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---+!! Notes about Installation and Configuration of WN using Torque with MPI support * *These notes are provided by site admins on a best effort base as a contribution to the IGI communities and MUST not be considered as a subsitute of the [[http://wiki.italiangrid.it/twiki/bin/view/IGIRelease/IgiEmi][Official IGI documentation]].* * This document is addressed to site administrators responsible for middleware installation and configuration. * The goal of this page is to provide some hints and examples on how to install and configure an *EMI WN + MPI* service based on EMI middleware using *TORQUE* as batch system %TOC% ---++ References 1. [[http://www.italiangrid.it/][About IGI - Italian Grid infrastructure]] 1. [[http://wiki.italiangrid.it/twiki/bin/view/IGIRelease/WebHome][About IGI Release]] 1. [[http://wiki.italiangrid.it/twiki/bin/view/IGIRelease/IgiEmi][IGI Official Installation and Configuration guide]] 1. [[https://twiki.cern.ch/twiki/bin/view/EMI/GenericInstallationConfigurationEMI1][Generic Installation & Configuration for EMI 1]] 1. [[https://twiki.cern.ch/twiki/bin/view/LCG/YaimGuide400][ Yaim Guide]] 1. [[https://twiki.cern.ch/twiki/bin/view/LCG/Site-info_configuration_variables#site_info_def][site-info.def yaim variables]] 1. [[https://twiki.cern.ch/twiki/bin/view/LCG/Site-info_configuration_variables#MPI][MPI yaim variables]] 1. [[https://twiki.cern.ch/twiki/bin/view/LCG/Site-info_configuration_variables#WN][WN yaim variables]] 1. [[https://twiki.cern.ch/twiki/bin/view/LCG/Site-info_configuration_variables#TORQUE][TORQUE Yaim variables]] 1. [[http://www.eu-emi.eu/products/-/asset_publisher/z2MT/content/emi-wn][EMI-WN v.1.0.0]] 1. [[http://www.eu-emi.eu/products/-/asset_publisher/z2MT/content/glite-mpi][gLite-MPI v.1.0.0]] 1. [[https://wiki.egi.eu/wiki/MAN03 ][MPI-Start Installation and Configuration]] 1. [[https://wiki.egi.eu/wiki/Tools/Manuals/SiteProblemsFollowUp][Troubleshooting Guide for Operational Errors on EGI Sites]] 1. [[https://wiki.egi.eu/wiki/Tools/Manuals/AdministrationFaq][Grid Administration FAQs page]] ---++ Service installation %TWISTY{ mode="div" showlink=" *O.S. and Repos* " hidelink=" *O.S. and Repos* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++ O.S. and Repos * Starts from a fresh installation of Scientific Linux 5.x (x86_64). <verbatim> # cat /etc/redhat-release Scientific Linux SL release 5.7 (Boron) </verbatim> * Install the additional repositories: EPEL, Certification Authority, UMD <verbatim> # yum install yum-priorities yum-protectbase # cd /etc/yum.repos.d/ # rpm -ivh http://mirror.switch.ch/ftp/mirror/epel//5/x86_64/epel-release-5-4.noarch.rpm # wget http://repo-pd.italiangrid.it/mrepo/repos/egi-trustanchors.repo # rpm -ivh http://repo-pd.italiangrid.it/mrepo/EMI/1/sl5/x86_64/updates/emi-release-1.0.1-1.sl5.noarch.rpm # wget http://repo-pd.italiangrid.it/mrepo/repos/igi/sl5/x86_64/igi-emi.repo </verbatim> * Be sure that SELINUX is disabled (or permissive). Details on how to disable SELINUX are [[http://fedoraproject.org/wiki/SELinux/setenforce][here]]: <verbatim> # getenforce Disabled </verbatim> * Check the repos list (sl-*.repo are the repos of the O.S. and they should be present by default). <verbatim> # ls /etc/yum.repos.d/ egi-trustanchors.repo emi1-third-party.repo emi1-base.repo emi1-updates.repo epel.repo epel-testing.repo igi-emi.repo sl-contrib.repo sl-fastbugs.repo sl-security.repo sl-testing.repo sl-debuginfo.repo sl.repo sl-srpms.repo </verbatim> *IMPORTANT*: remove the dag repository if present %ENDTWISTY% %TWISTY{ mode="div" showlink=" *yum install* " hidelink=" *yum install* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++ yum install <verbatim> # yum clean all Loaded plugins: downloadonly, kernel-module, priorities, protect-packages, protectbase, security, verify, versionlock Cleaning up Everything # yum install ca-policy-egi-core # yum install igi-wn_torque_noafs # yum install glite-mpi # yum install emi-version # yum install openmpi openmpi-devel # yum install mpich2 mpich2-devel # yum install nfs-utils </verbatim> see [[YumWNtorqueMPI][here]] for details %ENDTWISTY% ---++ Service configuration You have to copy the configuration files in another path, for example root, and set them properly (see later): <verbatim> # ls /opt/glite/yaim/examples/siteinfo/ services site-info.def # ls /opt/glite/yaim/examples/siteinfo/services/ glite-mpi glite-mpi_ce glite-mpi_sl4-x86 glite-mpi_sl5-x86_64 glite-mpi_wn glite-vobox glite-wn glite-wn_tar igi-mpi # cp -r /opt/glite/yaim/examples/siteinfo/* . </verbatim> in the services directory, keep and edit only these files: <verbatim> # ls services/ glite-mpi glite-mpi_ce glite-mpi_wn </verbatim> %TWISTY{ mode="div" showlink=" *vo.d directory* " hidelink=" *vo.d directory* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++ vo.d directory Create the vo.d directory for the VO configuration file (you can decide if keep the VO information in the site.def or putting them in the vo.d directory) <verbatim> # mkdir vo.d </verbatim> [[VoDirContent][here]] an example for some VOs. Information about the several VOs are available at the [[http://operations-portal.in2p3.fr/vo][CENTRAL OPERATIONS PORTAL]]. %ENDTWISTY% %TWISTY{ mode="div" showlink=" *users and groups configuration* " hidelink=" *users and groups configuration* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++ users and groups configuration here an example on how to define pool accounts ([[https://forge.cnaf.infn.it/plugins/scmsvn/viewcvs.php/branches/BRANCH-4_0_X/ig-yaim/examples/ig-users.conf?rev=6195&root=igrelease&view=markup][ig-users.conf]]) and groups ([[https://forge.cnaf.infn.it/plugins/scmsvn/viewcvs.php/*checkout*/branches/BRANCH-4_0_X/ig-yaim/examples/ig-groups.conf?rev=6193&root=igrelease][ig-groups.conf]]) for several VOs %ENDTWISTY% %TWISTY{ mode="div" showlink=" *site-info.def* " hidelink=" *site-info.def* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++ site-info.def SUGGESTION: use the same [[SiteDefCreamWNMPI][site-info.def]] for CREAM and WNs: for this reason in this example file there are yaim variable used by CREAM, TORQUE or emi-WN. It is also included the settings of some VOs For your convenience there is an explanation of each yaim variable. For more details look at [6, 7, 8, 9] %ENDTWISTY% %TWISTY{ mode="div" showlink=" *glite-mpi* " hidelink=" *glite-mpi* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++ glite-mpi in the following example, it is enabled the support for MPICH2 and OPENMPI; moreover the WNs are configured to use shared homes <verbatim> ############################################ # Mandatory parameters in services/mpi # ############################################ # N.B. this file contains common configuration for CE and WN # As such, it should be included in your site-info.def to ensure # that the configuration of the CE and WNs remains in sync. #---------------------------------- # MPI-related configuration: #---------------------------------- # Several MPI implementations (or "flavours") are available. # If you do NOT want a flavour to be configured, set its variable # to "no". Otherwise, set it to "yes". If you want to use an # already installed version of an implementation, set its "_PATH" and # "_VERSION" variables to match your setup (examples below). # # NOTE 1: the CE_RUNTIMEENV will be automatically updated in the file # functions/config_mpi_ce, so that the CE advertises the MPI implementations # you choose here - you do NOT have to change it manually in this file. # It will become something like this: # # CE_RUNTIMEENV="$CE_RUNTIMEENV # MPICH # MPICH-1.2.7p4 # MPICH2 # MPICH2-1.0.4 # OPENMPI # OPENMPI-1.1 # LAM" # # NOTE 2: it is currently NOT possible to configure multiple concurrent # versions of the same implementations (e.g. MPICH-1.2.3 and MPICH-1.2.7) # using YAIM. Customize "/opt/glite/yaim/functions/config_mpi_ce" file # to do so. ############### # The following example are applicable to default SL 5.3 x86_64 (gLite 3.2 WN) # Support for MPICH 1 is dropped MPI_MPICH_ENABLE="no" MPI_MPICH2_ENABLE="yes" MPI_OPENMPI_ENABLE="yes" MPI_LAM_ENABLE="no" #--- # Example for using an already installed version of MPI. # Just fill in the path to its current installation (e.g. "/usr") # and which version it is (e.g. "6.5.9"). #--- # DEFAULT Parameters # The following parameters are correct for a default SL 5.X x86_64 WN #MPI_MPICH_PATH="/opt/mpich-1.2.7p1/" #MPI_MPICH_VERSION="1.2.7p1" MPI_MPICH2_PATH="/usr/lib64/mpich2/" MPI_MPICH2_VERSION="1.2.1p1" MPI_OPENMPI_PATH="/usr/lib64/openmpi/1.4-gcc/" MPI_OPENMPI_VERSION="1.4" #MPI_LAM_VERSION="7.1.2" # If you provide mpiexec (http://www.osc.edu/~pw/mpiexec/index.php) # for MPICH or MPICH2, please state the full path to that file here. # Otherwise do not set this variable. (Default is to set this to # the location of mpiexec set by the glite-MPI_WN metapackage. # Most versions of MPI now distribute their own versions of mpiexec # However, I had some problems with the MPICH2 version - so use standard mpiexec MPI_MPICH_MPIEXEC="/usr/bin/mpiexec" MPI_MPICH2_MPIEXEC="/usr/bin/mpiexec" MPI_OPENMPI_MPIEXEC="/usr/lib64/openmpi/1.4-gcc/bin/mpiexec" ######### MPI_SHARED_HOME section # Set this variable to one of the following: # MPI_SHARED_HOME="no" if a shared directory is not used # MPI_SHARED_HOME="yes" if the HOME directory area is shared # MPI_SHARED_HOME="/Path/to/Shared/Location" if a shared area other # than the HOME dirirectory is used. # If you do NOT provide a shared home, set MPI_SHARED_HOME to "no" (default). #MPI_SHARED_HOME=${MPI_SHARED_HOME:-"no"} # If you do provide a shared home and Grid jobs normally start in that area, # set MPI_SHARED_HOME to "yes". MPI_SHARED_HOME="yes" # If you have a shared area but Grid jobs don't start there, then set # MPI_SHARED_HOME to the location of this shared area. The permissions # of this area need to be the same as /tmp (i.e. 1777) so that users # can create their own subdirectories. #MPI_SHARED_HOME=/share/cluster/mpi ######## Intra WN authentication # This variable is normally set to yes when shared homes are not used. # This allows the wrapper script to copy the job data to the other nodes # # If enabling SSH Hostbased Authentication you must ensure that # the appropriate ssh config files are deployed. # Affected files are the system ssh_config, sshd_config and ssh_know_hosts. # The edg-pbs-knownhosts can be use to generate the ssh_know_hosts # # If you do NOT have SSH Hostbased Authentication between your WNs, # set this variable to "no" (default). Otherwise set it to "yes". # MPI_SSH_HOST_BASED_AUTH=${MPI_SSH_HOST_BASED_AUTH:-"no"} </verbatim> %ENDTWISTY% %TWISTY{ mode="div" showlink=" *glite-mpi_ce* " hidelink=" *glite-mpi_ce* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++ glite-mpi_ce <verbatim> # Setup configuration variables that are common to both the CE and WN if [ -r ${config_dir}/services/glite-mpi ]; then source ${config_dir}/services/glite-mpi fi # The MPI CE config function can create a submit filter for # Torque to ensure that CPU allocation is performed correctly. # Change this variable to "yes" to have YAIM create this filter. # Warning: if you have an existing torque.cfg it will be modified. #MPI_SUBMIT_FILTER=${MPI_SUBMIT_FILTER:-"no"} MPI_SUBMIT_FILTER="yes" </verbatim> %ENDTWISTY% %TWISTY{ mode="div" showlink=" *glite-mpi_wn* " hidelink=" *glite-mpi_wn* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++ glite-mpi_wn <verbatim> # Setup configuration variables that are common to both the CE and WN # Most variables are common to CE and WN. It is easier to define # These in a common file ${config_dir}/services/glite-mpi if [ -r ${config_dir}/services/glite-mpi ]; then source ${config_dir}/services/glite-mpi fi </verbatim> %ENDTWISTY% %TWISTY{ mode="div" showlink=" *munge configuration* " hidelink=" *munge configuration* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++ munge configuration *IMPORTANT*: The updated EPEL5 build of torque-2.5.7-1 as compared to previous versions enables munge as an inter node authentication method. * verify that munge is correctly installed: <verbatim> # rpm -qa | grep munge munge-libs-0.5.8-8.el5 munge-0.5.8-8.el5 </verbatim> * On one host (for example the batch server) generate a key by launching: <verbatim> # /usr/sbin/create-munge-key # ls -ltr /etc/munge/ total 4 -r-------- 1 munge munge 1024 Jan 13 14:32 munge.key </verbatim> * Copy the key, /etc/munge/munge.key to every host of your cluster, adjusting the permissions: <verbatim> # chown munge:munge /etc/munge/munge.key </verbatim> * Start the munge daemon on each node: <verbatim> # service munge start Starting MUNGE: [ OK ] # chkconfig munge on </verbatim> %ENDTWISTY% %TWISTY{ mode="div" showlink=" *software area settings* " hidelink=" *software area settings* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++ software area settings you have to import the software area from CE (or another host). * Edit the file /etc/fstab by adding a line like the following: <verbatim> cremino.cnaf.infn.it:/opt/exp_soft/ /opt/exp_soft/ nfs rw,defaults 0 0 </verbatim> * check nfs and portmap status <verbatim> # service nfs status rpc.mountd is stopped nfsd is stopped # service portmap status portmap is stopped # service portmap start Starting portmap: [ OK ] # service nfs start Starting NFS services: [ OK ] Starting NFS daemon: [ OK ] Starting NFS mountd: [ OK ] Starting RPC idmapd: [ OK ] # chkconfig nfs on # chkconfig portmap on </verbatim> * after any modification in /etc/fstab launch <verbatim> mount -a </verbatim> * verify the mount: <verbatim> # df -h Filesystem Size Used Avail Use% Mounted on /dev/sda3 65G 1.9G 59G 4% / /dev/sda1 99M 18M 76M 19% /boot tmpfs 2.0G 0 2.0G 0% /dev/shm cremino.cnaf.infn.it:/opt/exp_soft/ 65G 4.4G 57G 8% /opt/exp_soft </verbatim> %ENDTWISTY% %TWISTY{ mode="div" showlink=" *yaim check* " hidelink=" *yaim check* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++yaim check <verbatim> # /opt/glite/yaim/bin/yaim -v -s site-info_batch.def -n MPI_WN -n WN_torque_noafs INFO: Using site configuration file: site-info_batch.def INFO: Sourcing service specific configuration file: ./services/glite-mpi_wn INFO: ################################################################### . /'.-. ') . yA,-"-,( ,m,:/ ) .oo. oo o ooo o. .oo . / .-Y a a Y-. 8. .8' 8'8. 8 8b d'8 . / ~ ~ / 8' .8oo88. 8 8 8' 8 . (_/ '====' 8 .8' 8. 8 8 Y 8 . Y,-''-,Yy,-.,/ o8o o8o o88o o8o o8o o8o . I_))_) I_))_) current working directory: /root site-info.def date: Apr 24 09:22 site-info_batch.def yaim command: -v -s site-info_batch.def -n MPI_WN -n WN_torque_noafs log file: /opt/glite/yaim/bin/../log/yaimlog Tue Apr 24 11:53:02 CEST 2012 : /opt/glite/yaim/bin/yaim Installed YAIM versions: glite-yaim-clients 5.0.0-1 glite-yaim-core 5.0.2-1 glite-yaim-mpi 1.1.10-10 glite-yaim-torque-client 5.0.0-1 glite-yaim-torque-utils 5.0.0-1 #################################################################### INFO: The default location of the grid-env.(c)sh files will be: /usr/libexec INFO: Sourcing the utilities in /opt/glite/yaim/functions/utils INFO: Detecting environment INFO: Executing function: config_mpi_wn_check INFO: Executing function: config_ntp_check INFO: Executing function: config_sysconfig_lcg_check INFO: Executing function: config_globus_clients_check INFO: Executing function: config_lcgenv_check INFO: Executing function: config_users_check INFO: Executing function: config_sw_dir_check INFO: Executing function: config_amga_client_check INFO: Executing function: config_wn_check INFO: Executing function: config_vomsdir_check INFO: Executing function: config_vomses_check INFO: Executing function: config_glite_saga_check INFO: Executing function: config_add_pool_env_check INFO: Executing function: config_wn_info_check INFO: Executing function: config_torque_client_check INFO: Checking is done. INFO: All the necessary variables to configure MPI_WN WN_torque_noafs are defined in your configuration files. INFO: Please, bear in mind that YAIM only guarantees the definition of variables INFO: controlled in the _check functions. INFO: YAIM terminated succesfully. </verbatim> %ENDTWISTY% %TWISTY{ mode="div" showlink=" *yaim config* " hidelink=" *yaim config* " remember="off" firststart="hide" showimgright="%ICONURLPATH{toggleopen}%" hideimgright="%ICONURLPATH{toggleclose}%" }% ---+++ yaim config <verbatim> # /opt/glite/yaim/bin/yaim -c -s site-info_batch.def -n MPI_WN -n WN_torque_noafs INFO: Using site configuration file: site-info_batch.def INFO: Sourcing service specific configuration file: ./services/glite-mpi_wn INFO: ################################################################### . /'.-. ') . yA,-"-,( ,m,:/ ) .oo. oo o ooo o. .oo . / .-Y a a Y-. 8. .8' 8'8. 8 8b d'8 . / ~ ~ / 8' .8oo88. 8 8 8' 8 . (_/ '====' 8 .8' 8. 8 8 Y 8 . Y,-''-,Yy,-.,/ o8o o8o o88o o8o o8o o8o . I_))_) I_))_) current working directory: /root site-info.def date: Apr 24 09:22 site-info_batch.def yaim command: -c -s site-info_batch.def -n MPI_WN -n WN_torque_noafs log file: /opt/glite/yaim/bin/../log/yaimlog Tue Apr 24 11:53:15 CEST 2012 : /opt/glite/yaim/bin/yaim Installed YAIM versions: glite-yaim-clients 5.0.0-1 glite-yaim-core 5.0.2-1 glite-yaim-mpi 1.1.10-10 glite-yaim-torque-client 5.0.0-1 glite-yaim-torque-utils 5.0.0-1 #################################################################### INFO: The default location of the grid-env.(c)sh files will be: /usr/libexec INFO: Sourcing the utilities in /opt/glite/yaim/functions/utils INFO: Detecting environment INFO: Executing function: config_mpi_wn_check INFO: Executing function: config_ntp_check INFO: Executing function: config_sysconfig_lcg_check INFO: Executing function: config_globus_clients_check INFO: Executing function: config_lcgenv_check INFO: Executing function: config_users_check INFO: Executing function: config_sw_dir_check INFO: Executing function: config_amga_client_check INFO: Executing function: config_wn_check INFO: Executing function: config_vomsdir_check INFO: Executing function: config_vomses_check INFO: Executing function: config_glite_saga_check INFO: Executing function: config_add_pool_env_check INFO: Executing function: config_wn_info_check INFO: Executing function: config_torque_client_check INFO: Executing function: config_mpi_wn_setenv INFO: Executing function: config_mpi_wn INFO: Executing function: config_ldconf INFO: config_ldconf: function not needed anymore, left empy waiting to be removed INFO: Executing function: config_ntp_setenv INFO: Executing function: config_ntp INFO: Storing old ntp settings in /etc/ntp.conf.yaimold.20120424_115316 INFO: Executing function: config_sysconfig_edg INFO: Executing function: config_sysconfig_globus INFO: Executing function: config_sysconfig_lcg INFO: Executing function: config_crl INFO: Now updating the CRLs - this may take a few minutes... Enabling periodic fetch-crl: [ OK ] INFO: Executing function: config_rfio INFO: Executing function: config_globus_clients_setenv INFO: Executing function: config_globus_clients INFO: Configure the globus service - not needed in EMI INFO: Executing function: config_lcgenv INFO: Executing function: config_users INFO: Executing function: config_sw_dir_setenv INFO: Executing function: config_sw_dir INFO: Executing function: config_nfs_sw_dir_client INFO: Variable $BASE_SW_DIR is not set! INFO: The directory /opt/exp_soft won't be mounted with NFS! INFO: Executing function: config_fts_client INFO: Executing function: config_amga_client_setenv INFO: Executing function: config_amga_client INFO: Executing function: config_wn_setenv INFO: Executing function: config_wn INFO: Executing function: config_vomsdir_setenv INFO: Executing function: config_vomsdir INFO: Executing function: config_vomses INFO: Executing function: config_glite_saga_setenv INFO: SAGA configuration is not required INFO: Executing function: config_glite_saga INFO: SAGA configuration is not required INFO: Executing function: config_add_pool_env_setenv INFO: Executing function: config_add_pool_env INFO: Executing function: config_wn_info WARNING: No subcluster has been defined for the WN in the WN_LIST file /root/wn-list.conf WARNING: YAIM will use the default subcluster id: CE_HOST -> cream-01.cnaf.infn.it INFO: Executing function: config_torque_client INFO: starting pbs_mom... Shutting down TORQUE Mom: pbs_mom already stopped [ OK ] Starting TORQUE Mom: [ OK ] INFO: Configuration Complete. [ OK ] INFO: YAIM terminated succesfully. </verbatim> %ENDTWISTY% ---++ Revisions | *Date* | *Comment* | *By* | |2012-05-25 | installation notes completed | Alessandro Paolini | | 2012-04-23 | First draft | Alessandro Paolini | -- Main.AlessandroPaolini - 2012-04-23
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Topic revision: r5 - 2012-05-25
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AlessandroPaolini
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