[gin-ops] FW: Status
Cindy Zheng
zhengc at sdsc.edu
Fri Apr 28 18:25:18 CDT 2006
Dear all,
There have been a lot of working discussions between
EGEE system supporters and TDDFT application drivers.
I bundled most of the email contents together below
for your information. There will be a summary report
when Yoshio and Yusuke get TDDFT running on EGEE's
cluster.
Thank you for everyone's effort!
Cindy
> From: Mona Aggarwal [mailto:m.aggarwal at imperial.ac.uk]
> Sent: Friday, April 28, 2006 10:12 AM
> To: 'Yoshio Tanaka'
> Cc: o.van-der-aa at imperial.ac.uk; zhengc at sdsc.edu;
> Erwin.Laure at cern.ch; yusuke.tanimura at aist.go.jp
> Subject: RE: Status
>
>
> > -----Original Message-----
> > From: Yoshio Tanaka [mailto:yoshio.tanaka at aist.go.jp]
> > Sent: 28 April 2006 17:38
> > To: m.aggarwal at imperial.ac.uk
> > Cc: o.van-der-aa at imperial.ac.uk; zhengc at sdsc.edu;
> > Erwin.Laure at cern.ch; yusuke.tanimura at aist.go.jp;
> > yoshio.tanaka at aist.go.jp
> > Subject: Re: Status
> >
> >
> >
> > Hi Aggarwal,
> >
> > I have two questions:
> >
> > 1. What's the difference between globus gatekeeper and edg
> > gatekeeper?
> It is the same thing with some modifications.
>
> The authorization decision is based upon the users' proxy
> certificate and the job specification in RSL (JDL) format.
> The certificate
> and RSL are passed to (plug-in) authorization modules, which grant or
> deny the access after checking the user in gridmap file on the CE.
>
>
> 2. How proxy cert is delegated to users's job?
>
> Once the VO have been granted a certificate to be used for
> job submission.
> Tools on a user-interface (UI) machine then allow the user to
> generate,
> from this certificate, a delegated proxy. This is sent along
> with the job,
> enabling the job to perform Grid operations on behalf of the user.
>
> For more information:
> https://edms.cern.ch/file/498081/1.0/UserScenario2.pdf
>
> Regards,
>
> Mona
-----Original Message-----
From: Mona Aggarwal [mailto:m.aggarwal at imperial.ac.uk]
Sent: Friday, April 28, 2006 7:51 AM
To: 'Yoshio Tanaka'; o.van-der-aa at imperial.ac.uk
Cc: zhengc at sdsc.edu; Erwin.Laure at cern.ch; yusuke.tanimura at aist.go.jp
Subject: RE: Status
> -----Original Message-----
> From: Yoshio Tanaka [mailto:yoshio.tanaka at aist.go.jp]
> Sent: 28 April 2006 06:49
> To: o.van-der-aa at imperial.ac.uk
> Cc: zhengc at sdsc.edu; Erwin.Laure at cern.ch;
> m.aggarwal at imperial.ac.uk; yusuke.tanimura at aist.go.jp;
> yoshio.tanaka at aist.go.jp
> Subject: Re: Status
>
>
>
> Hi Olivier,
>
> I think Globus GRAM doesn't work correctly if file system is
> not shared between the gatekeeper node and compute nodes.
> For example, Globus GRAM checks the existence of the
> executable on the gatekeeper node even if the executable will
> be launched on compute nodes via the batch scheduler. In
> addition, delegated proxy cert will be generated in ~/.globus
> directory on the gatekeeper node. The proxy cert will be
> required if the executable will connect to the other process
> via globus IO, i.e. the proxy cert must be readable in
> compute nodes as well.
>
> In order to confirm my understanding, I made a quick test, in
> which I made ~/.globus directory as a symbolic link to /tmp
> (in server machine). The test failed if I speidifed
> jobmanager-pbs. (the test was succeeded if I specified
> jobmanager-fork).
>
> Would you confirm that the globus/jobmanager-pbs work well
> again? Please accept my apologize if I'm missing something.
>
Yes, it works with LCG middleware software.
Please find attached file Job_submission_chain_diagram within
LCG.
Regards,
Mona
> From: Olivier van der Aa [mailto:o.van-der-aa at imperial.ac.uk]
> Sent: Thursday, April 27, 2006 2:42 AM
> To: Yoshio Tanaka
> Cc: zhengc at sdsc.edu; Erwin.Laure at cern.ch;
> m.aggarwal at imperial.ac.uk; yusuke.tanimura at aist.go.jp
> Subject: Re: Status
>
>
> > Does Globus GRAM and jobmanager-pbs work well in this
> configuration (home
> > directory is not shared between the gw39 and the other wn) ?
>
> Yes it should be ok.
>
> I also need the certificate of the gin voms
> (vomss://kuiken.nikhef.nl:8443/voms/gin.ggf.org).
>
> Thanks, Olivier.
> From: Yoshio Tanaka [mailto:yoshio.tanaka at aist.go.jp]
> Sent: Thursday, April 27, 2006 1:38 AM
> To: o.van-der-aa at imperial.ac.uk
> Cc: zhengc at sdsc.edu; Erwin.Laure at cern.ch;
> m.aggarwal at imperial.ac.uk; yusuke.tanimura at aist.go.jp;
> yoshio.tanaka at aist.go.jp
> Subject: Re: Status
>
>
>
> Hi Olivier and Mona,
>
> Let me ask one quick question.
>
> o.van-der-aa> -the worker nodes (wn) names are from
> gw01.hep.ph.ic.ac.uk to
> o.van-der-aa> gw35.hep.ph.ic.ac.uk.
> o.van-der-aa> - gcc 3.2.3 is installed on all wn
> o.van-der-aa> - All WN have a variable $VO_GIN_SW_DIR that
> points to a shared
> o.van-der-aa> directory (/opt/exp_soft/gin) where the ninf-g
> and intel9.0 are installed.
> o.van-der-aa> - For the gin vo the PATH and LD_LIBRARY_PATH
> has entries for ninf-g and
> o.van-der-aa> intel fortran 9.0.
> o.van-der-aa> - home directories are not shared only
> /opt/exp_soft/gin is shared
> o.van-der-aa> (read-only).
> o.van-der-aa> - each machine is a dual CPU Pentium III 1GHz.
> 1GB of memory per machine.
> o.van-der-aa>
> o.van-der-aa> - gw39, our gatekeeper, is not sharing
> directories with the wn.
>
> Does Globus GRAM and jobmanager-pbs work well in this
> configuration (home
> directory is not shared between the gw39 and the other wn) ?
>
> Thanks,
> From: Yoshio Tanaka [mailto:yoshio.tanaka at aist.go.jp]
> Sent: Wednesday, April 26, 2006 7:17 AM
> To: o.van-der-aa at imperial.ac.uk
> Cc: zhengc at sdsc.edu; Erwin.Laure at cern.ch;
> m.aggarwal at imperial.ac.uk; yusuke.tanimura at aist.go.jp;
> yoshio.tanaka at aist.go.jp
> Subject: Re: Status
>
>
>
> Hi Olivier and Kostas,
>
> Thanks for the detailed information of your cluster and License issues
> for Intel compiler. I'll summarize the answer shortly.
>
> Thanks,
> -----Original Message-----
> From: Kostas Georgiou [mailto:k.georgiou at imperial.ac.uk]
> Sent: Wednesday, April 26, 2006 6:47 AM
> To: Olivier van der Aa
> Cc: Yoshio Tanaka; zhengc at sdsc.edu; Erwin.Laure at cern.ch;
> m.aggarwal at imperial.ac.uk; yusuke.tanimura at aist.go.jp
> Subject: Re: Status
>
>
> On Wed, Apr 26, 2006 at 02:43:12PM +0100, Olivier van der Aa wrote:
>
> > Hi Yoshio,
> >
> > After looking at the intel licence it turns out that I
> cannot install
> > the free version even for an academic project. So I will
> have to remove
> > the fortran 9.0 installation.
>
> For details here is the FAQ for the license:
> http://www.intel.com/cd/software/products/asmo-na/eng/compiler
s/219692.htm
> From: Olivier van der Aa [mailto:o.van-der-aa at imperial.ac.uk]
> Sent: Wednesday, April 26, 2006 6:43 AM
> To: Yoshio Tanaka
> Cc: zhengc at sdsc.edu; Erwin.Laure at cern.ch;
> m.aggarwal at imperial.ac.uk; yusuke.tanimura at aist.go.jp; Kostas Georgiou
> Subject: Re: Status
>
>
> Hi Yoshio,
>
> After looking at the intel licence it turns out that I cannot install
> the free version even for an academic project. So I will have
> to remove
> the fortran 9.0 installation.
>
> Could you explain me why you really need the fortran
> compiler. Could you
> compile tddft on your machine to avoid the licence problem.
>
> Cheers, Olivier.
> From: Olivier van der Aa [mailto:o.van-der-aa at imperial.ac.uk]
> Sent: Wednesday, April 26, 2006 6:24 AM
> To: Yoshio Tanaka
> Cc: zhengc at sdsc.edu; Erwin.Laure at cern.ch;
> m.aggarwal at imperial.ac.uk; yusuke.tanimura at aist.go.jp
> Subject: Re: Status
>
>
> Hi Yoshio,
>
> -the worker nodes (wn) names are from gw01.hep.ph.ic.ac.uk to
> gw35.hep.ph.ic.ac.uk.
> - gcc 3.2.3 is installed on all wn
> - All WN have a variable $VO_GIN_SW_DIR that points to a shared
> directory (/opt/exp_soft/gin) where the ninf-g and intel9.0
> are installed.
> - For the gin vo the PATH and LD_LIBRARY_PATH has entries for
> ninf-g and
> intel fortran 9.0.
> - home directories are not shared only /opt/exp_soft/gin is shared
> (read-only).
> - each machine is a dual CPU Pentium III 1GHz. 1GB of memory
> per machine.
>
> - gw39, our gatekeeper, is not sharing directories with the wn.
>
> - On all the worker nodes a set of pool accounts have been created
> gin001-gin010 and ginsgm. ginsgm is the user that can install
> software
> in /opt/exp_soft/gin
>
> How will you access the nodes for compilation of the TDDFT software ?
> Will you submit a job ?
>
> Hope it helps, Olivier
> ps: i will be on holiday from 28/04-07/04 but Mona Aggarwal
> will be able
> to help if there are problems with the current install.
> From: Yoshio Tanaka [mailto:yoshio.tanaka at aist.go.jp]
> Sent: Wednesday, April 26, 2006 6:04 AM
> To: o.van-der-aa at imperial.ac.uk
> Cc: zhengc at sdsc.edu; Erwin.Laure at cern.ch;
> m.aggarwal at imperial.ac.uk; yusuke.tanimura at aist.go.jp;
> yoshio.tanaka at aist.go.jp
> Subject: Re: Status
>
>
> Hi Olivier,
>
> Thanks for your quick work.
>
> o.van-der-aa> Hi Yoshio,
> o.van-der-aa>
> o.van-der-aa> Thanks that worked. and I could compile ninf-g 2.4.1 on
> o.van-der-aa> gw05.hep.ph.ic.ac.uk. I have used ./configure
> --prefix=/home/ginsgm/gin/SW
> o.van-der-aa>
> o.van-der-aa> Is that ok ?
>
> Yes, I think this should be ok.
>
> o.van-der-aa> For the intel fortran compiler, is version 9 ok ?
>
> Yes, version 9 is ok.
>
> o.van-der-aa> I would like to understand more in detail how
> we are going to proceed.
> o.van-der-aa> As soon as I have installed the software on the
> compute node and the
> o.van-der-aa> worker node how are you going to access the
> compile node to build your
> o.van-der-aa> executable ?
> o.van-der-aa>
> o.van-der-aa> We have created a queue for the gin vo the end point is
> o.van-der-aa> gw39.hep.ph.ic.ac.uk:2119/jobmanager-lcgpbs-gin
>
> Would you let me know the configuration of your system?
> What kind of node do you have (e.g. compute, worker, compile, etc.)?
> What's the difference between the nodes? (sharing of file
> systems, accounts, etc.)?
>
> I could see that globus gatekeeper is running on gw39 and Ninf-G 2.4.1
> is installed in gw05. Is the home directory shared between these
> nodes? Is the home directory shared between the gatekeeper node and
> backend compute nodes?
>
> If you provide this kind of information on the web or on the other
> document, please let me know.
>
> P.S. We, in Japan, will have about 10 days holidays from this
> Saturday until May 7. Our application driver, Yusuke, will start his
> vacation from tomorrow. Thus, our response may be delayed.
>
> Thanks,
> From: Yoshio Tanaka [mailto:yoshio.tanaka at aist.go.jp]
> Sent: Tuesday, April 25, 2006 6:03 PM
> To: o.van-der-aa at imperial.ac.uk
> Cc: zhengc at sdsc.edu; Erwin.Laure at cern.ch;
> m.aggarwal at imperial.ac.uk; yusuke.tanimura at aist.go.jp;
> bacon at mcs.anl.gov; childers at mcs.anl.gov; ninf-developers at apgrid.org
> Subject: Re: Status
>
>
>
> Hi Olivier,
>
> # I'm Cc-ing to Charles and Lisa from Globus and Ninf-G developers.
>
> We believe that at least the following three RPMs are necessary for
> installing Ninf-G:
>
> gpt-VDT1.2.2rh9-1.i386.rpm
> vdt_globus_essentials-VDT1.2.2rh9-1.i386.rpm
> vdt_globus_sdk-VDT1.2.2rh9-1.i386.rpm
>
> In addition to installing these RPMs, you need to run the following
> command:
>
> $ gpt-build <flavor> -nosrc
>
> globus-build-env-gcc32dbg.sh is not included at least in these RPMs
> and I guess it does not appear in any RPM according to the following
> document in GT4 installation manual:
>
> ----------------------------------------------------------------------
> B.4. Using globus-makefile-header with a binary distribution
>
> We use a package called "globus_core" to detect the compiler and
> platform settings of the computer that the Toolkit is installed
> on. This package is excluded from binary distributions, because the
> compiler settings on your machine are likely to be different from
> those used on the machine that built the binaries.
>
> If you need to install a source update into a binary installation,
> globus_core will automatically be built for you. If you're building
> something using "globus-makefile-header", though, you will need to
> install globus_core yourself. Install it with the following command:
>
> $ $GLOBUS_LOCATION/sbin/gpt-build -nosrc <flavor>
>
> Where flavor is the flavor you're passing to globus-makefile-header.
> ----------------------------------------------------------------------
>
> Ninf-G uses various Globus API and it does require files and tools
> such as globus-makefile-header and globus-build-env-<flavor>.sh for
> compling GT-based middleware.
>
> Thanks,
>
> P.S. These three RPMs are minimum requirements for installing Ninf-G
> and of course you need to install the other RPMs such as
> rm_server for runtime.
> From: Olivier van der Aa [mailto:o.van-der-aa at imperial.ac.uk]
> Sent: Tuesday, April 25, 2006 1:31 AM
> To: Yoshio Tanaka
> Cc: zhengc at sdsc.edu; Erwin.Laure at cern.ch;
> m.aggarwal at imperial.ac.uk; yusuke.tanimura at aist.go.jp
> Subject: Re: Status
>
>
> > Hi Olivier,
> >
> > Let me ask two more questions:
> >
> > 1. Does /opt/globus/libexec/globus-build-env-gcc32dbg.sh exist?
>
> I only have the following sh files in /opt/globus/libexec/ directory
>
> /opt/globus/libexec/globus-gram-protocol-constants.sh
> /opt/globus/libexec/globus-personal-gatekeeper-version.sh
> /opt/globus/libexec/globus-sh-tools.sh
> /opt/globus/libexec/globus-sh-tools-vars.sh
>
> >
> > 2. How is the output of the following command?
> > % globus-makefile-header --flavor=gcc32dbg globus_io
>
> ERROR: Cannot open /opt/globus/libexec/globus-build-env-gcc32dbg.sh!
> (Hint: This error is most commonly caused when no packages of the
> specified flavor type
> are installed..)
>
> Our globus was installed from rpm that can be found in the vdt1.2.2
> toolkit: http://vdt.cs.wisc.edu/native_packages/1.2.2/rpm/stable/rh9/
>
> Could you check from which rpm the
> /opt/globus/libexec/globus-build-env-gcc32dbg.sh comes.
>
> Cheers, Olivier.
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