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Who is ID SIS HPC ?

What services are provided ID SIS HPC ?

Do I need to pay or are the services for free ?

Where can I find more information ?


Who can use the services of ID SIS HPC ?

Anyone within ETH may use the services provided by ID SIS HPC. Professors and institutes who participated in the purchase of the system are guaranteed a share of the resources proportional to their investment. Other users must share the public resources allocated to the IT Services. Researchers from other Swiss and international institutions can use the services, as long as they have a collaboration with an institute of ETH Zurich.

Do I need an account ?

For most services, you can directly login with the credentials of your NETHZ account. The only exceptions are the Brutus cluster and the CLC genomics service, where you still need to apply for an account. If you are interested in using these services, then please contact cluster support.

How do I log in ?

For security reasons, you can only access our services from within the ETH network. If you are outside the ETH network, you have to establish a VPN connection first. From a Linux or a Mac OS X computer, you can login with

ssh username@hostname

or for graphical applications with

ssh -Y username@hostname

If you are using Windows, then you need to make use of a third party application, as for instance PuTTY or Cygwin, that provide a console to enter the ssh command, analogue to the Linux users. For graphical applications, Windows users require a software called an X-server, which provides X11 forwarding. Common X-servers are Cygwin/X, Xming, Exceed, XWin-32.

X11-forwarding with -X does not work, what am I doing wrong?

As described above, you have to use the -Y option for X11-forwarding. Log in with:

ssh -Y username@hostname

How can I change my password?

Since the NETHZ password is used for the log in to our services, the users can change their password at


Can I change my default shell?

Bash is the default shell for all users. The configuration of our services is complex and everything is tested extensively using bash. It is therefore the only shell that we fully support. You are free to use a different shell, but you are doing so at your own risks.


Do you provide any software on your clusters ?

On our clusters, we provide a wide range of centrally installed applications and libraries. Our software stack contains commercial as well as open source software. An overview on all centrally installed applications can be found in our application tables.

Why does my 32-bit executable not work on your clusters ?

Our cluster are pure 64-bit systems. Your 32-bit executable might runs without problems in some cases, but there are certain limitations. A 32-bit executable can only use up to 3 GB of virtual memory. If you try to use more, this might results in a segmentation fault or an out of memory error message. The solution for this problem is to recompile your application for 64-bit.

Can I run Windows executables on the clusters ?

Windows executables do not run under Linux. In order to be able to run your application on our clusters, you need to make sure that it is a 64-bit binary for Linux.

Can you please update GLIBC on the clusters ?

The libc is part of the operating system. Updating libc is equivalent to updating the operating system on the cluster. Therefore we can not just update libc. If your executable requires a newer version of libc (GLIBC), then please consider recompiling the source code directly on the cluster, where you would like to run the executable.

Is it necessary to recompile or can I just copy my application to a cluster ?

Statically linked, single-processor executables built on standard x86 Linux platforms should run without any problem on our clusters. Recompliling may improves the performance, though. Dynamically linked executables will not run if the required shared libraries are either not available or not compatible (e.g. 32-bit executable and 64-bit library). Recompiling is recommended.

Are development tools available on the clusters ?

How do I compile MPI applications ?

What scientific libraries are available on the clusters ?

Can you please allow me to run sudo for installing my code ?

Why can't I install my application into /usr/bin and /usr/lib64 ?

Is there a license available for application XYZ ?

Environment modules

Can I automatically load modules on login ?

Is it possible to load modules in a script ?

Module load does not work properly, what am I doing wrong ?

In the application table version X is listed, why does module avail not list it ?

Version X is gone, why did you delete it ?

Submitting jobs

Can I run an application on the login nodes?

Can I access a compute node via ssh or rsh?

How do I execute a program on the cluster?

How do I submit a simple command ?

How do I submit a shell script ?

How do I submit a parallel job ?

What are the processor and time limits ?

What is the maximal amount of memory that I can use ?

Which queue should I choose ?

How many jobs can I submit ?

How much time should I request for my job ?

What happens when a job reaches its time limit ?

How do I submit a series of jobs (job chaining)?

Monitoring jobs

When does my job start ?

How can I check the status of my job(s) ?

Why is my job waiting for a long time in the queue ?

Where is my job's output ?

Can I see my job's output in real time ?

How do I know when my job is done ?

Can I see the resources used by my job(s) ?

How do I kill a job ?

Data management and file transfer

How much disk space is available on then clusters ?

How much space can I use ?

What happens when I reach my quota ?

What if I need more space ?

Why is there a limit for the number of files in my home/scratch directory ?

Why is storage in the cluster more expensive than cheap external USB 3 hard drives ?

How long can I keep files in the scratch directories ?

Why did you delete my files in scratch ?

Are my files backed up regularly ?

How do I restore a file from a backup ?

What is the fastest way to transfer files from/to the cluster ?

Why is file transfer very slow ?


Do I need to be logged in when a job is executed ?

Can I let my co-workers run jobs from my account ?

What are your recommendations regarding security ?

I have a problem, can I come to your office and bring my laptop ?