry and the Faculty of Information Technology. The current curriculum periods run from 2024–2025 through 2027–2028.

The programme connects high-performance computing technologies to computational science. Its stated themes include CPU and GPU parallel computing, distributed and multicore programming, data mining and machine learning, quantum computing, Computational Physics and Computational Chemistry.

A multidisciplinary HPC thesis is possible

The degree object explicitly allows a Master’s thesis on a multidisciplinary topic combining different sub-fields of the programme. A project may be connected to a JYU research group, based on the student’s own idea, or linked to an industry or technology partner outside the university. This gives considerable topic flexibility.

That flexibility does not erase the specialisation route. A multidisciplinary Chemistry student still follows the Chemistry thesis codes; a Physics student follows the Physics package; and a Computer Science student follows the IT Faculty package unless JYU formally places the work in another approved arrangement.

Shared HPC core is not a universal thesis method

All three specialisations share a 15 ECTS HPC core containing TIES3420 GPU Programming, TIES4523 Quantum Computer Programming and TIES4600 Machine Learning, each worth 5 ECTS. These courses explain why HPC graduates have broad computational competence.

Shared-core enrolment does not establish GPU use, quantum computing or machine learning as programme-wide thesis requirements. Nor do the current programme sources impose one universal programming language, software package, dataset or hardware platform. Method choice must follow the research problem and the specialisation-specific thesis expectations rather than being inferred mechanically from shared coursework.

Chemistry branch: the formal research package

For the Chemistry specialisation, the current advanced-studies module is KEMSYVHPC under the Department of Chemistry. Its Research and Training selection is 31–41 ECTS. The compulsory thesis-related components are KEMS903 Thesis Seminar 1 ECTS, KEMS9550 Master’s Thesis 30 ECTS and KEMS901 Maturity Exam for Master’s Degree 0 ECTS.

These Chemistry codes are not interchangeable with the Physics FYSS codes or the Computer Science TIES codes. When checking Sisu, Moodle, submission instructions or a supervisor’s advice, make sure the course object belongs to the Chemistry branch.

KEMS903 Chemistry thesis seminar

KEMS903 is a 1 ECTS advanced-studies seminar graded Pass/Fail and offered in English and Finnish. Students observe two other seminar presentations before their own thesis presentation and complete assignments based on what they hear. Before presenting, the student discusses the presentation with the supervisor.

The student then gives an oral presentation of roughly ten minutes on the Master’s thesis topic. The supervisor or an authorised substitute listens and gives feedback. Passing requires the assignments and an approved seminar presentation. The seminar therefore combines observation, critical discussion, presentation and supervisor feedback rather than functioning as a simple attendance requirement.

KEMS9550 Chemistry thesis: exact requirement

KEMS9550 is the 30 ECTS Chemistry Master’s Thesis, an advanced-studies course graded 0–5. Its most important branch-specific rule is structural: the thesis comprises both a literature review and an experimental or computational component. This is an explicit Chemistry requirement and should be stated exactly.

The literature review demonstrates scientific command of the topic, literature searching and critical handling of research material. The second component depends on the topic. Experimental work involves independent laboratory activity and appropriate measurement techniques; computational work requires relevant simulations using suitable computational software.

Do not export the Chemistry format to other branches

The Chemistry literature-review-plus-experimental-or-computational structure belongs to KEMS9550. It must not be presented as a universal HPC format. FYSS9490 does not state the same two-part requirement, and TIES502 sits under a different IT Faculty thesis framework with several recognised thesis types.

This distinction is central to accurate programme guidance. The degree is multidisciplinary, but the thesis rules remain scoped. If a Physics or Computer Science project happens to include a literature review and computation, that may be methodologically sensible, but it is not evidence that KEMS9550 rules govern that branch.

Chemistry topic, supervision and readiness

HPC Chemistry students normally work independently but often within a research group. Topics may come from departmental research, an external source or industry. The responsible supervisor must be employed by JYU and hold a doctoral degree. Student and supervisor agree the topic, schedule, guidance practices and assessment criteria through the Chemistry supervision process.

KEMS9550 also says advanced-level studies should be almost completed before thesis work begins. This makes the thesis a late-stage integration of subject expertise and research competence rather than an introductory project.

Chemistry assessment and originality workflow

KEMS9550 assessment focuses on the ability to produce an independent, comprehensive scientific report according to department guidelines. The assessment considers coherence, use of literature, writing, independence and timeliness, together with subject-specific quality.

Before formal review, HPC Chemistry uses Turnitin in the relevant Moodle workspace. Students register for KEMS9550 and KEMS901 in Sisu to access the workflow. When the final version is ready, it is checked for originality and then submitted to Vasara. The Chemistry instructions also provide a 14-day response window after the student receives notification of the grade.

KEMS901 Chemistry maturity exam

KEMS901 is a 0 ECTS Pass/Fail maturity course offered in English, Finnish and Swedish. In an English-medium programme the maturity exam is normally in English, and usually the thesis abstract written in the programme language is accepted as the maturity exam.

There is a language-history exception. If a student whose school education was Finnish or Swedish has not previously demonstrated the required school-language proficiency through an earlier maturity process, a separate exam route applies. Its content is evaluated by the discipline and language quality by an approved Movi language specialist. Check personal language history instead of copying another student’s route.

Physics branch: the formal research package

For the Physics specialisation, FYSSYVHPC is the current advanced-studies module under the Department of Physics. Its Research and Training selection is 33–43 ECTS. The compulsory thesis chain is FYSS9489 Master’s Seminar 3 ECTS, FYSS9490 MSc Thesis 30 ECTS and FYSS9495 Maturity Test 0 ECTS.

Physics therefore has a larger seminar than Chemistry and a different maturity course. Use the FYSS route for Physics even when the thesis topic overlaps computational chemistry, machine learning or another shared HPC field.

FYSS9489 Physics Master’s Seminar

FYSS9489 is a 3 ECTS advanced-studies course graded Pass/Fail and offered in English and Finnish. It combines thesis preparation with career and professional reflection. The course covers project planning, peer-group work, assessment criteria and process, scientific presentation, career paths and doctoral-study awareness.

For the thesis itself, the important outcomes are concrete: the student chooses a topic, finds a supervisor, drafts a realistic schedule with meaningful checkpoints, understands assessment criteria and rights/obligations, and learns to communicate research. The primary route includes seminar work, assignments and a public scientific presentation.

FYSS9490 Physics MSc Thesis

FYSS9490 is the formal 30 ECTS Physics MSc Thesis, graded 0–5. It covers information acquisition and criticism, research design and implementation, data management, scientific writing and structure, visualisation of data, literature management and citation, research communication and good scientific practice.

The course expects the student to design and conduct small-scale scientific research, write and visualise results, recognise ethical questions, use feedback and present the thesis competently. Unlike Chemistry KEMS9550, its current description does not impose a universal literature-review-plus-experimental-or-computational two-part structure.

Physics pair thesis and public record

FYSS9490 explicitly allows one author or two authors working as a pair. In a paired thesis or a larger research project, each student’s contribution must be specified clearly enough to permit independent assessment. The course also states that Master’s theses are public documents and are saved in JYX.

A pair thesis therefore needs more than shared authorship. Keep a traceable division of work and make individual scientific contribution visible. This is especially important in computational projects where code, model development, simulation, analysis and writing may be distributed between students.

Physics supervision agreement matters

The Department of Physics uses a thesis-project guideline and supervision agreement. The agreement is intended to make expectations explicit before work develops too far. It records the responsible and other supervisors, the estimated difficulty of the topic, completion schedule, supervision and meeting practices, checkpoints and assessment criteria.

The Physics guidance also says schedule performance can be considered against the estimate recorded in the agreement unless the schedule is formally updated. Treat the agreement as a living project-control document rather than a form completed and forgotten.

Physics originality check and Sisu access

For HPC Physics, the final thesis is submitted for plagiarism detection in the Moodle workspace of FYSS9490 before the formal assessment route continues. JYU’s branch instructions say students should register for FYSS9490 and FYSS9495 in Sisu to access the appropriate Moodle environment.

Do not use the Chemistry Moodle registration or IT seminar route just because the programme title is the same. Branch-specific course registration is part of the operational workflow.

FYSS9495 Physics maturity test

FYSS9495 is 0 ECTS and Pass/Fail. It is offered in English and Finnish. Where the required school-language proficiency has already been demonstrated, the master’s thesis summary can serve as the maturity test and is evaluated by the discipline. If the required school-language proficiency has not been demonstrated previously, an exam and separate language evaluation route applies.

The English-medium context therefore does not remove the need to check the student’s language-history condition. Use the current FYSS9495 implementation rather than another department’s maturity instructions.

Computer Science branch: the formal research package

For Computer Science, HPCITADV is the current advanced-studies module under the Faculty of Information Technology. Its Research and Training selection is 33–45 ECTS. The compulsory thesis chain is TIES501 Master’s thesis seminar 3 ECTS, TIES502 Master’s Thesis 30 ECTS and TIES503 Maturity Test (MSc) 0 ECTS.

This branch is governed by the IT Faculty thesis framework, which differs materially from Chemistry and Physics. It has its own topic approval process, thesis-type catalogue, assessment framework and template for AI and HPC.

TIES501 Computer Science thesis seminar

TIES501 is a 3 ECTS advanced-studies seminar graded Pass/Fail and offered in English and Finnish. Its main components include topic selection, literature search and analysis, research-method selection, development of a research plan, implementation of the thesis work and presentations. The topic should be agreed with the thesis supervisor and approved by the head of the study programme before the seminar process proceeds.

The course expects a completed bachelor degree, an up-to-date eHOPS that makes graduation within roughly a year realistic, and at least a preliminarily identified topic and supervisor.

Do not inherit the WISE/COIN CSD Project prerequisite

TIES501 contains a specific prerequisite note for IMDP WISE and IMDP COIN students: the CSD Project is required for those programmes. The wording is programme-specific. It must not be copied into the HPC Computer Science guide as though every HPC student has the same CSD Project prerequisite.

This is a good example of why a shared course object must be read with scope. TIES501 serves several programmes, so every prerequisite sentence is not automatically an HPC rule.

TIES502 Computer Science Master’s Thesis

TIES502 is the 30 ECTS Computer Science Master’s Thesis, an advanced-studies course graded 0–5 under the Faculty of Information Technology. The course allows a student to propose a topic, but the coordinating professor must approve the topic before thesis work officially begins. In an international Master’s programme the thesis is written in English.

The learning outcomes cover research or development problem formulation, scientific sources and synthesis, methodological choice and application, research ethics, reflection against prior research, scientific reporting and process management. The course also permits a jointly written thesis in justified cases.

Computer Science topic and responsible supervisor

The IT Faculty says students may suggest their own thesis topics, develop an idea from a workplace or other external partner, or use a topic connected to faculty research. The process formally begins once a responsible supervisor is appointed and approves the topic. The responsible supervisor must hold a doctoral degree and be employed by JYU.

HPC Computer Science uses the IT Faculty’s dedicated AI & HPC thesis template. Use the current programme template and supervisor guidance rather than borrowing a Chemistry or Physics template.

IT thesis type 1: empirical research

The Faculty of Information Technology recognises an empirical research-based thesis. In this form, research results are produced from empirical data using relevant scientific research methods and then linked to earlier studies and theories.

This is one valid route, not the only route. Although TIES501 refers to implementation of an empirical part in its generic seminar description, the faculty-level thesis guidance explicitly recognises several thesis types. Therefore do not infer that every HPC Computer Science thesis must be an empirical study.

IT thesis type 2: literature review with original contribution

The IT Faculty also recognises a systematic and comprehensive literature review tied to a defined research task, provided it uses an accepted review or mapping methodology and includes a significant original contribution. The guidance gives examples such as a new model or framework with novelty value.

This is more demanding than a narrative summary. The review method must be defensible and the original contribution must be visible. It is also different from the Chemistry requirement, where the literature review is one component of a larger thesis containing experimental or computational work.

IT thesis type 3: constructive or developmental work

A constructive or developmental thesis can systematically develop an artefact or construction such as software, an algorithm, model, method or material. The work must be connected to prior research and evaluated for effectiveness and functionality.

For HPC this can be especially relevant to computational systems or algorithms, but “I built software” is not by itself sufficient. The artefact must answer a defined research or development problem, be grounded in scientific knowledge and be evaluated in a way that supports defensible conclusions.

IT thesis type 4: article-based thesis

The IT Faculty permits an article-based Master’s thesis under its stated conditions. The faculty guidance requires one or more qualifying scientific articles together with a literature-review introduction that contextualises and complements the articles. The student’s independent and significant contribution must be identifiable, and the total workload must correspond to the thesis ECTS scope.

Because article-based rules are detailed and publication-status sensitive, confirm the current conditions with the responsible supervisor before committing to this format. Do not transfer article-thesis rules from Physics or another faculty.

Joint and dual-degree cases in IT

The IT Faculty also describes jointly written and dual-degree thesis cases. Pair theses must reflect the combined workload and make the division of labour clear. A thesis serving two degree programmes must demonstrate competence in both disciplines and be evaluated in the relevant programmes.

These are special cases, not default HPC arrangements. If a project crosses programmes, faculties or universities, secure formal approval early. The fact that HPC itself is multidisciplinary does not automatically turn a thesis into a dual-degree or pair thesis.

IT Faculty assessment for Computer Science

IT theses are graded 0–5. The Faculty of Information Technology assesses defined criteria cumulatively: every criterion must reach at least satisfactory level for the thesis to be accepted, and the overall grade is not calculated as a simple arithmetic average of criterion scores. The Vice Dean determines the final grade based on the examiners’ assessment.

Once an IT thesis has been accepted, the faculty guidance says it cannot be revised or retaken. This makes pre-submission supervisor review and the final quality check particularly important.

TIES503 maturity: read metadata and rule together

TIES503 Maturity Test (MSc) is 0 ECTS and Pass/Fail. Its Study Guide metadata lists Finnish, but its descriptive rule says Master’s maturity tests in the IT Faculty are primarily completed using the abstract of the Master’s thesis. A Finnish student whose bachelor-level degree was completed abroad is specifically directed to a Finnish maturity exam and Movi language checking.

Do not reduce this to “every HPC Computer Science student takes a Finnish exam.” The course metadata and the descriptive maturity route must be read together with the university-wide maturity rules and the student’s language history.

Vasara is the university-wide final submission route

Across JYU, the final Master’s thesis evaluation and archiving process runs electronically through Vasara. Before submission, confirm with the supervisor that the work is ready, complete the required originality check, ensure thesis and maturity implementations are registered in Sisu, and save the final work as an accessible PDF/A.

The version submitted to Vasara is the final version for assessment. Confidential background material must be kept outside the submitted public thesis. The overall return-and-review process may take up to about two months, so graduation timing should be planned accordingly.

Examiner and response rights

JYU Degree Regulations provide the formal examiner framework. A Master’s thesis has two examiners, at least one holding a doctoral degree. Students have the right to respond before final grading and may interrupt the assessment process once. The student is also responsible for the originality of the work.

Operational details can differ by branch. Chemistry explicitly notes departmental delegation of examiner/evaluation decisions; IT uses its Vice Dean grading process; Physics follows the Department of Physics framework. Use the branch page together with Degree Regulations instead of assuming one administrative signature applies everywhere.

Research data and personal data

HPC projects can involve simulation outputs, experimental measurements, source code, logs, benchmark data, industrial datasets or information about people. JYU treats information relating to an identifiable living person as personal data, and pseudonymised data can remain personal data when re-identification is possible.

Plan the research-data lifecycle before collection or generation. Decide storage, access control, documentation, backup, versioning, ownership, licensing, retention and disposal. If personal data are involved, also plan lawful processing, participant information and identifier handling before the data arrive.

Use a living Data Management Plan

JYU’s Data Management Plan guidance covers the full data lifecycle, including creation or collection, processing, storage, documentation, legal and ethical issues, rights, integrity, publication, archiving and disposal. The DMP is a living document.

For HPC, update it when compute environments, collaborators or datasets change. Record enough technical detail to reproduce and interpret the work: software versions, code repositories, parameter settings, random seeds where relevant, preprocessing, data provenance and the relationship between raw and derived outputs.

Ethics review is conditional

JYU’s Human Sciences Ethics Committee follows TENK principles. Ethical review is not automatic for every thesis involving people; prior review is required when an applicable TENK criterion is met. The researcher remains responsible for ethics regardless of whether a committee statement is required.

Many HPC theses have no human participants, but that does not remove ethical obligations. Consider dataset provenance, consent and licensing where applicable, security implications, dual-use risks, model bias, confidential partner data and the consequences of automated decisions.

AI use in HPC thesis work

JYU permits AI-based applications in studies subject to current teacher and unit instructions, but AI output is not a scientific source. Students remain responsible for submitted content, and scholarly claims assisted by AI must be verified against original sources. Relevant generative-AI use should be reported transparently.

For an HPC thesis, distinguish between AI as a research object or computational method and generative AI used to assist writing or coding. A model that is part of the experiment belongs in the methodology; a writing or coding assistant belongs under the university’s AI-use and disclosure rules.

Citation and reproducibility

JYU requires sources to be indicated when paraphrasing or quoting and requires consistent citation practice. The current citation guidance does not establish one universal named style across Chemistry, Physics and Computer Science HPC theses, so confirm the expected style within the specialisation.

In computational work, citation should extend beyond papers when appropriate. Cite datasets, software, libraries, standards, algorithms and external code according to disciplinary practice. A reproducible thesis should allow a reader to distinguish the student’s contribution from imported tools and prior methods.

Accessibility and PDF/A

The final thesis submitted through Vasara should be an accessible PDF/A. Accessibility is easier to achieve when built into the document from the beginning: use real heading styles, logical reading order, meaningful link text, accessible tables and figures, and alternative text where appropriate.

Use the correct specialisation template. Computer Science has the AI & HPC IT template; Chemistry and Physics have their own department guidance. A visually similar template from another branch can still encode the wrong structure or metadata.

Public thesis, JYX and confidential material

Master’s theses are public documents at JYU. Approved work is archived in JYX, and the final thesis should not contain confidential background material. If an industrial partner provides protected information, separate that background material from the assessed public thesis before submission.

TIES502 additionally states that the assessed Computer Science thesis must be published in JYX before credits are registered. Physics FYSS9490 also explicitly identifies JYX as the public archive. These branch statements align with the university-wide publication framework.

No universal word count or one thesis template

The current official HPC sources do not establish one universal thesis word count or page count covering all three specialisations. They also do not create one universal thesis template. Chemistry, Physics and Computer Science have different department or faculty guidance and, in Computer Science, multiple thesis types.

Use the correct branch template and current supervisor guidance for scale and formatting. Do not import an unofficial page target from another university, from a different JYU faculty, or from another HPC specialisation and present it as a programme-wide rule.

A practical Chemistry sequence

For Chemistry, complete the shared HPC core and advanced Chemistry preparation, identify a research topic and responsible supervisor, and agree the supervision plan. Use KEMS903 to observe other theses and prepare your own seminar presentation. Build KEMS9550 as a literature review plus experimental or computational research component, maintaining the data-management and ethics requirements relevant to the project.

When the final manuscript is ready, complete the Moodle originality check, confirm KEMS9550 and KEMS901 registrations, prepare the accessible PDF/A and submit through Vasara. Monitor email and use the stated response window if necessary.

A practical Physics sequence

For Physics, use FYSS9489 to establish the topic, supervisor, project schedule, checkpoints and assessment awareness. Document the supervision agreement and update it when the plan changes. Develop FYSS9490 as a scientifically coherent research project with proper data management, literature handling, ethical reflection and clear communication of results.

Before final submission, register FYSS9490 and FYSS9495, complete the Moodle plagiarism check, finalise the accessible thesis and follow the Vasara route. If the project has two authors, make individual contributions explicitly assessable.

A practical Computer Science sequence

For Computer Science, identify a topic and responsible IT Faculty supervisor, obtain programme approval, and enter TIES501 with an up-to-date study plan. Choose the thesis type that fits the problem: empirical, literature review with original contribution, constructive/developmental, or article-based if all current conditions are met. Use the AI & HPC template and TIES502 learning outcomes to structure the work.

Keep the maturity route under TIES503 distinct from the thesis itself. Complete originality and final-submission requirements, publish through JYX and ensure the IT assessment criteria are met across all required dimensions.

Final HPC branch-selection checklist

Before acting on any thesis instruction, ask four questions. First, which HPC specialisation are you officially enrolled in? Second, are you looking at the correct seminar, thesis and maturity course codes? Third, is the rule programme-wide, faculty-wide or branch-specific? Fourth, is the instruction current for the 2024–2028 curriculum and current academic year?

For Chemistry the anchor is KEMS903/KEMS9550/KEMS901. For Physics it is FYSS9489/FYSS9490/FYSS9495. For Computer Science it is TIES501/TIES502/TIES503. Keeping that branch identity visible prevents most administrative and methodological errors.