SEE-GRID ESM Software Installation Guide

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This page is OBSOLETE! Please go to Software Installation Management Guide!

--Bmarovic 19:06, 7 Sep 2005 (EEST)

1 Site Configuration
- 1.1 Setting up shared application software filesystem
- 1.2 Publishing of software tags
2 Software Installation Management
3 Example Scripts

Site Configuration

Make sure that your site has valid SEEGRID VO certificates and uses SEEGRID VOMS with user certificates. Also check

SG Using file replicas and RFIO: UI configuration, rfiod, usage in apps, limitations and workarounds.

Setting up shared application software filesystem

It is agreed that all SEEGRID sites should set up a file system shared among all WNs of the same cluster. The jobs that want to use the installed software just need to use the VO_SEEGRID_SW_DIR environment variable in order to access it.

To create a shared directory on your do the following, preferably on your storage element:

mkdir /opt/exp_soft/seegrid
chown seegridsgm.seegrid /opt/exp_soft/seegrid
chmod 755 /opt/exp_soft/seegrid

add a line to /etc/exports:

/opt/exp_soft/seegrid      *.<YourDomain>(rw,no_root_squash)

Execute

$ exportfs -rv

on all WNs a line to /etc/fstab:

<YourStorageElement>:/opt/exp_soft/seegrid      /opt/exp_soft/seegrid      nfs hard,intr,nodev,nosuid  0 0

Create the mountpoint for /opt/exp_soft/seegrid, and mount new filesystem:

mkdir /opt/exp_soft/seegrid
chown seegridsgm.seegrid /opt/exp_soft/seegrid
mount -av

Finally, set VO_SEEGRID_SW_DIR to /opt/exp_soft/seegrid in site-info.def and reconfigure all WNs. This will update /etc/profile.d/lcgenv.csh and /etc/profile.d/lcgenv.sh.

Publishing of software tags

The tags of published software are managed using lcg-ManageVOTag. Tags published on your site can be checked using

lcg-ManageVOTag -host <Target-CE-machine> -vo seegrid --list

It a good idea to check and, if needed, set permissions of seegrid.list on your CE. Its initial content may be left empty.

$ ls -ld /opt/edg/var/info/seegrid/ /opt/edg/var/info/seegrid/seegrid.list
drwxr-xr-x    2 seegridsgm seegrid      4096 Apr 12  2005 /opt/edg/var/info/seegrid/
-rw-r--r--    1 seegridsgm seegrid        24 Jan 13 13:55 /opt/edg/var/info/seegrid/seegrid.list

Software Installation Management

First of all, read

https://edms.cern.ch/file/454439/2/LCG-2-UserGuide.html#SECTION000144000000000000000 http://goc.grid.sinica.edu.tw/gocwiki/Experiments_Software_Installation

Request /seegrid/sgmadmin role from SEEGRID VOMS administrator.

Prepare your JDL and shell scripts for installation, validation, and uninstallation. Prepare and publish installation tarball(s). You may choose to submit only a script with the job, especially if the installation tarball is large, and then use wget or lcg-cp. To do so, you need to publish your tarball on the web or to place on a SE using lcg-cr.

voms-proxy-init -voms seegrid:/seegrid/Role=sgmadmin

Manage your installation jobs to SEEGRID sites using edg-job-submit. Instead of using lcg-asis, we recomend dymanic creation of JDL by job submission scripts, whicg place proper

Requirements = other.GlueCEUniqueID == "<Target-CE>:2119/jobmanager-lcgpbs-seegrid"

in install JDL. Another option for target CE selection is using -r option of edg-job-submit. The usage of -r is problematic if "edg-brokerinfo getCE" is used in the install script, since the chosen CE will not be properly set in job's .brokerinfo file.

Also note that "--notify" option of lcg-ManageSoftware does not seem to work, and that in validation "--validate_script validate_sw" is required.

lcg-ManageVOTag is also useful in clearing of published tags, especially during development of your installation scripts:

lcg-ManageVOTag -host <Target-CE> -vo seegrid --remove -tag VO-seegrid-vive-0.2-aborted-validate

Example Scripts

Installation

site_VIVE_install scipt dynamically creates JDL and submits the installation job using CE given on invocation as a parameter, thus avoiding "edg-job-submit -r" .brokerinfo problem:

#!/bin/bash

#args: CE
echo VIVE install Startup $*

CE=$1
VER=`cat /storage/VIVE/programs/version_VIVE`

# do not use "edg-job-submit -r" because of ./BrokerInfo

cat > site_VIVE_install_tmp.jdl <<EOF
 Executable = "/opt/lcg/bin/lcg-ManageSoftware";
 InputSandbox = {"/storage/VIVE/programs/install_sw"};
 OutputSandbox={"out", "err"};
 StdOutput="out";
 StdError="err";
 Requirements = other.GlueCEUniqueID == "$CE" \
   && !Member("VO-seegrid-vive-$VER",other.GlueHostApplicationSoftwareRunTimeEnvironment) \
   && !Member("VO-seegrid-vive-$VER-to-be-validated",other.GlueHostApplicationSoftwareRunTimeEnvironment) \
   && !Member("VO-seegrid-vive-$VER-processing-validate",other.GlueHostApplicationSoftwareRunTimeEnvironment) \
   && !Member("VO-seegrid-vive-$VER-processing-install",other.GlueHostApplicationSoftwareRunTimeEnvironment) \
   && !Member("VO-seegrid-vive-$VER-aborted-validate",other.GlueHostApplicationSoftwareRunTimeEnvironment) \
   && !Member("VO-seegrid-vive-$VER-aborted-install",other.GlueHostApplicationSoftwareRunTimeEnvironment);
 Arguments = "--install --vo seegrid --tag vive-$VER --notify Branko.Marovic@rcub.bg.ac.yu";
 VirtualOrganisation="seegrid";
 RetryCount=0;
EOF

edg-job-list-match site_VIVE_install_tmp.jdl
edg-job-submit site_VIVE_install_tmp.jdl
#cat site_VIVE_install_tmp.jdl
rm -f site_VIVE_install_tmp.jdl

install_sw:

#!/bin/bash
#required
#  voms-proxy-init -voms seegrid:/seegrid/Role=sgmadmin
#check tags with
#  lcg-infosites --vo seegrid tag
#  lcg-info --vo seegrid --list-ce --attrs Tag --query 'Tag=*VO-seegrid-vive*'
#  lcg-ManageVOTag -host <Target-CE> -vo seegrid --list
#manage with
#  yes yes | lcg-ManageVOTag -vo seegrid --remove -tag VO-seegrid-vive-0.3.2-aborted-validate -host Target-CE

export VER=0.3.2

echo "############ starting install_sw $VER ############"
echo "Running on: $HOSTNAME(`hostname -i`) as `whoami`"
echo Belonging to CE: `$EDG_LOCATION/bin/edg-brokerinfo getCE`

if [ x$VO_SEEGRID_SW_DIR = 'x' ]; then #failure?
   echo "VO_SEEGRID_SW_DIR is not set in the environment"
   echo "############ ending install_sw $VER returning 1 ############"
   exit 1
fi

if [ $VO_SEEGRID_SW_DIR = '.' ]; then #failure?
   echo "The site does not provide a shared file system: VO_SEEGRID_SW_DIR=$VO_SEEGRID_SW_DIR"
   echo "############ ending install_sw $VER returning 1 ############"
   exit 1
fi

if [ ! X`whoami` = 'Xseegridsgm' ]; then #failure?
   echo "invalid username" `whoami`
   echo "############ ending install_sw $VER returning 1 ############"
   exit 1
fi

export TAR_LOC=`pwd`  #this is the temporary directory where is
                      #supposed to be the steering script and the tarballs

#this also tests outbound access to VIVE portal
wget http://grid02.rcub.bg.ac.yu/VIVE/seegrid-vive-$VER.tar.gz
                      #in this case the script doesn't need tarball from the grid but
                      #it fetches from the WEB requiring OUTBOUND connectivity
                      #it is needed anyway for VIVE software to run

cd $VO_SEEGRID_SW_DIR #go to software installation root directory
pwd
ls -al                #and check its content

#remove previously created junk caused by uninstall
#this is related to undocumented lcg-ManageSoftware behavior
rm -r -f seegrid-vive-0.1*_tmp 
rm -r -f seegrid-vive-0.2*_tmp 
rm -r -f seegrid-vive-0.3_tmp
rm -r -f seegrid-vive-0.3.1_tmp
rm -f seegrid.*

rm -r -f -v vive-$VER #remove only the current version of the software

#for initial development and testing only:
#remove previously created installation attempts
#this also destroys valid old software versions which we may want to preserve
echo "#cleaning $VO_SEEGRID_SW_DIR"
rm -r -f vive-_tmp
rm -r -f vive-0.1*
rm -r -f vive-0.2*
#cannot rm -r -f vive-0.3* because of seegrid-vive-$VER_tmp
rm -r -f vive-0.3
rm -r -f vive-0.3.1*
rm -r -f vive-$VER
ls -al                #and check its content

mkdir vive-$VER
if [ ! $? = 0 ]; then #failure?
   echo "Directory vive-$VER already exists in" `pwd`
   echo "############ ending install_sw $VER returning 1 ############"
   exit 1
fi

cd vive-$VER          #create installation directory
echo "Installing into" `pwd`

echo "running the command: tar xzvf $TAR_LOC/seegrid-vive-$VER.tar.gz"
tar xzvf $TAR_LOC/seegrid-vive-$VER.tar.gz
if [ ! $? = 0 ]; then #failure?
   echo "Failure unpacking $TAR_LOC/seegrid-vive-$VER.tar.gz"
   echo "############ ending install_sw $VER returning 1 ############"
   exit 1
fi

echo "Installation into " `pwd` " finished"
ls -al                #list what has been installed
echo "############ ending install_sw $VER returning $? ############"
exit $? #This is the relevant return code

Validation

site_VIVE_validate:

#!/bin/bash

#args: CE
echo VIVE validate Startup $*

CE=$1
VER=`cat /storage/VIVE/programs/version_VIVE`

# do not use "edg-job-submit -r" because of ./BrokerInfo

cat > site_VIVE_validate_tmp.jdl <<EOF
 Executable = "/opt/lcg/bin/lcg-ManageSoftware";
 InputSandbox = {"/storage/VIVE/programs/validate_sw"};
 OutputSandbox = {"out", "err"};
 StdOutput="out";
 StdError="err";
 #InputData = {"lfn:/grid/seegrid/VIVE/PACSimages/seegrid/SoftwareValidation.CSFE"};
 #DataAccessProtocol={"rfio","gsidcap"};
 Requirements = other.GlueCEUniqueID == "$CE" && (Member("VO-seegrid-vive-$VER-to-be-validated",other.GlueHostApplicationSoftwareRunTimeEnvironment));
 Arguments = "--validate --vo seegrid --tag vive-$VER --notify Branko.Marovic@rcub.bg.ac.yu --validate_script validate_sw";
 RetryCount=0;
 VirtualOrganisation="seegrid";
EOF

edg-job-list-match  site_VIVE_validate_tmp.jdl
edg-job-submit site_VIVE_validate_tmp.jdl
rm -f site_VIVE_validate_tmp.jdl

validate_sw:

#!/bin/bash
#see the comments at the beginning of install_sw

export VER=0.3.2

#set up LFC/GFAL environment
export LFC_HOST=grid02.rcub.bg.ac.yu
export LCG_CATALOG_TYPE=lfc
export LCG_GFAL_VO=seegrid

export CE=`$EDG_LOCATION/bin/edg-brokerinfo getCE`

echo "############ starting validate_sw $VER ############"
echo "# VO_SEEGRID_SW_DIR (e.g. /opt/exp_soft/seegridi) should be writable only by seegridsgm user"
echo "# and only seegridsgm should be able to manage published application tags"
echo "Running job $EDG_WL_JOBID on: $HOSTNAME(`hostname -i`) as `whoami`"
echo "VO_SEEGRID_SW_DIR (e.g. /opt/exp_soft/seegrid) should be writable only by seegridsgm user"
echo " and only seegridsgm should be able to manage published application tags"
echo "VO_SEEGRID_SW_DIR is $VO_SEEGRID_SW_DIR"
echo Belonging to CE: $CE
echo Close SE is $VO_SEEGRID_DEFAULT_SE


if [ x$VO_SEEGRID_SW_DIR = 'x' ]; then #failure?
   echo "VO_SEEGRID_SW_DIR is not set in the environment"
   echo "############ ending validate_sw $VER returning 1 ############"
   exit 1
fi

if [ $VO_SEEGRID_SW_DIR = '.' ]; then #failure?
   echo "The site does not provide a shared file system: VO_SEEGRID_SW_DIR=$VO_SEEGRID_SW_DIR"
   echo "############ ending validate_sw $VER returning 1 ############"
   exit 1
fi

#useful in diagnosing sites that do not pass the validation
echo "### Checking lcg-cp"
lcg-cp --vo seegrid -v lfn:/grid/seegrid/VIVE/PACSimages/seegrid/SoftwareValidation.CSFE  file:`pwd`/SoftwareValidation.CSFE
if [ ! $? = 0 ]; then #failure?
   echo "Command lcg-cp does not work, suspicious but not required"
fi
ls -ld `pwd`
ls -al
rm -f `pwd`/SoftwareValidation.CSFE

cd $VO_SEEGRID_SW_DIR #software installation root directory

echo "### Listing `pwd`"
ls -alt
cd vive-$VER
if [ ! $? = 0 ]; then #failure?
   echo "Directory vive-$VER does not exists in" `pwd`
   echo "############ ending validate_sw $VER returning $? ############"
   exit 1
fi

echo "### Checking FieldServer operation"
echo "# This starts a server process that loads a file from the closeSE using RFIO"
echo "# based on the information from SEEGRID LFC, then connects to TCP port 443 on"
echo "# grid02.rcub.bg.ac.yu and, if OK, exits returning 113"
./FieldServer $CE "$HOSTNAME(`hostname -i`)" \
 p grid02.rcub.bg.ac.yu 443 grid02.rcub.bg.ac.yu ANY \
 . /VIVE-cache3D . . 300000000 0 SoftwareValidation@seegrid

if [ $? = 113 ]; then
   echo "Dataset load and binder connectivity test passed, installation validated"
   echo "############ ending validate_sw $VER returning 0 ############"
   exit 0
fi

echo "FieldServer returned $?"
echo "Validation failed"
echo "############ ending validate_sw $VER returning 255 ############"
exit 255

Removal

uninstall-vive.jdl:

Executable = "/opt/lcg/bin/lcg-ManageSoftware";
InputSandbox = {"/storage/programs/VIVE/uninstall_sw"};
OutputSandbox = {"out", "err"};
stdoutput = "out";
stderror = "err";
Arguments = "--uninstall --vo seegrid --tag seegrid-vive-0.2 --uninstall_script uninstall_sw";
Requirements = (Member("VO-seegrid-vive-0.2",other.GlueHostApplicationSoftwareRunTimeEnvironment) \
 && (other.GlueCEUniqueID == "<Target-CE>:2119/jobmanager-lcgpbs-seegrid))";
VirtualOrganisation="seegrid";

uninstall_sw:

#!/bin/bash
#see the comments at the beginning of install_sw

export VER=0.2

echo "############ starting uninstall_sw $VER ############"
echo "Running on: $HOSTNAME(`hostname -i`) as `whoami`"
echo Belonging to CE: `$EDG_LOCATION/bin/edg-brokerinfo getCE`

if [ x$VO_SEEGRID_SW_DIR = 'x' ]; then #failure?
   echo "VO_SEEGRID_SW_DIR is not set in the environment"
   echo "############ ending uninstall_sw $VER returning 1 ############"
   exit 1
fi

if [ $VO_SEEGRID_SW_DIR = '.' ]; then #failure?
   echo "The site does not provide a shared file system: VO_SEEGRID_SW_DIR=$VO_SEEGRID_SW_DIR"
   echo "############ ending uninstall_sw $VER returning 1 ############"
   exit 1
fi

cd $VO_SEEGRID_SW_DIR #go to software installation root directory
ls -al                #and check its content

rm -f -v -r vive-$VER #remove only the current version of the software
if [ ! $? = 0 ]; then #failure?
   echo "Removal of vive-$VER from" `pwd` "failed"
   echo "############ ending uninstall_sw $VER returning $? ############"
   exit 1
fi

echo "Removal of vive-$VER from" `pwd` "finished"
echo "############ ending uninstall_sw $VER returning $? ############"
exit 0 # This is the relevant return code

Retrieved from "http://wiki.egee-see.org/index.php/SEE-GRID_ESM_Software_Installation_Guide"

SEE-GRID ESM Software Installation Guide

From EGEE-see WIki

Contents

Site Configuration

Setting up shared application software filesystem

Publishing of software tags

Software Installation Management

Example Scripts

Installation

Validation

Removal

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