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SuperMUC Instructions

Send an email with the personal information template from below filled in to grid-support@lrz.de to request an account on SuperMUC.

If you're a Mac or Linux user, you can extract your DN from your certificate with the following command (the point of the Python script is to automagically convert the DN to the right format):

openssl x509 -in ~/.globus/usercert.pem -noout -subject | python -c "import sys; print ','.join(reversed(sys.stdin.read().strip()[9:].split('/')[1:]))"

Template Email Request

Dear grid-support,

I would like to request an account on SuperMUC as part of 
the ComPat project. 

My personal information is as follows:

Academic Title (if any):
First Name: 
Last Name: 
Nationality: 
Office Address: 
Telephone no:         
Email address: 
Certificate DN (distinguished name, also called subject) :

Many thanks in advance.

Best rgds,
Your name

Getting on SuperMUC

To get on SuperMUC you will need gsissh which is part of the Globus Toolkit . Download and install the version for your operating system. On a Mac it will be put under /Library/Globus/bin. You will want to add it to your .bash_profile path. You will want to set-up your trust roots by running myproxy-get-trustroots -b -s myproxy.lrz.de -p 80. Also, you need to create a proxy (a short-lived copy) of your certificate by running grid-proxy-init and typing your certificate passphrase. After that you can log on by running gsissh gridmuc.lrz.de -p 2222.

You can put your intermediate results on $SCRATCH and use $WORK to store your data and software.

Optional: You can create directories under $WORK and make them readable/writable by the ComPat project group (pr92ge) to share software or data with your colleagues. Use the command chmod g+rw $WORK.

To get data in and out of SuperMUC you can use GridFTP command (globus-url-copy -r ./filetoupload.txt gsiftp://gridmuc.lrz.de/~/ to copy from your machine to your home on SuperMUC; -r means recursive and also copies directories). Or use or the convenient Globus Online website.

To use Globus Online follow the instructions below:

  1. Create a Globus Online account here .
  2. Go to https://www.globus.org/app/transfer and choose Globus ID as your organisation, and click No thanks, continue when it's asking if you want to use an existing account.
  3. When using the Globus Online web app you need to specify gridmuc as your endpoint.
    1. Upload a proxy certificate to a myproxy server. We recommend using myproxy.lrz.de and you can do this by running myproxy-init -l username -s myproxy.lrz.de -p 80. This username can be freely chosen and is not related to anything else. When asked for myproxy passphrase invent a new password specific to myproxy.
    2. In the Globus Online website select GridMUC as one of the end-points. Just type GridMUC in one of the search fields and it should pop-up.
    3. In the GridMUC endpoint log-in window specify the user name and password you used in the myproxy-init command. Screenshot
  4. To set-up the other endpoint you need to install Globus Connect Personal by following the steps outlined on the website. BEWARE: there seems to be a bug in the Linux version of Globus Connect. After following the usage instructions you will receive a very non-descript error message. You can ignore it (just click OK), but you have to quit Globus Connect application and start it again before you can connect.
  5. In Globus Online specify the name you chose above as the other endpoint.
  6. If you did everything right, the transfer window should look something like this.

Extensive instructions on using SuperMUC can be found on the LRZ website:

Getting on SuperMUC

Using LoadLeveller on SuperMUC

SuperMUC currently uses LoadLeveller as it's batch system. You can find some common usage scenarios, queue descriptions and other information by following the link below.

https://www.lrz.de/services/compute/supermuc/loadleveler/

Accessing the Shared Directory

To access the shared directory that contains tools and data that are meant to be shared between the ComPat group, once logged in to SuperMUC, do:

cd $WORK
cd ../di25pul

This is the shared directory. The agreed upon directory tree structure is:

di25pul/
  Astro/
  Bio/
  Common/
  Fusion/

You should put commonly used tools (NAMD, MUSCLE2, AMUSE, …) in the Common subdirectory.

supermuc_instructions.txt · Last modified: 2017/09/29 15:30 (external edit)