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 experiments, 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 beamposition monitor tool. Other software can be accessed from the Applications menu on the Desktop top bar.
All the beamline computers as well as the biomax-remote are located in the MAX IV blue network. The blue network is rather isolated to protect the beamline control software that runs 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 during the beamtime. The front end machine is clu0-fe-1. The online cluster can be accessed from the beamline workstations or biomax-remote via the Thinlinc desktop client, by clicking the Applications menu on the top panel and selecting the Internet submenu.
- The offline cluster, a smaller cluster that can be used to reprocess data manually after or during the beamtime. The front end is offline-fe1. The offline cluster is not accessible from the beamline computers o biomax-remote, but it is possible to establish to log in to it remotely from the users’ home computer. Please refer to these instructions.
Unlike the beamline computers, The HPC clusters are on the MAX IV white (office) network and it is possible to connect to outside sites from them.
Important: The HPC clusters are shared resources. There are limits to the maximum number of users who can log in at one time. Therefore, please log out always when you have finished working. There is also a limit to the available processors. Although the data processing needs of crystallographic experiments are relatively modest, for special projects that require many hours of computation and several nodes on a regular basis, please consider requesting access to LUNARC.
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).