Non-public templates: Coordination of Scientific Computing
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Here, for documentation, completeness and availability I will list some templates of e-mails and further things I used on a regular basis.
Application for a new user account
So as to apply for a new user account, an eligible user needs to specify three things:
- his/her anonymous user-name in the form abcd1234,
- the working group (or ideally the unix-group) he will be associated to, and
- an approximate data until when the user account will be needed.
No university user account, yet
If the user has no university-wide anonymous user account, yet, he first needs to apply for one. An exemplary e-mail with advice on how to get such a (guest) user account is listed below
Sehr geehrter Herr NAME, um einen Nutzeraccount für das HPC System erhalten zu können müssen Sie bereits über einen universitätsweiten, anonymen Nutzeraccount verfügen. Als Gast einer Arbeitsgruppe können sie einen entsprechenden Guest-Account bei den IT-Diensten beantragen. Besuchen Sie dazu bitte die Seite http://www.uni-oldenburg.de/itdienste/services/nutzerkonto/gaeste-der-universitaet/ und wählen Sie die Option "Gastkonto einrichten". Starten sie den Workflow für das Anlegen eines Gastkontos. Tragen Sie als Verantwortlichen den Leiter der universitären Organisationseinheit ein, der Ihr Vorhaben unterstützt. Bitten Sie diesen, die E-Mail die er erhält zu öffnen, den darin enthaltenen Link aufzurufen und den Antrag zu genehmigen. Das Konto wird dann automatisch erstellt. Ihr anonymer Nutzeraccount wird die Form "abcd1234" haben. Um nun ihren Nutzeraccount für das HPC System freischalten zu können senden Sie mir bitte folgende Details: 1) den anonymen Nutzernamen für den der HPC account erstellt werden soll, 2) den Namen der Arbeitsgruppe der Sie zugeordnet werden sollen, 3) einen voraussichtlichen Gültigkeitszeitraum für den benötigten HPC account. Sobald Ihr HPC account aktiviert ist werde ich mich mit weiteren Informationen bei Ihnen melden. Mit freundlichen Grüßen Oliver Melchert
User account HPC system: Mail to IT-Services
Once the user supplied the above information, you can apply for a HPC user account at the IT-Service using an e-mail similar to:
Mail to: felix.thole@uni-oldenburg.de; juergen.weiss@uni-oldenburg.de Betreff: [HPC-HERO] Einrichtung eines Nutzeraccounts Sehr geehrter Herr Thole, sehr geehrter Herr Weiss, Hiermit bitte ich um die Einrichtung eines HPC Accounts für Herrn NAME abcd124; UNIX-GROUP der Account wird voraussichtlich bis DATUM benötigt. Mit freundlichen Grüßen Oliver Melchert
If no proper unix group exists, yet, send instead an email similar to the following:
Mail to: felix.thole@uni-oldenburg.de; juergen.weiss@uni-oldenburg.de Betreff: [HPC-HERO] Einrichtung eines Nutzeraccounts Hallo Felix, hallo Jürgen, Hiermit bitte ich um die Einrichtung eines HPC Accounts für Herrn NAME abcd1234 der Account wird voraussichtlich bis DATUM benötigt. Herr NAME ist Mitarbeiter der AG "AG-NAME" (AG-URL) von Herrn Prof. NAME AG-LEITER. Die entsprechede AG hat noch keine eigene Unix Group! Kann daher eine neue Unix Group für die AG angelegt und in die bestehende Gruppenhierarchie eingebunden werden? Ich schlage hier den Namen agUNIX-GROUP-NAME für die Unix Gruppe vor. Die AG gehört zur Fak. FAKULTAET. Mit freundlichen Grüßen Oliver Melchert
User account HPC system: Mail back to user
As soon as you get feedback from the IT-Services that the account was created, send an email to the user similar to the following:
Betreff: [HPC-HERO] HPC user account Sehr geehrter Herr NAME, die IT-Dienste haben Ihren HPC Account bereits freigeschaltet. Ihr Loginname ist abcd1234 und Sie sind der Unix-gruppe UNIX-GROUP-NAME zugeordnet. Sie verfügen über 100GB Plattenspeicher auf dem lokalen Filesystem (mit vollem Backup). Wenn Sie über einen begrenzten Zeitraum mehr Speicherplatz benötigen können Sie mich gerne diesbezüglich anschreiben. Ihren aktuellen Speicherverbrauch auf dem HPC System können Sie mittels "iquota" einsehen. An jedem Sonntag werden Sie eine Email mit dem Betreff "Your weekly HPC Quota Report" erhalten, die Ihren aktuellen Speicherverbrauch zusammenfasst. Anbei sende ich Ihnen einen Link zu unserem HPC user wiki, auf dem Sie weitere Details über das lokale HPC System erhalten http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Main_Page Der Beitrag "Brief Introduction to HPC Computing" unter http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Brief_Introduction_to_HPC_Computing illustriert einige einfache Beispiele zur Nutzung der verschiedenen (hauptsächlich parallelen) Anwendungsumgebungen die auf HERO zur Verfügung stehen und ist daher besonders zu empfehlen. Er diskutiert außerdem einige andere Themen, wie z.B. geeignetes Alloziieren von Ressourcen und Debugging. Wenn Sie planen die parallelen Ressourcen von MATLAB auf HERO zu nutzen kann ich Ihnen die Beiträge "MATLAB Distributed Computing Server" (MDCS) unter http://wiki.hpcuser.uni-oldenburg.de/index.php?title=MATLAB_Distributing_Computing_Server und "MATLAB Examples using MDCS" unter http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Matlab_Examples_using_MDCS empfehlen. Der erste Beiträge zeigt wie man das lokale Nutzerprofil für die Nutzung von MATLAB auf HERO konfigurieren kann und der Zweite beinhaltet einige Beispiele und diskutiert gelegentlich auftretende Probleme im Umgang mit MDCS. Viele Grüße Oliver Melchert
english variant of the above email:
Betreff: [HPC-HERO] HPC user account Dear NAME, the IT-Services were now able to activate your HPC account. Your login name to the HPC system is abcd1234 and you are integrated in the group UNIX-GROUP-NAME Per default you have 100GB of storage on the local filesystem which is fully backed up. If you need some more storage over a limited period in time you can contact me. Note that you can check your memory consumption on the HPC system via the command "iquota". In addition, on each Sunday you will receive an email, titled "Your weekly HPC Quota Report", summarizing your current memory usage. Below I sent you a link to the HPC user wiki where you can find further details on the HPC system http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Main_Page In particular I recommend the "Brief Introduction to HPC Computing" at http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Brief_Introduction_to_HPC_Computing which illustrates several basic examples related to different (mostly parallel) environments the HPC system HERO offers and discusses a variety of other topics, as, e.g., proper resource allocation and debugging. Further, if you plan to use the parallel capabilities of MATLAB on HERO, I recommend the "MATLAB Distributed Computing Server" (MDCS) page at http://wiki.hpcuser.uni-oldenburg.de/index.php?title=MATLAB_Distributing_Computing_Server and the "MATLAB Examples using MDCS" wiki page at http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Matlab_Examples_using_MDCS These pages summarize how to properly set up your profile for using MATLAB on HERO and discuss some of the frequently appearing problems. With kind regards Oliver
User account HPC system: Mail back to user; Fak 2 (STATA users)
New users from Fak 2 most likely want to use the STATA software. An adapted version of the above email reads
Dear MY_NAME, the IT-Services activated your HPC account already. Your login name to the HPC system is LOGIN_NAME and you are associated to the unix group UNIX_GROUP This is also reflected by the structure of the filesystem on the HCP system. Per default you have 100GB of storage on the local filesystem which is fully backed up. If you need some more storage over a limited period in time you can contact me. Note that you can check your memory consumption on the HPC system via the command "iquota". In addition, on each Sunday you will receive an email, titled "Your weekly HPC Quota Report", summarizing your current memory usage. Below I sent you a link to the HPC user wiki where you can find further details on the HPC system: http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Main_Page If you plan to use the parallel capabilities of STATA on HERO, I recommend the "STATA" entry at Main Page > Application Software and Libraries > Mathematics/Scripting > STATA see: http://wiki.hpcuser.uni-oldenburg.de/index.php?title=STATA The above page summarizes how to access the HPC System and how to successfully submit a STATA job. With kind regards Dr. Oliver Melchert
Temporary extension of disk quota
Sometimes a user from the theoretical chemistry group needs an temporary extension of the available backed-up disk space. Ask him to provide
- the total amount of disk space needed (he might check his current limit by means of the unix command iquota)
- an estimated data until the extension is required
Mail to IT-Servies
Then send an email similar to the one listed below to the IT-Service
Mail to: felix.thole@uni-oldenburg.de; juergen.weiss@uni-oldenburg.de Betreff: [HPC-HERO] Erhöhung des verfügbaren Festplattenspeichers eines Nutzers Hallo Felix, hallo Jürgen, der HPC User NAME abcd1234; UNIX-GROUP hat darum gebeten seinen Disk Quota vorübergehend zu erhöhen. Er bittet um eine Erhöhung auf ein Gesamtvolumen von 500GB die bis Ende Dezember 2013 benötigt wird. Danach kann er die Daten entsprechend archivieren und der Disk Quota könne wider zurückgesetzt werden. Viele Grüße, Oliver
List of users with nonstandard quota
Users that currently enjoy an extended disk quota:
NAME ID MEM LIMIT jan.mitschker@uni-oldenburg.de dumu7717 1TB no limit given hendrik.spieker@uni-oldenburg.de rexi0814 300GB Ende September 2013 wilke.dononelli@uni-oldenburg.de juro9204 700GB Ende Dezember 2013 eike.mayland.quellhorst@uni-oldenburg.de auko1937 500GB Ende März 2014
Cluster downtime
In case there needs to be a maintenance downtime for the cluster, send an email similar to the following to the mailing list of the HPC users
Mail to: hpc-hero@listserv.uni-oldenburg.de Betreff: [HPC-HERO] Maintenance downtime 11-13 June 2013 (announcement) Dear Users of the HPC facilities, this is to inform you about an overly due THREE-DAY MAINTENANCE DOWNTIME FROM: Tuesday 11th June 2013, 7 am TO: Thursday 13th June 2013, 16 pm This downtime window is required for essential maintenance work regarding particular hardware components of HERO. Ultimately, the scheduled downtime will fix longstanding issues caused by malfunctioning network switches. Please note that all running Jobs will be killed if they are not finished up to 11th June 7 am. During the scheduled downtime, all queues and filesystems will be unavailable. We expect the HPC facilities to resume on Thursday afternoon. I will remind you about the upcoming three-day maintenance downtime in unregular intervals. Please accept my apologies for any inconvenience caused Oliver Melchert
In case the downtime needs to be extended send an email similar to:
Mail to: hpc-hero@listserv.uni-oldenburg.de Betreff: [HPC-HERO] Delay returning the HPC system HERO to production status Dear Users of the HPC Facilities, we currently experience a DELAY RETURNING THE hpc SYSTEM TO PRODUCTION STAUTS since the necessary change of the hardware components took longer than originally expected. The HPC facilities are expected to finally resume service by Friday 14th June 2013, 15:00 We will notify you as soon as everything is back online. With kind regards Oliver Melchert
you do not need to supply much details, yet. However, if another extension is necessary, you should provide some details otherwise prepare for complaints by the users. So, your email could look similar to:
Mail to: hpc-hero@listserv.uni-oldenburg.de Betreff: [HPC-HERO] Further delay returning the HPC system HERO to production status Dear Users of the HPC Facilities, as communicated already yesterday, we currently experience a DELAY RETURNING THE hpc SYSTEM TO PRODUCTION STATUS. The delay results from difficulties related to the maintenance work on the hardware components of HERO. The original schedule for the maintenance work could not be kept. Some details of the maintenance process are listed below: According to the IT-services, the replacement of the old (malfunctioning) network switches by IBM engineers worked out well (with no delay). However, the configuration of the components by pro-com engineers took longer that the previously estimated single day, causing the current delay. Once the configuration process is completed, the IT-service staff needs to perform several tests, firmware updates and application test which will take approximately one day. After the last step is completed, the HPC facilities will finally return to production status. In view of the above difficulties we ask for your understanding that the HPC facilities will not be up until today 15:00. We hope that the HPC facilities resume service by Monday 17th June 2013, 16:00 We will notify you as soon as everything is back online and apologize for the inconvenience. With kind regards Oliver Melchert
once the HPC is up and ready send an email similar to:
Mail to: hpc-hero@listserv.uni-oldenburg.de Betreff: [HPC-HERO] HPC systems have returned to production Dear Users of the HPC Facilities, this is to inform you that the maintenance work on the HPC systems have been completed and the HPC component HERO has returned to production: HERO accepts logins and has already started to process jobs. Thank you for your patience and please accept my apologies for the extension of the maintenance downtime and any inconvenience this might have caused Oliver Melchert
MOLCAS academic license
My question to the MOLCAS contact
Dear Dr. Veryazov, my Name is Oliver Melchert and currently I'm in charge of the coordination of the scientific computing at the University of Oldenburg. Previously this position was occupied by Reinhard Leidl who had correspondence with you. I write to you since I have a question regarding a licensed Software product which was purchased earlier for our local HPC facilities. The Software product I'm referring to is the Quantum Chemistry Software MOLCAS, for which we own an academic group license which will expire on 18.10.2013. Now, my question is, in order to extend the license validity what steps do I have to follow and can you guide me through these steps? With kind regards Dr. Oliver Melchert
And their response
Dear Dr. Melchert,
In order to update the academic license for Molcas you should place a
new order http://www.molcas.org/order.html
Please, print and sign the forms generated during the ordering.
These forms should be sent to me (e-mail attachment is OK).
After receiving the forms I will send you the updated license file.
There are two possibilities for the payment. By default - we will send
you an invoice to be paid via bank transfer.
It is also possible to pay by a credit card.
Best Regards,
Valera.
--
=================================================================
Valera Veryazov * Tel: +46-46-222 3110
Theoretical Chemistry * Fax: +46-46-222 8648
Chemical Center, *
P.O.B. 124 * Valera.Veryazov@teokem.lu.se
S-221 00 Lund, Sweden * http://www.teokem.lu.se/~valera
About MOLCAS: http://www.molcas.org/
-----------------------------------------------------------------
Large Matlab Jobs
Some Matlab users send jobs with the maximally allowed number of workers (i.e. slots in Matlab jargon), i.e. 36. Usually these Jobs get distributed over lots of hosts. E.g.:
job-ID prior name user state submit/start at queue master ja-task-ID
----------------------------------------------------------------------------------------------------------
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs004 MASTER
mpc_std_shrt.q@mpcs004 SLAVE
mpc_std_shrt.q@mpcs004 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs008 SLAVE
mpc_std_shrt.q@mpcs008 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs032 SLAVE
mpc_std_shrt.q@mpcs032 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs034 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs036 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs038 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs043 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs045 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs052 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs066 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs070 SLAVE
mpc_std_shrt.q@mpcs070 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs076 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs080 SLAVE
mpc_std_shrt.q@mpcs080 SLAVE
mpc_std_shrt.q@mpcs080 SLAVE
mpc_std_shrt.q@mpcs080 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs087 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs089 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs090 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs091 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs099 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs107 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs110 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs111 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs112 SLAVE
mpc_std_shrt.q@mpcs112 SLAVE
1040328 0.51109 Job16 nixi9106 r 10/07/2013 18:19:48 mpc_std_shrt.q@mpcs117 SLAVE
mpc_std_shrt.q@mpcs117 SLAVE
mpc_std_shrt.q@mpcs117 SLAVE
mpc_std_shrt.q@mpcs117 SLAVE
mpc_std_shrt.q@mpcs117 SLAVE
mpc_std_shrt.q@mpcs117 SLAVE
If the jobs have lots of I/O this puts a big strain on the filesystem. For these large jobs the "parallel job memory issue" is a problem. I.e. the master process has to account (in terms of memory) for all the connections to the other host machines. Then, if the master process runs out of memory the job gets killed. More common are 8 slot jobs and even more common are jobs with even less slots.
Login problems
Every now and then external guests or regular users try to login to the HPC system from outside the university and the straightforward attempt via
ssh abcd1234@hero.hpc.uni-oldenburg.de
fails, of course. Then, the user might report
Dear Oliver, My name is Pavel Paulau, I tried today for the first time to log in in cluster: ssh exwi4008@hero.hpc.uni-oldenburg.de and got message: "Permission denied, please try again." Could You say what is the reason? What should I do to get access? Thanks. Kind wishes, Pavel
A possible response then might read
Dear Pavel, on the first sight your command line statement looks right, provided that you try to login to the HPC system from a terminal within the University of Oldenburg. I also checked that your HPC account indeed exists (and it does :)). As pointed out in the HPC user wiki it makes a difference whether you attempt to login from a Terminal within the University of Oldenburg or from outside the university: http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Logging_in_to_the_system#From_within_the_University_.28intranet.29 In case you want to login to the HPC system from outside the university I recommend to setup a VPN connection via the gateway vpn2.uni-oldenburg.de as pointed out in the above user-wiki entry. However, sometimes, even though the VPN tunnel is correctly set up, the login procedure might fail due to problems resolving the hostname. Then you might try to access the cluster via the ip address of the master node. Just establish the VPN tunnel and try to access HERO via ssh exwi4008@10.140.1.61 this should resolve the name issues. With kind regards Oliver
HPC tutorial
Requesting seminar rooms
Hallo Herr Melchert, die Buchungen habe ich eingetragen! Gruß Silke Harms Raum- und Veranstaltungsbüro Dezernat 4 / Gebäudemanagement Carl von Ossietzky Universität Oldenburg Telefon: 0441 / 798-2483 -----Ursprüngliche Nachricht----- Von: Oliver Melchert Gesendet: Donnerstag, 24. Oktober 2013 10:28 An: Silke Ulrike Harms Betreff: RE: Anfrage Raum für Einzel-/Blockveranstaltung Hallo Frau Harms, vielen Dank für die Liste der freien Termine. Nach Rücksprache mit meinem Kollegen würden wir gerne folgende Räume/Zeiten buchen: W04 1-162: Di: 19.11.13 - 14-16 Uhr Mi: 20.11.13 - 16-18 Uhr W01 0-008: Do: 21.11.13 - 09-12 Uhr der Einzelveranstaltung/Blockveranstaltung ist keine Nr. zugeordnet, es ist ein Pilotprojekt das, wenn erfolgreich, in den kommenden Semestern regulär (dann mit Veranstaltungsnummer) angeboten werden soll. Der Name der Veranstaltung lautet "A brief HPC Tutorial" und wird von Dr. Oliver Melchert und Dr. Stefan Albensoeder angeboten. Mit herzlichen Grüßen Oliver Melchert ________________________________________ From: Silke Ulrike Harms Sent: Wednesday, October 23, 2013 10:09 AM To: Oliver Melchert Subject: AW: Anfrage Raum für Einzel-/Blockveranstaltung Hallo Herr Melchert, Sie können die freien Zeiten über Stud.IP in den jeweiligen Räumen einsehen (unter Raumbelegungen). Ich habe Ihnen jetzt die derzeitigen Lücken rausgesucht: W01 0-008 Mo 11.11.13 - 10-12 Uhr, Di 12.11.13 - 12-14 Uhr, Mi 13.11.13 - 08-10 + 16-18 Uhr, Do 14.11.13 - 08-10 + 14-16 Uhr, Fr 15.11.13 - 12-14 Uhr Mo 18.11.13 - ab 16 Uhr, Di 19.11.13 - 12-14 Uhr, Mi 20.11.13 - 08-10 Uhr, Do 21.11.13 - 08-12 + 14-16 Uhr, Fr 22.11.13 - ab 12 Uhr Mo 25.11.13 - ab 16 Uhr, Di 26.11.13 - 12-14 Uhr, Mi 27.11.13 - 08-10 Uhr, Do 28.11.13 - 08-12 + 14-16 Uhr W04 1-162 Di 12./19./26.11.13 - jeweils 14-16 Uhr Mi 13./20./27.11.13 - jeweils ab 16 Uhr Fr 15./22./29.11.13 - jeweils ab 14 Uhr Bitte entscheiden Sie sich schnell, weil es zurzeit noch vielen Anfragen/Buchungen gibt. Gruß Silke Harms Raum- und Veranstaltungsbüro Dezernat 4 / Gebäudemanagement Carl von Ossietzky Universität Oldenburg Telefon: 0441 / 798-2483 -----Ursprüngliche Nachricht----- Von: Oliver Melchert Gesendet: Dienstag, 22. Oktober 2013 11:13 An: Silke Ulrike Harms Betreff: RE: Anfrage Raum für Einzel-/Blockveranstaltung Sehr geehrte Frau Harms, vielen Dank für Ihre Antwort. Aufgrund von Urlaub/Krankeit konnten mein Kollege und ich uns auf keinen der vorgeschlagenen Ternime festlegen. Hiermit möchte erneut einen Anfrage für dieselben Räume (siehe unten angehängte e-Mail) im Zeitraum 11.11.2013 - 29.11.2013 stellen. Mit herzlichen Grüßen Oliver Melchert ________________________________________ From: Silke Ulrike Harms Sent: Monday, September 23, 2013 1:42 PM To: Oliver Melchert Subject: AW: Anfrage Raum für Einzel-/Blockveranstaltung Guten Tag Herr Melchert, ich kann Ihnen folgende Raumangebote machen: Montag 14. Oktober 2013 14-20 Uhr - W04 1-162 + 16-20 Uhr - W01 0-008 Dienstag 15. Oktober 2013 14-16 Uhr - W04 1-162 + 18-20 Uhr - W01 0-008 Mittwoch 16. Oktober 2013 16-20 Uhr - W04 1-162 + 08-12 Uhr - W01 0-008 Bitte teilen Sie mir mit, welche Buchungen ich vornehmen soll und unter welcher Nr. ich Ihre Veranstaltung finde (und die Räume buchen soll). Gruß Silke Harms Raum- und Veranstaltungsbüro Dezernat 4 / Gebäudemanagement Carl von Ossietzky Universität Oldenburg Telefon: 0441 / 798-2483 -----Ursprüngliche Nachricht----- Von: Oliver Melchert Gesendet: Freitag, 20. September 2013 10:00 An: Silke Ulrike Harms Betreff: Anfrage Raum für Einzel-/Blockveranstaltung Sehr geehrte Frau Harms, mein Name ist Oliver Melchert und ich begleite derzeit die Stelle des "Koordinators für das wissenschaftliche Rechnen". Für die Nutzer des Oldenburger Großrechners möchte ich, zusammen mit einem Kollegen, die Einzelveranstaltung/Blockveranstaltung "A brief HPC tutorial" anbieten. Für die Veranstaltung planen wir die Dauer von 4 x 1.5 Stunden ein. Optimal wäre es, wenn wir an zwei aufeinanderfolgenden Tagen jeweils 2 x 1.5h anbieten könnten. Wir rechnen mit max. 30 Teilnehmern und suchen einen geeigneten Raum für unser Vorhaben. Wir würden, sofern das möglich ist, die Veranstaltung gerne an zwei aufeinanderfolgenden Tagen im Zeitraum Oktober/November in den Wochen 14.10. - 19.10. oder 28.10. - Ende November anbieten. Die Veranstaltung soll neben Vorträgen auch praktische Übungen bieten. Daher wäre es optimal, wenn wir für den letzten 1.5h Block in einen Rechnerraum ausweichen könnten. Da die meisten Nutzer am Standord Wechloy sitzen wäre es super wenn wir dort einen Seminarraum finden könnten. Geeignete Räume wären z.B. W2-1-143 W2-1-148 W3-1-156 W4-1-162 Ein geeigneter Rechnerraum wäre z.B. W1-0-008 Bezüglich der Urzeit sind wir flexibel. Wäre denn überhaupt noch Raum unsere geplante Veranstaltung unterzubringen? Mit freundlichen Grüßen Dr. Oliver Melchert
Mail to users
Betr.: [HPC-HERO] Tutorial on High Performance Computing (19.-21. Nov)
Dear User of the HPC System,
this is to announce the first tutorial on "High Performance Computing" which
will take place from 19.11.2013 to 21.11.2013. More precisely, the tutorial
will be split into three sessions. The first two sessions feature the parts
0.-IV. (listed below) and are held at the following dates:
Seminar-Room: W04 1-162:
Tue, 19.11.13 - 14-16 Uhr
Wed, 20.11.13 - 16-18 Uhr
The third session (part V.) comprises practical exercises which are meant to
illustrate some of the content presented in the earlier parts and is held at:
Computer-Lab: W01 0-008:
Thu, 21.11.13 - 09-12 Uhr
The target audience of this 1st HPC tutorial are new Users of the local HPC
system, for whom, in order to benefit from the tutorial, the skills of reading
and writing C-programs are of avail. However, we are optimistic that we will
be able to announce a quite similar tutorial for all Matlab-focused users,
soon. If you would like to attend the HPC tutorial, please sent a brief response
to this email.
The planned programme of this 1st HPC tutorial is
0. Introduction to HPC
1. Motivation
2. Architectures
3. Overview over parallel models
I. Cluster Overview:
1. System Overview
2. Modification of user environments via "module"
3. Available compiler
4. Available parallel environments
5. Available Libraries
6. Performance hints
II. Introduction to the usage of SGE:
1. Introduction
2. General Job submission
3. Single Slot jobs
4. Parallel Jobs
5. Monitoring and Controlling jobs
III. Debugging and Profiling:
1. Compiling programs for debugging
2. Tracking memory issues
3. Profiling
IV. Misc:
1. Logging in from outside the university
2. Mounting the HPC home directory
3. Parallel environment memory issue
4. Importance of allocating proper resources
V. Exercises (Computer-Lab):
1. Try out the examples given in part II
2. Estimate pi using Monte Carlo simulation
(code provided serial+parallel using mpi;
compile, submit and monitor jobs for different
parameter settings)
With kind regards
Oliver Melchert and Stefan Albensoeder
Confirmation for users
Dear USER, this is to confirm your registration for the first tutorial on "High Performance Computing" which will be held at the following dates: Seminar-Room W04 1-162: Tue, 19.11.13 - 14-16 Uhr Wed, 20.11.13 - 16-18 Uhr Computer-Lab W01 0-008: Thu, 21.11.13 - 09-12 Uhr Thank you for signing up Oliver Melchert and Stefan Albensoeder
Mail to IT Services
Contact the IT services and ask to make sure that the participants of the HPC Tutorial can logon to the HPC system from the Computer lab.
Hallo Oliver, wir haben das Subnetz freigeschaltet. Kannst du mal probieren ob alles funktioniert. Heute kann ich nicht an deiner Veranstaltung teilnehmen, da ich schon um 17 Uhr einen Termin habe. Viele Grüße Felix -----Ursprüngliche Nachricht----- Von: Oliver Melchert Gesendet: Mittwoch, 20. November 2013 10:14 An: Jürgen Weiß; Felix Thole Betreff: IP Adressen in Raum W01-0-008 Hallo Jürgen, hallo Felix, ich habe die IP Adressen der Rechner im Raum W01-0-008 nachgeschaut. Die ersten 3 Oktetts lauten auf: 134.106.45.XXX Die Übungen sollen morgen von 9-12 Uhr in diesem Raum stattfinden. Ist die obige Information ausreichend oder soll ich eine genaue Liste der vollständigen IP Adressen senden? Viele Grüße Oliver
User-Wiki entry
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=HPC_Tutorial_No1
Corresponding mail to all users
Betr.: [HPC-HERO] Accompanying documents for HPC Tutorial Dear User of the HPC System, this is to inform you that the User Wiki page that collects the material related to the first tutorial on "High Performance Computing", which took place from 19.11.2013 to 21.11.2013, is available at Main Page > Basic Information > Examples > HPC Tutorial No1 under the link http://wiki.hpcuser.uni-oldenburg.de/index.php?title=HPC_Tutorial_No1 We would like to thank all users of the HPC components FLOW/HERO that attended this first HPC tutorial and we are looking forward to host a further educational workshop tailored to suit all "MATLAB distributed computing server" (MDCS) users at the end of January 2014 (more information will follow in due time). Best regards Oliver Melchert and Stefan Albensoeder
List of HPC publications
This page is intended to list publications that were supported by simulations on the HPC components FLOW/HERO. If you want to contribute to this list, please send an e-mail with subject:
[HPC-HERO or HPC-FLOW] Contribution to the list of HPC publications
to the coordinator of scientific computing (position currently substituted by: oliver.melchert@uni-oldenburg.de). It would be highly appreciated if you could provide the digital object identifier (DOI) that refers to your article within that mail. If the journal you published your article(s) in offers to export citations you might alternatively send one of the formats supported by the journal (preverably: BibTex).
NOTE: We kindly ask you to acknowledge the HPC components FLOW/HERO within research articles that were supported by simulations on the HPC facilities.
2012
- Claussen, G. and Apolo, L. and Melchert, O. and Hartmann, A. K.,
Analysis of the loop length distribution for the negative-weight percolation problem in dimensions d=2 through d=6,
Physical Review E 86, 5 (2012), 10.1103/PhysRevE.86.056708.
2013
- Melchert, O.,
Percolation thresholds on planar Euclidean relative-neighborhood graphs,
Physical Review E 87, 4 (2013), 10.1103/PhysRevE.87.042106. - Melchert, O. and Hartmann, A. K.,
Information-theoretic approach to ground-state phase transitions for two- and three-dimensional frustrated spin systems,
Physical Review E 87, 2 (2013), 10.1103/PhysRevE.87.022107. - Melchert, O.,
Universality class of the two-dimensional randomly distributed growing-cluster percolation model,
Physical Review E 87, 2 (2013), 10.1103/PhysRevE.87.022115. - Norrenbrock, C. and Melchert, O. and Hartmann, A. K.,
Paths in the minimally weighted path model are incompatible with Schramm-Loewner evolution,
Physical Review E 87, 3 (2013), 10.1103/PhysRevE.87.032142. - Melchert, O. and Hartmann, A. K.,
Typical and large-deviation properties of minimum-energy paths on disordered hierarchical lattices,
The European Physical Journal B 86, 7 (2013), 10.1140/epjb/e2013-40230-1.
- Wiki Ref-generator: http://reftag.appspot.com/doiweb.py?doi=10.1103%2FPhysRevE.87.022107
- style example: http://en.wikipedia.org/wiki/Wikipedia:Citing_sources
List of user wiki pages
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Brief_Introduction_to_HPC_Computing
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Matlab_Examples_using_MDCS
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Queues_and_resource_allocation
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Unix_groups
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Mounting_Directories_of_FLOW_and_HERO#OSX
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=File_system (Snapshot functionality)
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=STATA
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Memory_Overestimation
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Debugging
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=Profiling_using_gprof
http://wiki.hpcuser.uni-oldenburg.de/index.php?title=HPC_Tutorial_No1
MISC
Limited resource quota sets
Slot limits for different user groups are set using resource quota sets (rqs)
alxo9476@hero01:~$ qconf -srqs
{
name max_slots_for_express_queue_FLOW
description "limits number of slots for express queue on FLOW"
enabled TRUE
limit users {@flowusers} queues {cfd_xtr_expr.q} to slots=40
}
{
name max_slots_for_pe_mdcs
description "limits number of slots for PE mdcs"
enabled TRUE
limit users {*} pes {mdcs} to slots=36
}
{
name max_slots_for_user_groups_HERO
description "limits number of slots of users on HERO"
enabled TRUE
limit users {@herousers} to slots=360
}
