A worldwide e-Infrastructure for NMR and structural biology

Quick gLite HOW-TO for WeNMR users

 


The WeNMR Grid Infrastructure is available and running the latest EMI/UMD release. Its present layout and a few hints for administrators on how to deploy a new site are available here. The test-bed has been accessible since December 2007, and only a few steps are needed to access it from almost any Linux PC.
You will need to:

  • Own a personal certificate issued by a IGTF recognized CA (i.e. ASGCCA, INFN CA, LCG catch-all,...); 
  • Register with the '''enmr.eu VO''' filling the form available here. Having the personal certificate installed in your browser is required for the registration procedure; in case of problems with the browser, please have a look at this link;
  • Install in your Linux PC the Miramare Interoperable Lite UI (MILU) version of the gLite User Interface (a.k.a. gLite-UI); no root privileges are needed for this installation; this UI has been tested on several linux-based distributions; you can download it from here; please read the documentation available here to install and properly configure it for working with WeNMR in few minutes.
  • Put your usercert.pem and userkey.pem under $HOME/.globus directory (have a look  here to learn how to convert formats).
  • Create a proxy using the command ''voms-proxy-init -voms enmr.eu'' and start to submit jobs (see the  gLite User Guide for more details). Please notice that since September 2007 the NS component of the WMS has been removed, so '''you must use the WMProxy''' component which is accessed through the '''glite-wms-job-*''' commands. Therefore the edg-job-* and glite-job-* commands will not work anymore. 
  • Be sure that the administrative network domain from where you perform these operations is configured in order to allow communications with external hosts and ports as described in the document available here. In particular, most of the grid services has to be run on hosts with public IP address, and only the WNs can run under NAT with an appropriate configuration. Another important requirement is time synchronisation among grid elements, typically achieved making use of NTP. As an example, for the UI you should make sure that the following ports are open for communication with the enmr.eu VO services:
from port  to port service
 localhost  >1023  wms-enmr.cerm.unifi.it  7443  WMProxy
 localhost  >1023  wms-enmr.cerm.unifi.it  2811  GridFTP server
 localhost  >1023  lb-enmr.cerm.unifi.it  9000  LB
 localhost  >1023  lb-enmr.cerm.unifi.it  9003  LB
 localhost  >1023  voms2.cnaf.infn.it  15014

VOMS server

 


For a quick test, try the command below and look at the output message:

$ glite-wms-job-list-match -a test.jdl

Connecting to the service https://wms-enmr.cerm.unifi.it:7443/glite_wms_wmproxy_server

==========================================================================

COMPUTING ELEMENT IDs LIST
The following CE(s) matching your job requirements have been found:

        *CEId*

 - as-ce01.euasiagrid.org:8443/cream-pbs-enmr
 - ce03.ncg.ingrid.pt:8443/cream-sge-gridq
 - ce1-enmr.science.uu.nl:8443/cream-pbs-long
 - ce1-enmr.science.uu.nl:8443/cream-pbs-medium
 - ce1-enmr.science.uu.nl:8443/cream-pbs-short
 - ce1-enmr.science.uu.nl:8443/cream-pbs-verylong
 - cert-37.pd.infn.it:8443/cream-lsf-grid
 - cream-ge-1-kit.gridka.de:8443/cream-sge-core1
 - cream-ge-2-kit.gridka.de:8443/cream-sge-core1
 - cream-ge-3-kit.gridka.de:8443/cream-sge-core1
 - cream-ge-4-kit.gridka.de:8443/cream-sge-core1
 - cream-ge-5-kit.gridka.de:8443/cream-sge-core1
 - cream-ge-6-kit.gridka.de:8443/cream-sge-core1
 - cream-ge-7-kit.gridka.de:8443/cream-sge-core1
 - cream-ge-8-kit.gridka.de:8443/cream-sge-core1
 - creamce2.gina.sara.nl:8443/cream-pbs-medium
 - creamce2.gina.sara.nl:8443/cream-pbs-short
 - creamce3.gina.sara.nl:8443/cream-pbs-medium
 - creamce3.gina.sara.nl:8443/cream-pbs-short
 - grid-ce-00.sgai.csic.es:8443/cream-pbs-grid-csic
 - grid-cr2.desy.de:8443/cream-pbs-emi2-sl6
 - grid-cr5.desy.de:8443/cream-pbs-desy
 - gridce.ilc.cnr.it:8443/cream-pbs-grid
 - gridsrv2-4.dir.garr.it:8443/cream-pbs-enmr
 - khaldun.biruni.upm.my:8443/cream-pbs-academicgrid
 - pbs-enmr.cerm.unifi.it:8443/cream-pbs-long
 - pbs-enmr.cerm.unifi.it:8443/cream-pbs-medium
 - pbs-enmr.cerm.unifi.it:8443/cream-pbs-short
 - pbs-enmr.cerm.unifi.it:8443/cream-pbs-verylong
 - prod-ce-01.pd.infn.it:8443/cream-lsf-grid
 - srvslngrd004.uct.ac.za:8443/cream-pbs-enmr.eu
 - wario.univ-lille1.fr:8443/cream-pbs-enmr.eu
 - grid-cr3.desy.de:8443/cream-pbs-desy
 - grid-cr6.desy.de:8443/cream-pbs-desy
 - cream-ce-2.ba.infn.it:8443/cream-pbs-infinite
 - cream-ce-2.ba.infn.it:8443/cream-pbs-long
 - cream-ce-2.ba.infn.it:8443/cream-pbs-short
 - cream-ce-3.ba.infn.it:8443/cream-pbs-infinite
 - cream-ce-3.ba.infn.it:8443/cream-pbs-long
 - cream-ce-3.ba.infn.it:8443/cream-pbs-short
 - cream-ce.cat.cbpf.br:8443/cream-pbs-enmr
 - cream-ce02.cat.cbpf.br:8443/cream-pbs-enmr
 - dissel.nikhef.nl:2119/jobmanager-pbs-medium
 - dissel.nikhef.nl:2119/jobmanager-pbs-short
 - juk.nikhef.nl:8443/cream-pbs-medium
 - juk.nikhef.nl:8443/cream-pbs-short
 - klomp.nikhef.nl:8443/cream-pbs-medium
 - klomp.nikhef.nl:8443/cream-pbs-short
 - gazon.nikhef.nl:8443/cream-pbs-medium
 - gazon.nikhef.nl:8443/cream-pbs-short
 - ce-01.roma3.infn.it:8443/cream-pbs-eumed
 - t2-ce-06.lnl.infn.it:8443/cream-lsf-enmr1
 - t2-ce-01.lnl.infn.it:8443/cream-lsf-enmr1
 - t2-ce-04.lnl.infn.it:8443/cream-lsf-enmr1
 - t2-ce-03.lnl.infn.it:8443/cream-lsf-enmr1
 - t2-ce-02.lnl.infn.it:8443/cream-lsf-enmr1
 - t2-ce-05.lnl.infn.it:8443/cream-lsf-enmr1
 - cce.ihep.ac.cn:8443/cream-pbs-enmr.eu
 - ce1.dur.scotgrid.ac.uk:8443/cream-pbs-q1d
 - ce1.dur.scotgrid.ac.uk:8443/cream-pbs-q2d
 - ce1.dur.scotgrid.ac.uk:8443/cream-pbs-q30m
 - ce1.dur.scotgrid.ac.uk:8443/cream-pbs-q3d
 - ce1.dur.scotgrid.ac.uk:8443/cream-pbs-q6h
 - ce-02.roma3.infn.it:8443/cream-pbs-eumed
 - ce-enmr.chemie.uni-frankfurt.de:8443/cream-pbs-long
 - ce-enmr.chemie.uni-frankfurt.de:8443/cream-pbs-medium
 - ce-enmr.chemie.uni-frankfurt.de:8443/cream-pbs-short
 - ce-enmr.chemie.uni-frankfurt.de:8443/cream-pbs-verylong
 - cream-ce-grid.obspm.fr:8443/cream-pbs-enmr.eu
 - grid-cr4.desy.de:8443/cream-pbs-desy
 - svr009.gla.scotgrid.ac.uk:8443/cream-pbs-q1d
 - svr009.gla.scotgrid.ac.uk:8443/cream-pbs-q2d
 - svr010.gla.scotgrid.ac.uk:8443/cream-pbs-q1d
 - svr010.gla.scotgrid.ac.uk:8443/cream-pbs-q2d
 - svr011.gla.scotgrid.ac.uk:8443/cream-pbs-q1d
 - svr011.gla.scotgrid.ac.uk:8443/cream-pbs-q2d
 - svr014.gla.scotgrid.ac.uk:8443/cream-pbs-q1d
 - svr014.gla.scotgrid.ac.uk:8443/cream-pbs-q2d
 - svr026.gla.scotgrid.ac.uk:8443/cream-pbs-q1d
 - svr026.gla.scotgrid.ac.uk:8443/cream-pbs-q2d
 

==========================================================================


If you are planning to access the WMProxy via its web-services interface, you may want to generate voms proxies programatically, e.g. from java code. In this case, it can be useful to know the Port and the DN of the enmr.eu VOMS server, which are publicly available in the 3rd and 4th string of the second line of the web page here.

For more details about gLite EMI/UMD and its use have also a look at this on-line Training Material produced by the  EMI team.

If you have any problems please contact us here.

 

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Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life