Life Science Grid clusters¶
The current page provides information about the Life Science Grid (LSG) clusters and their locations, local support contact persons, and DNS addresses of User Interface (UI) and Storage Element (SE) machines.
Contents
Warning
The Life Science Grid infrastructure is scheduled to be decommissioned mid 2018. After the decommissioning the smaller LSG clusters within the UMC’s and other universities will cease to exist; the large central Grid clusters at NIKHEF and SURFsara will remain. More details about the decommissioning can be found here: https://userinfo.surfsara.nl/documentation/decommissioning-life-science-grid
About¶
The Life Science Grid is a compute and data processing infrastructure that is available for all Life Science researchers working in the Netherlands. The Life Science Grid consists of a series of computer clusters that can be used either as a local facility or as an integrated Grid environment. For both types of usage, you will need an account on a User Interface machine. Accounts on the user interface machines are managed via a central system at SURFsara, and can be arranged after verification by a local site support contact person. To arrange access, the most efficient way is to ask (one of) your local support contact(s) to send a request to our helpdesk for access to the local User Interface machine. Your local support person will need your name, e-mail address, telephone number and nationality, and will verify that you are employed at the relevant institution and an active researcher in one of the Life Science disciplines.
Locations and local support contacts¶
| Location | LSG Site | Local support contact(s) | Notes |
|---|---|---|---|
| AMC, Amsterdam | LSG_AMC | Silvia Olabarriaga
|
|
| Delft University of Technology | LSG_TUD | Robbert Eggermont | |
| UMCG, Groningen | LSG_RUG | Peter Horvatovich
Morriz Swertz
|
|
| LUMC, Leiden | LSG_LUMC | Michèle Huijberts | |
| Maastricht University | LSG_UM | Maarten Coonen
Nuno Nunes
|
|
| Radboud University, Nijmegen | LSG_KUN | Christian Gilissen
Gert Vriend
Janita Bralten
|
Includes a 2TB RAM High-memory node; contact helpdesk@surfsara.nl for access. |
| Erasmus MC, Rotterdam | LSG_EMC | Henri Vrooman | |
| Utrecht University | LSG_BCBR | Alexandre Bonvin
Johan van der Zwan
|
|
| VU University, Amsterdam | LSG_VU | René Pool | |
| Wageningen University | LSG_WUR | Harm Nijveen |
Cluster details¶
The following table lists the DNS addresses of the User Interface and Storage Element services, for each of the LSG sites.
| LSG Site | User interface | Storage element | LSG Storage SURL |
|---|---|---|---|
| LSG_AMC | gb-ui-amc.amc.nl |
gb-se-amc.amc.nl |
srm://gb-se-amc.amc.nl:8446/dpm/amc.nl/home/lsgrid/ |
| LSG_TUD | gb-ui-tud.ewi.tudelft.nl |
gb-se-tud.ewi.tudelft.nl |
srm://gb-se-tud.ewi.tudelft.nl:8446/dpm/ewi.tudelft.nl/home/lsgrid |
| LSG_RUG | gb-ui-rug.sara.usor.nl |
gb-se-rug.sara.usor.nl |
srm://gb-se-rug.sara.usor.nl:8446/dpm/sara.usor.nl/home/lsgrid |
| LSG_LUMC | gb-ui-lumc.lumc.nl |
gb-se-lumc.lumc.nl |
srm://gb-se-lumc.lumc.nl:8446/dpm/lumc.nl/home/lsgrid |
| LSG_UM | ui.lsg.maastrichtuniversity.nl |
se.lsg.maastrichtuniversity.nl |
srm://se.lsg.maastrichtuniversity.nl:8446/dpm/lsg.maastrichtuniversity.nl/home/lsgrid |
| LSG_KUN | gb-ui-kun.els.sara.nl |
gb-se-kun.els.sara.nl |
srm://gb-se-kun.els.sara.nl:8446/dpm/els.sara.nl/home/lsgrid |
| LSG_EMC | gb-ui-emc.erasmusmc.nl |
gb-se-emc.erasmusmc.nl |
srm://gb-se-emc.erasmusmc.nl:8446/dpm/erasmusmc.nl/home/lsgrid |
| LSG_BCBR | ui.lsg.bcbr.uu.nl |
se.lsg.bcbr.uu.nl |
srm://se.lsg.bcbr.uu.nl:8446/dpm/lsg.bcbr.uu.nl/home/lsgrid |
| LSG_VU | ui.lsg.psy.vu.nl |
se.lsg.psy.vu.nl |
srm://se.lsg.psy.vu.nl:8446/dpm/lsg.psy.vu.nl/home/lsgrid |
| LSG_WUR | gb-ui-wur.els.sara.nl |
gb-se-wur.els.sara.nl |
srm://gb-se-wur.els.sara.nl:8446/dpm/els.sara.nl/home/lsgrid |
User Interface machines can be accessed with any SSH client. To learn how to access the Storage Elements, see Grid storage
| LSG Site | Computing element queue |
|---|---|
| LSG_AMC | gb-ce-amc.amc.nl:8443/cream-pbs-<queue> |
| LSG_TUD | gb-ce-tud.ewi.tudelft.nl:8443/cream-pbs-<queue> |
| LSG_RUG | gb-ce-rug.sara.usor.nl:8443/cream-pbs-<queue> |
| LSG_LUMC | gb-ce-lumc.lumc.nl:8443/cream-pbs-<queue> |
| LSG_UM | ce.lsg.maastrichtuniversity.nl:8443/cream-pbs-<queue> |
| LSG_KUN | gb-ce-kun.els.sara.nl:8443/cream-pbs-<queue> |
| LSG_EMC | gb-ce-emc.erasmusmc.nl:8443/cream-pbs-<queue> |
| LSG_BCBR | ce.lsg.bcbr.uu.nl:8443/cream-pbs-<queue> |
| LSG_VU | ce.lsg.psy.vu.nl:8443/cream-pbs-<queue> |
| LSG_WUR | gb-ce-wur.els.sara.nl:8443/cream-pbs-<queue> |
The possible <queue> values can be express, medium and long. For
and update listing of the available queues use the command lcg-infosites.
Aditional Storage Elements¶
The following Storage Elements are also availble when you are member of the lsgrid VO.
| Site | Storage element | LSG Storage SURL | Remarks |
| SURFsara | srm://srm.grid.sara.nl |
srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/lsgrid |
See dCache |
| Test Cluster SURFsara | srm://gb-se-ams.els.sara.nl |
srm://gb-se-ams.els.sara.nl:8446/dpm/els.sara.nl/home/lsgrid |
Do not use: testing purpose only |
Security¶
The default permissions on the LSG clusters for /home, /home/nobackup and /scratch directories is:
- read+write+execute for the user
- read+execute for the group
- read+execute for others
In general, where security is important, we advise you to verify and set the permissions to abide by your data access regulations, especially for temporary working directories under /scratch and /tmp. For example, you can do $ umask 0077 to keep all data invisible to other users or $ umask 0007 to keep it closed for everone outside the group. Another point of attention is cleaning up intermediate data before job exit.