The system is named Cartesius in honour of René Descartes (Cartesius in Latin), a French philosopher, mathematician, and writer who spent most of his adult life in the Dutch Republic.
A comprehensive description of Descartes and his work can be found here.
In order to make use of the Cartesius services you need to read and accept the Usage Agreement. For this you need to visit https://portal.surfsara.nl/home/ and login with your login and password.
This usually happens when a maintenance session is planned. You can see planned maintenance on the system status page or in the message of the day when logging in on Cartesius.
Jobs with a maximum wall clock time longer than the time until the start of the maintenance, will not start until after the maintenance and are indicated with a status 'ReqNodeNotAvail' in the squeue output.
A workaround is to use a shorter maximum wall clock time.
There can be different reasons why this happens:
So, you might find that the system cannot be accessed while travelling. For these moments, please use the doornode.
If you need access from a location that you will use regularly and long-term, please contact the helpdesk and fill in your external IP address. Please take care that you report the CORRECT public IP address. As many sites nowadays use private IP space and a network address translation scheme, your public IP address is NOT necessarily an address that is configured directly on your local system and hence not necessarily known to your system. The following ranges are by definition private IP address ranges that cannot be white-listed:
You can easily find out the public IP address that you use, by visiting site like http://www.whatismyip.com, https://whatismyipaddress.com, or https://www.whatsmyip.org, with your web-browser.
If your program is compiled with the GNU gfortran compiler, set the following environment variable:
export GFORTRAN_UNBUFFERED_ALL=y
For C programs, the buffering can be changed using the command setvbuf
. E.g. standard output can be unbuffering using:
#include <stdio.h> ... setvbuf(stdout, NULL, _IONBF, 0);
Cartesius does not support the default remote shell 'rsh' for security reasons. Please use:
export CVS_RSH=ssh
The SLURM batch scheduler logs the memory usage of your application and it can be retrieved after your job has ended:
$ job-statistics -j 1155623 ... AveRSS : 11077K MaxRSS : 11576K MaxRSSTask : 46 MaxRSSNode : tcn828 ...
it shows the average and maximum memory use per MPI task, which MPI task used the maximum memory and on what node.
If you want to print the memory usage as part of your application, note that the linux system call getrusage() isn't fully implemented under linux, see 'man 2 getrusage'. Please compile and use the C routine printmem(), which prints the memory usage.
The environment variable $SLURM_NODELIST contains the names of the nodes. The format is something like: tcn[9006-9008]
. Using the program scontrol you can obtain the nodenames, one name per line:
$ scontrol show hostname $SLURM_NODELIST tcn9006 tcn9007 tcn9008
Using the command nodeset, you get all nodenames on one line:
$ nodeset -e $SLURM_NODELIST tcn9006 tcn9007 tcn9008
The SURFsara Data Archive allows the user to safely archive up to petabytes of valuable research data.
Persistent identifiers (PIDs) ensure the findability of your data. SURFsara offers a PID provisioning service in cooperation with the European Persistent Identifier Consortium (EPIC).
B2SAFE is a robust, secure and accessible data management service. It allows common repositories to reliably implement data management policies, even in multiple administrative domains.
The grid is a transnational distributed infrastructure of compute clusters and storage systems. SURFsara is active as partner in various...
Spider is a dynamic, flexible, and customizable platform locally hosted at SURF. Optimized for collaboration, it is supported by an ecosystem of tools to allow for data-intensive projects that you can start up quickly and easily.
The Data Ingest Service is a service provided by SURFsara for users that want to upload a large amount of data to SURFsara and who not have the sufficient amount...
The Collaboratorium is a visualization and presentation space for science and industry. The facility is of great use for researchers that are faced with...
Data visualization can play an important role in research, specifically in data analysis to complement other analysis methods, such as statistical analysis.