Compute Resources

• In general, the offers are limited to members of I-MATH and their students.

• Other UZH members are welcome to contact support@math.uz.ch .

• First time user: contact support@math.uzh.ch first.

Reservations

• Short (<1day) computations don't need a reservation,

• Longer (>1day) are reccomended to be done with a reservation.

• With reservation: In case of maintenance need, we typically schedule the maintenance according to the needs of the user.
• Without reservation: We try to contact the user and wait several hours for an answer.
• General: if we see running computations, we always contact the user first (independent of whether or not a reservation exists). If the user doesn't answer (weekend, holiday, ...) we decide on our own what to do.

Offers

• For small / ad hoc computations, just start the compute software via the thinlinc environment.

• For medium computations, please contact support@math.uzh.ch to ask for the best fitting possibilty and to reserve nodes.

• For large computations and professional support please check http://www.s3it.uzh.ch/.

Resources at IMATH

CPU

GPU

Old

Concept

Access

• The compute nodes can be accessed by SSH only from inside I-MATH.

• Use thinlinc

  • matlab, mathematica, maple, R, rstudio: just start the application via menu 'Applications > Science > ...' - you'll automatically be redirected to the appropriate compute server.

  • For non standard compute software please first log on the compute node via 'ssh', then start the program.
• SSH: Log onto 'ssh.math.uzh.ch' and jump to the compute node again via 'ssh'.

Operating System

• Ubuntu LTS (Linux) - all compute servers.
• Very very limited software might be installed on some Windows virtual machines.

Storage

• If you need more disk space, please contact support@math.uzh.ch .

• Remote (NFS)
  • Personal Home directory

  • /compute/<account>

• Local

  • /export/user/<account>

Programs / Software

• All compute servers use the same applications and versions as installed on the thinlinc terminals.

• Please report missing or outdated software or wishes to support@math.uzh.ch .

• There is no Intel C or Intel Fortran Compiler.
• If you need other program versions than the default one: open a terminal, type the program name followed by two 'TAB' presses: this will show all available installed versions of the specified program.

Parallel computing

• Cluster software
  • Not installed / offered at I-MATH.
  • Various MPI packages and libs are installed. Compiling and preparation to run programs later on a distributed compute cluster are possible.

• Some programs, like matlab, offer limited built-in auto parallelization.

• All of the compute nodes are shared memory machines. It's reasonable to start as many programs in parallel as long the load is less or equal the number of cores.

  • Determine the load by using the command uptime via a terminal. The last three numbers are the average number of jobs (=load) in the run queue over the last 1, 5 and 15 minutes.

    $ uptime
     15:55:20 up 22 days, 24 min,  1 user,  load average: 11.97, 11.73, 11.62

Limitations

• Memory
  • Soft: 64GB
  • Hard: unlimited
• Number of processes per user
  • Soft: 2048
  • Hard: 4096
• Change limitations

$ ulimit -m unlimited
$ ulimit -u 4096

• Make sure to increase a hard limit only one time. If you try to increase it a second time, you'll get an error. You have to log out and log in again to get a new chance.