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Uppsala Multidisciplinary Center for Advanced Computational Science

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Uppsala Multidisciplinary Center for Advanced Computational Science

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Support
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Resources
Projects and collaborations
About us

Home
Support
Apply for account or project
Resources
Projects and collaborations
About us

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Uppsala University Uppsala Multidisciplinary Center ... Support FAQ

Frequently Asked Questions

Below you can find all the FAQ's, grouped into the following categories:

Login problems
Projects, accounts and quotas
Running jobs
Software
Resources
General/Miscellaneous

Login Problems FAQs

When I connect with ssh, my client asks me to verify the key is correct, what should it say?
My connection to UPPMAX times out
How can I upload and download files from UPPMAX to my local computer?
Why can't I scp/sftp to UPPMAX when I can connect with ssh?
When I try to log in, I get "Please enter the current code from your second factor:"
How do I use SSH keys to login to UPPMAX?
How do I choose a good password?

Projects, accounts, and quotas FAQs

I belong to more than one project. How do I specify which project I am running my job on?
I want to use resources at UPPMAX to give a course or workshop, what should I think about?
How can I see how much time there is left on my project?
How to check my disk quota limits?
What rules apply to my activities at UPPMAX?
Should I use Bianca or Rackham?

Running jobs FAQs

How do I use Matlab's Distributed Computing features?
How can I run X11 applications inside GNU screen?
Looking at "jobinfo" output, PRIORITY and REASON for my waiting jobs change over time. Please explain what is going on!
What is causing the sbatch script error "Unknown shell type 'load'"?
How can I see my job's memory usage?
How to run interactively on a compute node?
I want my program to send data to both stdout and to a file but nothing comes until the program ends
My job has very low priority! What can be wrong?
I have strange problems with my text-files / scripts when they have been copied from other computers
How can I compile MPI and OpenMP programs on UPPMAX computers?
My program suddenly seems to stop executing but it does not crash, the process is still alive. What is wrong?
My program crashes with the error message "Bus error". Why?
How do I use the modules?

Software FAQs

How do I recognise and manage dependency conflicts between modules?
How can I resolve problems with conflicting modules?
"Undefined reference" when compiling program, what to do?
How do I install local Perl packages?
I have a Mac and have problems running perl on UPPMAX, with error messages like "Perl: warning: Setting locale failed." and "Perl: warning: Please check that your locale settings".
How can I use ScaLAPACK/BLACS?
How can I compile MPI programs on UPPMAX?
How can I use BLAS/LAPACK routines?
Can I install my own software on the UPPMAX systems?
Avoid timeouts in FileZilla

Resources FAQs

How can I compress my files as quickly and efficiently as possible?
How should I compress FastQ-format files?
Which compression format should I use for NGS-related files (FastQ, Fasta, VCF, GFF, etc.)?
How can I access the data that was uploaded to Swestore using the old way (with the "drophere2archive" folder), through iRODS?
How to move files to and from Swestore using iRODS?
Why don't I see any bioinformatics software with the 'module avail' command?
What do I need to do to get access to UPPNEX resources?
How can I request new software to be installed?
What is this "glob" folder in my home folder?

General/miscellaneous FAQs

"Disk quota exceeded" error when copying files
"slurmstepd: error: _get_pss: ferror() indicates error on file /proc/$$/smaps"
When is the maintenance window (service stop)?
How to acknowledge UPPMAX, SNIC and UPPNEX in papers, or presentations on workshops or conferences?
How to make selected files in my project available over the web?
I have a large datasets that I want to store in the project folder but that I do not need to back-up. Can I specify that?
Where can I ask questions about UPPNEX?
What is the relation between UPPNEX and UPPMAX?

Contact UPPMAX

Support: support@uppmax.uu.se
Director: Elisabeth Larsson
Office: Johanna Feiff
Post: P.O. Box 337, 751 05 Uppsala

Visit UPPMAX

Floor 1, House 4, ITC, Polacksbacken
Lägerhyddsvägen 2
752 37 Uppsala

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Apply for a project or user account

List of Installed Software

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