22112 - Recent changes [en]

22112 High Performance Computing in Life Science

WikiSysop — Thu, 20 Aug 2026 08:15:39 GMT

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	'''Tools:''' Various servers will be introduced.<br>		'''Tools:''' Various servers will be introduced.<br>
	'''Textbooks:''' There are no text books for the course. I will make do with powerpoints, videos and references to online resources. You can find the material under the individual lessons in the [[Programme]].<br>		'''Textbooks:''' There are no text books for the course. I will make do with powerpoints, videos and references to online resources. You can find the material under the individual lessons in the [[Programme]].<br>
	'''Location:''' Building 208, room ~~001~~.<br>		'''Location:''' Building 208, room 012.<br>
	'''Time:''' Thursday 13:00 - 17:00, module E1-B.<br>		'''Time:''' Thursday 13:00 - 17:00, module E1-B.<br>

MySQL

WikiSysop — Mon, 17 Aug 2026 10:51:24 GMT

Exercises

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	== Exercises ==		== Exercises ==
			'''1)'''
	<!-- Exercises are ready, but not shown - for reasons.....		<!-- Exercises are ready, but not shown - for reasons.....
	~~'''1)'''~~
	In /home/projects/pr_course there are 3 files: persons.csv, marriage.csv and disease.csv. That is data that corresponds to the database design exercise 2 last week.		In /home/projects/pr_course there are 3 files: persons.csv, marriage.csv and disease.csv. That is data that corresponds to the database design exercise 2 last week.
	Your task is to investigate the data, so you know how it looks. Then you must create a database on '''pupil1''' MySQL database system with the ’mysql’ command. <span style="color: red;">You have the privilege to create a database with your DTU username, (the name of the database is your username)</span>, nothing else. In that database, create tables that match the 3 files. Load the files into the tables.		Your task is to investigate the data, so you know how it looks. Then you must create a database on '''pupil1''' MySQL database system with the ’mysql’ command. <span style="color: red;">You have the privilege to create a database with your DTU username, (the name of the database is your username)</span>, nothing else. In that database, create tables that match the 3 files. Load the files into the tables.

Databases

WikiSysop — Mon, 17 Aug 2026 10:49:58 GMT

Exercises

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	'''1) Logging in to a server'''<br>		'''1) Logging in to a server'''<br>
	In the course we will change between using our personal laptop and the student ~~server: pupil1.healthtech.dtu.dk~~. There are currently 5 ~~pupil~~ servers; 1 to 5, but pupil1 is the login server and you can only reach the others from pupil1.~~<br>~~		In the course we will change between using our personal laptop and the student cluster. There are currently 5 servers in the cluster; 1 to 5, but pupil1 is the login server and you can only reach the others from pupil1. It is important to spread out on the servers, especially when you make programs that use CPU intensively.
	In the database exercises we use ''pupil1''. Log into ''pupil1'':
			In the database exercises we only use ''pupil1''. Log into ''pupil1'':
	ssh -X s123456@pupil1.healthtech.dtu.dk		ssh -X s123456@pupil1.healthtech.dtu.dk
	Remember to replace s123456 with your s-number or DTU username		Remember to replace s123456 with your s-number or DTU username
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	gedit X11-based		gedit X11-based
	jedit X11-based		jedit X11-based
	nano text-based		nano text-based Recommended editor
	vim text-based		vim text-based
	This entire exercise is just proof of concept and will make you ready for next week.		This entire exercise is just proof of concept and will make you ready for next week.<br>
			Some people set up VScode for editing files on the cluster. This is not without dangers, as you can inadvertently block both yourself and others for access.

	'''2) Design your own relational database'''<br>		'''2) Design your own relational database'''<br>

MySQL

WikiSysop — Mon, 17 Aug 2026 10:40:46 GMT

Exercises

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	== Exercises ==		== Exercises ==
	<!-- Exercises are ready, but not shown - for reasons.....		<!-- Exercises are ready, but not shown - for reasons.....
	~~-->~~
	'''1)'''		'''1)'''
	In /home/projects/pr_course there are 3 files: persons.csv, marriage.csv and disease.csv. That is data that corresponds to the database design exercise 2 last week.		In /home/projects/pr_course there are 3 files: persons.csv, marriage.csv and disease.csv. That is data that corresponds to the database design exercise 2 last week.
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	disease.csv		disease.csv
	cpr, name of disease, date of discovery		cpr, name of disease, date of discovery
			-->

	'''2)'''		'''2)'''

Distributed computing

WikiSysop — Mon, 17 Aug 2026 10:38:32 GMT

Exercises

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	collect data		collect data

	It is more difficult to solve this exercise - so do number 1 first. You need to find a way of waiting for your worker jobs to be done before your start collecting. However, you can see if this distributed method is faster than last week’s sequential method.		It is more difficult to solve this exercise - so do number 1 first. You need to find a way of waiting for your worker jobs to be done before your start collecting. However, you can see if this distributed method is faster than last week’s sequential method. Try to explain the results you find.

	Some ideas to wait for the jobs to be done.		Some ideas to wait for the jobs to be done.

Databases

WikiSysop — Mon, 17 Aug 2026 10:33:05 GMT

Exercises

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	'''1) Logging in to a server'''<br>		'''1) Logging in to a server'''<br>
	In the course we will change between using our personal laptop and the student server: pupil1.healthtech.dtu.dk<br>		In the course we will change between using our personal laptop and the student server: pupil1.healthtech.dtu.dk. There are currently 5 pupil servers; 1 to 5, but pupil1 is the login server and you can only reach the others from pupil1.<br>
	In the database exercises we use ''pupil1''. Log into ''pupil1'':		In the database exercises we use ''pupil1''. Log into ''pupil1'':
	ssh -X s123456@pupil1.healthtech.dtu.dk		ssh -X s123456@pupil1.healthtech.dtu.dk