A worldwide e-Infrastructure for NMR and structural biology

Quick gLite Middleware Deployment HOW-TO for WeNMR

This page provides support on the following topics:

  1. Grid elements deployment
  2. enmr.eu VO service configuration

Grid Elements deployment

WeNMR sites willing to deploy EMI/UMD services (CE, SE, UI, WN) might consider to follow the installation/configuration instructions of the IGI Release EMI/UMD SL5/SL6 x86_64 guide.
 
Commodity PCs are typically enough powerful to run the majority of the grid services. A minimal hardware configuration can be the following: a biprocessor machine with 1GB/core of RAM and 80GB SATA of HD. Most recent machines with 2-CPU quad-core and 2GB/core RAM can even be virtualized to host 4 different grid services with minimal loss of performances. All of the grid elements you may want to deploy at your site are EMI/UMD on Scientific Linux 5 or Scientific Linux 6, both x86_64.
 
Most of grid services needs a X509 certificate issued by a IGTF recognized Certification Authority (e.g. DutchGrid CA, GridKa CA, INFN CA, LCG catch-all,...). European sites should identify here their national CA and verify if their Institute is already a Registration Authority (RA) of that CA. If not, they should ask the CA to become a qualified RA, in order to be able to issue both host and personal certificates needed for grid operations.
 
 
Be sure that the administrative network domain hosting the gLite services to be deployed 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;
  • you need '''DNS Reverse Name Resolution''' to make Grid Security Infrastructure (GSI) to work properly;
  • time synchronisation (within minutes) among interacting grid elements is also required by GSI. The use of Network Time Protocol (NTP) is reccomended;
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

The IGI Release is 100% compatible with EMI/UMD release, but has some additional advanced accounting and monitoring features. Furthermore it allows you to automatically enable the '''enmr.eu VO''' at your site. The updates of IGI Release are very frequent and important, please pay attention to them checking periodically the link.

The release is of course fully supported by the Italian NGI with a ticketing system, a knowledge base, and 4 people a day weekly rotating on duty covering 11 hours during the working days (11x5).

More infos are available at the IGI portal.
 

enmr.eu VO service configuration

At the link https://voms2.cnaf.infn.it:8443/voms/enmr.eu/configuration/configuration.action
you'll find the data needed to configure the Grid services you might want to deploy at your site.

If you are using the IGI Release, you can automatically enable the enmr.eu VO in your EMI services using ig-yaim.
Particularly the file /opt/glite/yaim/examples/siteinfo/vo.d/enmr.eu already contains the needed lines:

SW_DIR=$VO_SW_DIR/enmr
DEFAULT_SE=$SE_HOST
VOMS_SERVERS="'vomss://voms2.cnaf.infn.it:8443/voms/enmr.eu?/enmr.eu' 'vomss://voms-02.pd.infn.it:8443/voms/enmr.eu?/enmr.eu'"
VOMSES="'enmr.eu voms2.cnaf.infn.it 15014 /C=IT/O=INFN/OU=Host/L=CNAF/CN=voms2.cnaf.infn.it enmr.eu' 'enmr.eu voms-02.pd.infn.it 15014 /C=IT/O=INFN/OU=Host/L=Padova/CN=voms-02.pd.infn.it enmr.eu'"
VOMS_CA_DN="'/C=IT/O=INFN/CN=INFN CA' '/C=IT/O=INFN/CN=INFN CA'"
WMS_HOSTS="prod-wms-01.pd.infn.it wms-enmr.cerm.unifi.it wms-enmr.chem.uu.nl mb-enmr.chemie.uni-frankfurt.de"
BDII_HOST=bdii-wenmr.pd.infn.it
#for Nagios:
NCG_DEFAULT_VO_FQAN=/enmr.eu/ops

 

 
while 20 pool accounts + sgmenmr are included in the relevant files /opt/glite/yaim/examples/ig-users.conf and /opt/glite/yaim/examples/ig-groups.conf

When installing e.g. a Computing Element with ig-yaim then automatically you get the VOMS mapping in the three files /etc/grid-security/grid-mapfile, /etc/grid-security/voms-grid-mapfile and /etc/grid-security/groupmapfile. As an example we see below the portion of file:

[root@prod-ce-01 root]# cat /etc/grid-security/grid-mapfile
...
"/enmr.eu/Role=SoftwareManager/Capability=NULL" .sgmenmr
"/enmr.eu/Role=SoftwareManager" .sgmenmr
"/enmr.eu/*/Role=NULL/Capability=NULL" .enmr
"/enmr.eu/*" .enmr
"/enmr.eu/Role=NULL/Capability=NULL" .enmr
"/enmr.eu" .enmr

If you are not using the IGI Release, e.g. you are just re-configuring a previous existing pure LCG/EGI site, you'll need to install the enmr.eu VOMS server certificate, which is not included in the gLite official rpms.

You can download the latest released certificate packed in a rpm from here.

In addition, be sure that in your yaim groups.conf file you have the following lines:

"/enmr.eu/ROLE=SoftwareManager":::sgm:
"/enmr.eu/*"::::
"/enmr.eu"::::

Please be careful, do not forget the wildcard "/enmr.eu/*" in the above configurations, because WeNMR uses VOMS groups for enabling the application accounting. Thus, the various WeNMR applications run with a proxy containing a VOMS group AC (the group names are available in https://voms2.cnaf.infn.it:8443/voms/enmr.eu/group/search.action).
 
For enmr.eu VO a specific structure is needed for sgm pool accounts. To fit these requirements some manual steps have to be performed in the software area exported to WNs. Assuming that the directory $VO_ENMR_EU_SW_DIR is already present with sgmenmr001.sgmenmr ownership, the following commands have to be
issued:

mkdir $VO_ENMR_EU_SW_DIR/BCBR $VO_ENMR_EU_SW_DIR/BMRZ $VO_ENMR_EU_SW_DIR/CIRMMP $VO_ENMR_EU_SW_DIR/EMBL-HH
chown sgmenmr001.sgmenmr $VO_ENMR_EU_SW_DIR/BCBR; chmod g+w $VO_ENMR_EU_SW_DIR/BCBR
chown sgmenmr001.sgmenmr $VO_ENMR_EU_SW_DIR/BMRZ; chmod g+w $VO_ENMR_EU_SW_DIR/BMRZ
chown sgmenmr001.sgmenmr $VO_ENMR_EU_SW_DIR/CIRMMP; chmod g+w $VO_ENMR_EU_SW_DIR/CIRMMP
chown sgmenmr001.sgmenmr $VO_ENMR_EU_SW_DIR/EMBL-HH; chmod g+w $VO_ENMR_EU_SW_DIR/EMBL-HH

 

For those sites that use CernVM-FS things are simpler: have a look here to properly configure your site to access the WeNMR area.

A WeNMR supported application, Gromacs, run in multithreading mode on multiprocessor boxes (MPI not needed), as described in http://www.egi.eu/blog/2011/10/31/running_multiprocessor_jobs_on_the_grid.html.
Please inform the VO managers if your site does not support this kind of jobs.

Further, multiple queues should ideally be enabled with different Job Wall Clock Time limits:

  1. very short: 30 minutes max - for NAGIOS probes, that run with the VO FQAN: /enmr.eu/ops/Role=NULL/Capability=NULL
  2. short : 120 minutes max
  3. medium : 12 hours max
  4. long : 48 hours

 


enmr.eu VO dedicated gLite services

Some high-level gLite services have been set-up at INFN-CNAF and CIRMMP.
These are:
Users members of enmr.eu VO can exploit the EMI-WMS to submit jobs to Computing Elements of the test-bed (see here how to become an enmr.eu VO member).

Up to now several CEs have been enabled enmr.eu VO, as you can see running from your UI the following command using a simple JDL file:

$ 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

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

When other sites will to join the test-bed, they will be match-ables by the EMI-WMS, as soon as they'll send us the LDAP address of their site-BDII. This is a string like:

ldap://prod-bdii-02.pd.infn.it:2170/mds-vo-name=INFN-PADOVA,o=grid

and it allows us to include your site to our Top-BDII bdii-wenmr.pd.infn.it

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