IT environment at BioMAX
The following is a summary of the IT facilities for BioMAX users. Click on each of the titles below to expand the contents.
BioMAX has several CentOS Linux workstations running the GNOME desktop dedicated for data collection. The naming convention for these workstations is b-biomax-controlroom-c-‘#’. There is also a dedicated machine for remote experimentes, biomax-remote. The desktop in all these machines contains several icons that fast link to useful applications for the experiment, like the Albula monitor to view diffraction images, links to MXCuBE, ISPyB and the data processing cluster front end. Other software can be accessed from the Applications menu on the Desktop top bar.
All the beamline computers are located in the MAX IV blue network. The blue network is rather isolated to protect all the beamline control software running on it, and in general, it is not possible to access other computers outside this network from it (the only exception is the online cluster for data processing, see next section) or link to web sites outside MAX IV.
There are two HPC clusters available to all MAX IV users:
- The online cluster, dedicated to data analysis (automated and manual) during the beamtime. The front end machine is clu0-fe-1
- The offline cluster, a smaller cluster that can be used outside beamtime by users without access to LUNARC. The front end is offline-fe1.
Both clusters can be accessed with the ThinLinc remote desktop client. The ThinLinc client is available on the beamline workstations and can be easily installed on any machine for remote access to the offline cluster. It is also possible to open a shell window on the online cluster front end by clicking on the HPC or the PReSTO desktop icons (which loads the MX data processing environment) in the beamline workstation.
The HPC clusters are on the MAX IV white network and it is possible to connect to outside sites from them.
See also Data handling and processing at BioMAX.
All the MAX IV computers available to the user mount the
/data disk and the
/mxn/visitors/'yourusername' is the home directory of the beamline workstations. Note, however, that the home directory in the HPC clusters (
/home/'yourusername') is different and not mounted on other machines, and it will not be visible from the beamline control computers or, when transferring files, the sftp server.
All the raw data and automated processing results are stored in subdirectories under
/data/visitors/biomax. The data directories are not backed up (but plans to implement a tape archive are underway), so please take care not to delete or overwrite any images.
The home directory can be used to store files related to the experiments, such as PDB files and processing scripts. They should not be used to store data images under any circumstances. Both the home directory under
/home (in the clusters) are backed up and up to four images are saved. To access the backups of a directory, go to the subdirectory .ckpt (this directory is not be visible until one accesses it).