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Quick help

Each request to the Bioinforma service is managed via the ticketing web system that can be reached at https://ticketing.bioinfo.szn.it. You can login to it using the same credentials you use for your mailbox @szn.it. It is important to note that for our support system your account will exist only after your first successful login.

HPC cluster access

You can request access to our HPC cluster systems by filing a request to the BioinForMa service. Few easy steps:
  • open a ticket on this ticketing platform asking for access to HPC computational resources: you can login to the ticketing platform using the same credentials you use for your @szn.it mailbox
  • we will take your request in charge and will ask you to come to our offices (third floor, near the canteen, server room corridor)
  • we will provide you a form to fill with some informations and sign, read it carefully!
  • you will receive your access credentials. The ticketing platform is the main way to ask for support, software installation, bug reporting and troubleshooting

At the moment our stable HPC cluster is Falkor, which is composed of8 nodes, running on Debian GNU/Linux)

Falkor access

  • You can access Falkor via SSH at host 192.168.16.35 from the internal network or using 193.205.231.59 from the external network
    ssh <your_username>@192.168.16.35
    

    ssh <your_username>@193.205.231.59
    

If you receive an error similar to the following when connecting from external networks

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@    WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!     @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that a host key has just been changed.
The fingerprint for the ECDSA key sent by the remote host is
SHA256:5Dfoz4xuiPNosKOrqfIXlKRuVQJNQPI6VwxX93/o6J0.
Please contact your system administrator.
Offending ECDSA key in /Users/xxyyyxx/.ssh/known_hosts:117
ECDSA host key for 193.205.231.59 has changed and you have requested strict checking.
Host key verification failed.

Please, modify your local .ssh/known_hosts file removing the offending key. The error is due to the fact that the same external IP is now pointing to a different machine

  • You can transfer files from and to the HPC cluster via scp
  • We are not enforcing an user quota on your home, but we are monitoring usage. Once in a while we could ask you to operate a cleanup to make room on the storage. We rely on a policy of fair usage of resources at the moment

Main rules

  • All your jobs must be submitted to the scheduler queue. Our cluster uses the SLURM workload manager for job queuing. Please, have a look at the documentation below
  • As a consequence, please do__not__start jobs on the HPC cluster frontend

HPC user environment

  • Our HPC cluster use
    module
    to setup software environments according to the needs. Type
    module avail
    to get a list of available environments
  • To use a module you can use the "module load" syntax. E.g.: to load bowtie 2.3.1 environment
    module load bowtie/2.3.1
    If you want to unload a module:
    module unload bowtie/2.3.1
  • You are very welcome to suggest and propose new module files. You can even prepare your own modulefiles. You can find a quick guide at this URL

Software

  • There is a moltitude of software installed at the moment. Have a look at this page for more details
  • You can request the installation of new software. According to the software programming language and/or software dependencies, we will find the optimal way to install it. This process is usually cooperative: please expect to be asked for feedback

Workload manager: SLURM

  • You are asked to launch your jobs using the default workload manager, SLURM. SLURM is a very flexible and customizable software with a moderate learning curve. Please, have a look at the SLURM documentation. For a quick guide have a look at this page also
  • To get informations about nodes current status and the available queues you can type the following command in a bash shell on the cluster:
    sinfo
  • We are giving some sample SLURM batch file on this page
  • SLURM and the MPICH2 talk each other in different ways. An early knowledge base is here

Data backup

  • The HPC cluster is now running quite stable after having suffered bad faults in the past. At the moment, we have no backup facilities. Please, keep a copy of your data.

Programming languages knowledge base

This section will collect documentation about language specific tasks, parallelization and task running under SLURM

Quick links

Some quick links you can reach from the internal SZN network segment (at the moment):