SGE
- SGE
- ROADMAP
- Instalation Guide SGE YAIM
- Integrating SGE with Yaim
- LIP SGE implementation
- CESGA SGE Implementation
- Imperial SGE implementation
- SA3 SGE TESTBED
ROADMAP
| Name | Date | Status | Responsible |
|---|---|---|---|
| Common Documentation | DONE | ALL | |
| IP on lcg-CE | DONE | IC | |
| jobmanager on lcg-CE | DONE | CESGA | |
| yaim on lcg-CE | DONE | LIP | |
| Stress tests on lcg-CE | DONE | CESGA | |
| Optimized SGE configuration | DONE | CESGA | |
| Documentation: Installation Guide, Batch System Cookbook | June | DONE | LIP, CESGA |
| Official realease of SGE on lcg-CE | July | ||
| IP on gLite-CE | DONE | ||
| blah on gLite-CE | June | in progress | IC |
| APEL on gLite-CE | June | in progress | CESGA |
| yaim on gLite-CE | July | LIP | |
| Stress tests on gLite-CE | August | CESGA | |
| Installation Guide | August | LIP, CESGA | |
| Official release of SGE on gLite-CE | October |
Instalation Guide SGE YAIM
If you just want to install SGE in your site the easiest would be to use yaim. The installation procedure is described in the "Installation Guide": Installation Guide Version2 Installation Guide SGE gLite 3.1 If you want to know more details about how the integration has been done or if you want to do then installation manually you can find the details below.Integrating SGE with Yaim
DISCLAIMER: THIS WORK IS STILL INCOMPLETE AND UNDER TESTING! THANKS: THIS WORK WOULD NOT BE POSSIBLE WITHOUT JOAO PAULO MARTINS HELP, LIP SYSTEM ADMINISTRATOR. This section reports the work which has been developed to distribute and install Sun Grid Engine together with the gLite/LCG middleware. Sun Grid Engine needs a qmaster machine (which can be installed in the CE Gatekeeper) and several execution hosts (which must be installed in Grid Worker Nodes). Following the SGE V60u7_1 distribution, we have compiled the original source code under 32 bit machines running SL4, and built different rpms modules. The basic rpm packages which have to be present in Qmaster/Exec SGE machines are:- edg-sge-utils-1.0.0-1: The equivalent SGE package of edg-pbs-utils-*_sl3 for configuring ssh
- /opt/edg/etc/edg-sge-knownhosts.conf.template
- /opt/edg/sbin/edg-sge-knownhosts
- sge-daemons-V60u7_1-2: The SGE daemons
- /usr/local/sge/V60u7_1/bin/lx26-x86/sge_execd
- /usr/local/sge/V60u7_1/bin/lx26-x86/sge_qmaster
- /usr/local/sge/V60u7_1/bin/lx26-x86/sge_schedd
- /usr/local/sge/V60u7_1/bin/lx26-x86/sge_shadowd
- sge-docs-V60u7_1-2: Documentation, Manuals and examples
- /usr/local/sge/V60u7_1/3rd_party/3rd_party_licscopyrights
- /usr/local/sge/V60u7_1/3rd_party/qmon/copyrights
- /usr/local/sge/V60u7_1/3rd_party/qmon/ltree_changed.tar.gz
- /usr/local/sge/V60u7_1/catman/cat/cat1/gethostbyaddr.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/gethostbyname.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/gethostname.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/getservbyname.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/hostnameutils.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qacct.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qalter.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qconf.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qdel.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qhold.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qhost.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qlogin.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qmake.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qmod.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qmon.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qping.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qresub.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qrls.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qrsh.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qselect.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qsh.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qstat.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qsub.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/qtcsh.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/sge_ckpt.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/sge_intro.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/sge_types.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/sgepasswd.1
- /usr/local/sge/V60u7_1/catman/cat/cat1/submit.1
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_allocate_job_template.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_attributes.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_control.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_delete_job_template.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_exit.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_get_DRM_system.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_get_attribute.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_get_attribute_names.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_get_contact.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_get_next_attr_name.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_get_next_attr_value.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_get_next_job_id.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_get_vector_attribute.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_get_vector_attribute_names.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_init.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_job_ps.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_jobcontrol.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_jobtemplate.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_misc.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_release_attr_names.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_release_attr_values.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_release_job_ids.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_run_bulk_jobs.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_run_job.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_session.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_set_attribute.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_set_vector_attribute.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_strerror.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_submit.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_synchronize.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_version.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_wait.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_wcoredump.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_wexitstatus.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_wifaborted.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_wifexited.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_wifsignaled.3
- /usr/local/sge/V60u7_1/catman/cat/cat3/drmaa_wtermsig.3
- /usr/local/sge/V60u7_1/catman/cat/cat5/access_list.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/accounting.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/bootstrap.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/calendar_conf.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/checkpoint.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/complex.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/host_aliases.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/host_conf.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/hostgroup.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/project.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/qtask.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/queue_conf.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/reporting.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/sched_conf.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/sge_aliases.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/sge_conf.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/sge_pe.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/sge_priority.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/sge_qstat.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/sge_request.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/sgepasswd.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/share_tree.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/user.5
- /usr/local/sge/V60u7_1/catman/cat/cat5/usermapping.5
- /usr/local/sge/V60u7_1/catman/cat/cat8/sge_execd.8
- /usr/local/sge/V60u7_1/catman/cat/cat8/sge_qmaster.8
- /usr/local/sge/V60u7_1/catman/cat/cat8/sge_schedd.8
- /usr/local/sge/V60u7_1/catman/cat/cat8/sge_shadowd.8
- /usr/local/sge/V60u7_1/catman/cat/cat8/sge_shepherd.8
- /usr/local/sge/V60u7_1/doc/README-Autoinstall.txt
- /usr/local/sge/V60u7_1/doc/README-DRMAA.txt
- /usr/local/sge/V60u7_1/doc/arc_depend_irix.asc
- /usr/local/sge/V60u7_1/doc/arc_depend_solaris.asc
- /usr/local/sge/V60u7_1/doc/load_parameters.asc
- /usr/local/sge/V60u7_1/doc/logfile-trimming.asc
- /usr/local/sge/V60u7_1/examples/drmaa
- /usr/local/sge/V60u7_1/examples/drmaa/example.c
- /usr/local/sge/V60u7_1/examples/drmaa/howto1.c
- /usr/local/sge/V60u7_1/examples/drmaa/howto2.c
- /usr/local/sge/V60u7_1/examples/drmaa/howto2_1.c
- /usr/local/sge/V60u7_1/examples/drmaa/howto3.c
- /usr/local/sge/V60u7_1/examples/drmaa/howto3_1.c
- /usr/local/sge/V60u7_1/examples/drmaa/howto3_2.c
- /usr/local/sge/V60u7_1/examples/drmaa/howto4.c
- /usr/local/sge/V60u7_1/examples/drmaa/howto5.c
- /usr/local/sge/V60u7_1/examples/drmaa/howto6.c
- /usr/local/sge/V60u7_1/examples/jobs
- /usr/local/sge/V60u7_1/examples/jobs/array_submitter.sh
- /usr/local/sge/V60u7_1/examples/jobs/jobnet_submitter.sh
- /usr/local/sge/V60u7_1/examples/jobs/pascal.sh
- /usr/local/sge/V60u7_1/examples/jobs/pminiworm.sh
- /usr/local/sge/V60u7_1/examples/jobs/simple.sh
- /usr/local/sge/V60u7_1/examples/jobs/sleeper.sh
- /usr/local/sge/V60u7_1/examples/jobs/step_A_array_submitter.sh
- /usr/local/sge/V60u7_1/examples/jobs/step_B_array_submitter.sh
- /usr/local/sge/V60u7_1/examples/jobs/worker.sh
- /usr/local/sge/V60u7_1/examples/jobsbin
- /usr/local/sge/V60u7_1/examples/jobsbin/lx26-x86
- /usr/local/sge/V60u7_1/examples/jobsbin/lx26-x86/work
- /usr/local/sge/V60u7_1/man/man1/gethostbyaddr.1
- /usr/local/sge/V60u7_1/man/man1/gethostbyname.1
- /usr/local/sge/V60u7_1/man/man1/gethostname.1
- /usr/local/sge/V60u7_1/man/man1/getservbyname.1
- /usr/local/sge/V60u7_1/man/man1/hostnameutils.1
- /usr/local/sge/V60u7_1/man/man1/qacct.1
- /usr/local/sge/V60u7_1/man/man1/qalter.1
- /usr/local/sge/V60u7_1/man/man1/qconf.1
- /usr/local/sge/V60u7_1/man/man1/qdel.1
- /usr/local/sge/V60u7_1/man/man1/qhold.1
- /usr/local/sge/V60u7_1/man/man1/qhost.1
- /usr/local/sge/V60u7_1/man/man1/qlogin.1
- /usr/local/sge/V60u7_1/man/man1/qmake.1
- /usr/local/sge/V60u7_1/man/man1/qmod.1
- /usr/local/sge/V60u7_1/man/man1/qmon.1
- /usr/local/sge/V60u7_1/man/man1/qping.1
- /usr/local/sge/V60u7_1/man/man1/qresub.1
- /usr/local/sge/V60u7_1/man/man1/qrls.1
- /usr/local/sge/V60u7_1/man/man1/qrsh.1
- /usr/local/sge/V60u7_1/man/man1/qselect.1
- /usr/local/sge/V60u7_1/man/man1/qsh.1
- /usr/local/sge/V60u7_1/man/man1/qstat.1
- /usr/local/sge/V60u7_1/man/man1/qsub.1
- /usr/local/sge/V60u7_1/man/man1/qtcsh.1
- /usr/local/sge/V60u7_1/man/man1/sge_ckpt.1
- /usr/local/sge/V60u7_1/man/man1/sge_intro.1
- /usr/local/sge/V60u7_1/man/man1/sge_types.1
- /usr/local/sge/V60u7_1/man/man1/sgepasswd.1
- /usr/local/sge/V60u7_1/man/man1/submit.1
- /usr/local/sge/V60u7_1/man/man3/drmaa_allocate_job_template.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_attributes.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_control.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_delete_job_template.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_exit.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_get_DRM_system.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_get_attribute.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_get_attribute_names.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_get_contact.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_get_next_attr_name.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_get_next_attr_value.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_get_next_job_id.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_get_vector_attribute.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_get_vector_attribute_names.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_init.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_job_ps.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_jobcontrol.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_jobtemplate.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_misc.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_release_attr_names.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_release_attr_values.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_release_job_ids.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_run_bulk_jobs.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_run_job.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_session.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_set_attribute.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_set_vector_attribute.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_strerror.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_submit.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_synchronize.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_version.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_wait.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_wcoredump.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_wexitstatus.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_wifaborted.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_wifexited.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_wifsignaled.3
- /usr/local/sge/V60u7_1/man/man3/drmaa_wtermsig.3
- /usr/local/sge/V60u7_1/man/man5/access_list.5
- /usr/local/sge/V60u7_1/man/man5/accounting.5
- /usr/local/sge/V60u7_1/man/man5/bootstrap.5
- /usr/local/sge/V60u7_1/man/man5/calendar_conf.5
- /usr/local/sge/V60u7_1/man/man5/checkpoint.5
- /usr/local/sge/V60u7_1/man/man5/complex.5
- /usr/local/sge/V60u7_1/man/man5/host_aliases.5
- /usr/local/sge/V60u7_1/man/man5/host_conf.5
- /usr/local/sge/V60u7_1/man/man5/hostgroup.5
- /usr/local/sge/V60u7_1/man/man5/project.5
- /usr/local/sge/V60u7_1/man/man5/qtask.5
- /usr/local/sge/V60u7_1/man/man5/queue_conf.5
- /usr/local/sge/V60u7_1/man/man5/reporting.5
- /usr/local/sge/V60u7_1/man/man5/sched_conf.5
- /usr/local/sge/V60u7_1/man/man5/sge_aliases.5
- /usr/local/sge/V60u7_1/man/man5/sge_conf.5
- /usr/local/sge/V60u7_1/man/man5/sge_pe.5
- /usr/local/sge/V60u7_1/man/man5/sge_priority.5
- /usr/local/sge/V60u7_1/man/man5/sge_qstat.5
- /usr/local/sge/V60u7_1/man/man5/sge_request.5
- /usr/local/sge/V60u7_1/man/man5/sgepasswd.5
- /usr/local/sge/V60u7_1/man/man5/share_tree.5
- /usr/local/sge/V60u7_1/man/man5/user.5
- /usr/local/sge/V60u7_1/man/man5/usermapping.5
- /usr/local/sge/V60u7_1/man/man8/sge_execd.8
- /usr/local/sge/V60u7_1/man/man8/sge_qmaster.8
- /usr/local/sge/V60u7_1/man/man8/sge_schedd.8
- /usr/local/sge/V60u7_1/man/man8/sge_shadowd.8
- /usr/local/sge/V60u7_1/man/man8/sge_shepherd.8
- sge-utils-V60u7_1-2: Instalation scripts and SGE utilities
- /usr/local/sge/V60u7_1/inst_sge
- /usr/local/sge/V60u7_1/install_execd
- /usr/local/sge/V60u7_1/install_qmaster
- /usr/local/sge/V60u7_1/util
- /usr/local/sge/V60u7_1/util/arch
- /usr/local/sge/V60u7_1/util/arch_variables
- /usr/local/sge/V60u7_1/util/bdb_checkpoint.sh
- /usr/local/sge/V60u7_1/util/create_settings.sh
- /usr/local/sge/V60u7_1/util/dl.csh
- /usr/local/sge/V60u7_1/util/dl.sh
- /usr/local/sge/V60u7_1/util/dl1.csh
- /usr/local/sge/V60u7_1/util/dl2.csh
- /usr/local/sge/V60u7_1/util/install_modules
- /usr/local/sge/V60u7_1/util/install_modules/DB_CONFIG
- /usr/local/sge/V60u7_1/util/install_modules/backup_template.conf
- /usr/local/sge/V60u7_1/util/install_modules/inst_berkeley.sh
- /usr/local/sge/V60u7_1/util/install_modules/inst_common.sh
- /usr/local/sge/V60u7_1/util/install_modules/inst_execd.sh
- /usr/local/sge/V60u7_1/util/install_modules/inst_execd_uninst.sh
- /usr/local/sge/V60u7_1/util/install_modules/inst_qmaster.sh
- /usr/local/sge/V60u7_1/util/install_modules/inst_qmaster_uninst.sh
- /usr/local/sge/V60u7_1/util/install_modules/inst_schedd_high.conf
- /usr/local/sge/V60u7_1/util/install_modules/inst_schedd_max.conf
- /usr/local/sge/V60u7_1/util/install_modules/inst_schedd_normal.conf
- /usr/local/sge/V60u7_1/util/install_modules/inst_template.conf
- /usr/local/sge/V60u7_1/util/install_modules/inst_update.sh
- /usr/local/sge/V60u7_1/util/logchecker.sh
- /usr/local/sge/V60u7_1/util/qtask
- /usr/local/sge/V60u7_1/util/rctemplates
- /usr/local/sge/V60u7_1/util/rctemplates/darwin_template
- /usr/local/sge/V60u7_1/util/rctemplates/sgebdb_template
- /usr/local/sge/V60u7_1/util/rctemplates/sgeexecd_template
- /usr/local/sge/V60u7_1/util/rctemplates/sgemaster_template
- /usr/local/sge/V60u7_1/util/resources
- /usr/local/sge/V60u7_1/util/resources/calendars
- /usr/local/sge/V60u7_1/util/resources/calendars/day
- /usr/local/sge/V60u7_1/util/resources/calendars/day_s
- /usr/local/sge/V60u7_1/util/resources/calendars/night
- /usr/local/sge/V60u7_1/util/resources/calendars/night_s
- /usr/local/sge/V60u7_1/util/resources/centry
- /usr/local/sge/V60u7_1/util/resources/centry/arch
- /usr/local/sge/V60u7_1/util/resources/centry/calendar
- /usr/local/sge/V60u7_1/util/resources/centry/cpu
- /usr/local/sge/V60u7_1/util/resources/centry/h_core
- /usr/local/sge/V60u7_1/util/resources/centry/h_cpu
- /usr/local/sge/V60u7_1/util/resources/centry/h_data
- /usr/local/sge/V60u7_1/util/resources/centry/h_fsize
- /usr/local/sge/V60u7_1/util/resources/centry/h_rss
- /usr/local/sge/V60u7_1/util/resources/centry/h_rt
- /usr/local/sge/V60u7_1/util/resources/centry/h_stack
- /usr/local/sge/V60u7_1/util/resources/centry/h_vmem
- /usr/local/sge/V60u7_1/util/resources/centry/hostname
- /usr/local/sge/V60u7_1/util/resources/centry/load_avg
- /usr/local/sge/V60u7_1/util/resources/centry/load_long
- /usr/local/sge/V60u7_1/util/resources/centry/load_medium
- /usr/local/sge/V60u7_1/util/resources/centry/load_short
- /usr/local/sge/V60u7_1/util/resources/centry/mem_free
- /usr/local/sge/V60u7_1/util/resources/centry/mem_total
- /usr/local/sge/V60u7_1/util/resources/centry/mem_used
- /usr/local/sge/V60u7_1/util/resources/centry/min_cpu_interval
- /usr/local/sge/V60u7_1/util/resources/centry/np_load_avg
- /usr/local/sge/V60u7_1/util/resources/centry/np_load_long
- /usr/local/sge/V60u7_1/util/resources/centry/np_load_medium
- /usr/local/sge/V60u7_1/util/resources/centry/np_load_short
- /usr/local/sge/V60u7_1/util/resources/centry/num_proc
- /usr/local/sge/V60u7_1/util/resources/centry/qname
- /usr/local/sge/V60u7_1/util/resources/centry/rerun
- /usr/local/sge/V60u7_1/util/resources/centry/s_core
- /usr/local/sge/V60u7_1/util/resources/centry/s_cpu
- /usr/local/sge/V60u7_1/util/resources/centry/s_data
- /usr/local/sge/V60u7_1/util/resources/centry/s_fsize
- /usr/local/sge/V60u7_1/util/resources/centry/s_rss
- /usr/local/sge/V60u7_1/util/resources/centry/s_rt
- /usr/local/sge/V60u7_1/util/resources/centry/s_stack
- /usr/local/sge/V60u7_1/util/resources/centry/s_vmem
- /usr/local/sge/V60u7_1/util/resources/centry/seq_no
- /usr/local/sge/V60u7_1/util/resources/centry/slots
- /usr/local/sge/V60u7_1/util/resources/centry/swap_free
- /usr/local/sge/V60u7_1/util/resources/centry/swap_rate
- /usr/local/sge/V60u7_1/util/resources/centry/swap_rsvd
- /usr/local/sge/V60u7_1/util/resources/centry/swap_total
- /usr/local/sge/V60u7_1/util/resources/centry/swap_used
- /usr/local/sge/V60u7_1/util/resources/centry/tmpdir
- /usr/local/sge/V60u7_1/util/resources/centry/virtual_free
- /usr/local/sge/V60u7_1/util/resources/centry/virtual_total
- /usr/local/sge/V60u7_1/util/resources/centry/virtual_used
- /usr/local/sge/V60u7_1/util/resources/loadsensors
- /usr/local/sge/V60u7_1/util/resources/loadsensors/calendar.sh
- /usr/local/sge/V60u7_1/util/resources/loadsensors/ibm-loadsensor
- /usr/local/sge/V60u7_1/util/resources/loadsensors/interix-loadsensor.sh
- /usr/local/sge/V60u7_1/util/resources/loadsensors/load.sh
- /usr/local/sge/V60u7_1/util/resources/loadsensors/maui.sh
- /usr/local/sge/V60u7_1/util/resources/loadsensors/nuser.sh
- /usr/local/sge/V60u7_1/util/resources/loadsensors/sgi_tty_sensor.sh
- /usr/local/sge/V60u7_1/util/resources/loadsensors/solaris-iidle.sh
- /usr/local/sge/V60u7_1/util/resources/pe
- /usr/local/sge/V60u7_1/util/resources/pe/make
- /usr/local/sge/V60u7_1/util/resources/pe/make.sge_pqs_api
- /usr/local/sge/V60u7_1/util/resources/schemas
- /usr/local/sge/V60u7_1/util/resources/schemas/qstat
- /usr/local/sge/V60u7_1/util/resources/schemas/qstat/detailed_job_info.xsd
- /usr/local/sge/V60u7_1/util/resources/schemas/qstat/message.xsd
- /usr/local/sge/V60u7_1/util/resources/schemas/qstat/qstat.xsd
- /usr/local/sge/V60u7_1/util/resources/spooling
- /usr/local/sge/V60u7_1/util/resources/spooling/disable_history.sql
- /usr/local/sge/V60u7_1/util/resources/spooling/history.sh
- /usr/local/sge/V60u7_1/util/resources/spooling/init_postgres.sh
- /usr/local/sge/V60u7_1/util/resources/spooling/init_postgres.sql
- /usr/local/sge/V60u7_1/util/resources/starter_methods
- /usr/local/sge/V60u7_1/util/resources/starter_methods/settaskid.sh
- /usr/local/sge/V60u7_1/util/resources/usersets
- /usr/local/sge/V60u7_1/util/resources/usersets/deadlineusers
- /usr/local/sge/V60u7_1/util/resources/usersets/defaultdepartment
- /usr/local/sge/V60u7_1/util/setfileperm.sh
- /usr/local/sge/V60u7_1/util/sgeCA
- /usr/local/sge/V60u7_1/util/sgeCA/renew_all_certs.csh
- /usr/local/sge/V60u7_1/util/sgeCA/sge_ca
- /usr/local/sge/V60u7_1/util/sgeCA/sge_ssl.cnf
- /usr/local/sge/V60u7_1/util/sgeCA/sge_ssl_template.cnf
- /usr/local/sge/V60u7_1/util/sge_aliases
- /usr/local/sge/V60u7_1/util/sge_log_tee
- /usr/local/sge/V60u7_1/util/sge_request
- /usr/local/sge/V60u7_1/util/sgeremoterun
- /usr/local/sge/V60u7_1/utilbin
- /usr/local/sge/V60u7_1/utilbin/lx26-x86
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/adminrun
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/checkprog
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/checkuser
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/filestat
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/fstype
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/gethostbyaddr
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/gethostbyname
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/gethostname
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/getservbyname
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/infotext
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/loadcheck
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/now
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/qrsh_starter
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/rlogin
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/rsh
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/rshd
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/sge_share_mon
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/spooldefaults
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/spooledit
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/spoolinit
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/testsuidroot
- /usr/local/sge/V60u7_1/utilbin/lx26-x86/uidgid
- sge-V60u7_1-2: Contains the binaries and libraries needed to run sge commands:
- /usr/local/sge/V60u7_1/bin/lx26-x86
- /usr/local/sge/V60u7_1/bin/lx26-x86/qacct
- /usr/local/sge/V60u7_1/bin/lx26-x86/qalter
- /usr/local/sge/V60u7_1/bin/lx26-x86/qconf
- /usr/local/sge/V60u7_1/bin/lx26-x86/qdel
- /usr/local/sge/V60u7_1/bin/lx26-x86/qhold
- /usr/local/sge/V60u7_1/bin/lx26-x86/qhost
- /usr/local/sge/V60u7_1/bin/lx26-x86/qlogin
- /usr/local/sge/V60u7_1/bin/lx26-x86/qmake
- /usr/local/sge/V60u7_1/bin/lx26-x86/qmod
- /usr/local/sge/V60u7_1/bin/lx26-x86/qping
- /usr/local/sge/V60u7_1/bin/lx26-x86/qresub
- /usr/local/sge/V60u7_1/bin/lx26-x86/qrls
- /usr/local/sge/V60u7_1/bin/lx26-x86/qrsh
- /usr/local/sge/V60u7_1/bin/lx26-x86/qselect
- /usr/local/sge/V60u7_1/bin/lx26-x86/qsh
- /usr/local/sge/V60u7_1/bin/lx26-x86/qstat
- /usr/local/sge/V60u7_1/bin/lx26-x86/qsub
- /usr/local/sge/V60u7_1/bin/lx26-x86/qtcsh
- /usr/local/sge/V60u7_1/bin/lx26-x86/sgepasswd
- /usr/local/sge/V60u7_1/lib/lx26-x86/libXltree.so
- /usr/local/sge/V60u7_1/lib/lx26-x86/libcrypto.so
- /usr/local/sge/V60u7_1/lib/lx26-x86/libcrypto.so.0.9.7a
- /usr/local/sge/V60u7_1/lib/lx26-x86/libdrmaa.so
- /usr/local/sge/V60u7_1/lib/lx26-x86/libspoolb.so
- /usr/local/sge/V60u7_1/lib/lx26-x86/libspoolc.so
- /usr/local/sge/V60u7_1/lib/lx26-x86/libssl.so
- /usr/local/sge/V60u7_1/lib/lx26-x86/libssl.so.0.9.7a
- sge-ckpt-V60u7_1-2: For checkpointing purposes;
- sge-parallel-V60u7_1-2: For running parallel environments, as OpenMpi, Mpich, etc;
- sge-qmon-V60u7_1-2: The SGE GUI.
[root@sgetest ~]# rpm -ivh sge-V60u7_1-2.i386.rpm Preparing... ########################################### [100%] 1:sge ########################################### [100%] [root@sgetest ~]# rpm -ivh sge-utils-V60u7_1-2.i386.rpm Preparing... ########################################### [100%] 1:sge-utils ########################################### [100%] [root@sgetest ~]# rpm -ivh sge-daemons-V60u7_1-2.i386.rpm Preparing... ########################################### [100%] 1:sge-daemons ########################################### [100%] [root@sgetest ~]# rpm -ivh sge-docs-V60u7_1-2.i386.rpm Preparing... ########################################### [100%] 1:sge-docs ########################################### [100%] [root@sgetest ~]# rpm -ivh edg-sge-utils-1.0.0-1.noarch.rpm Preparing... ########################################### [100%] 1:edg-sge-utils ########################################### [100%] [root@sgetest ~]#The SGE rpms will install all files under the directory /usr/local/sge/V60u7_1. Automatically, the rpms will link /usr/local/sge/pro to /usr/local/sge/V60u7_1 and $SGE_ROOT will be later defined as /usr/local/sge/pro. In this way, we can keep old SGE versions and use them when needed. For that, we just have to change the "pro link".
[root@sgetest ~]# ll /usr/local/sge total 4 lrwxrwxrwx 1 root root 7 Nov 9 16:40 pro -> V60u7_1 drwxr-xr-x 11 root root 4096 Nov 9 16:41 V60u7_1
Grid WNs instalation
To automatically install SGE GRID WNs using yaim we have created the glite-yaim-sge-3.0.0-1.i386.rpm ( glite-yaim-sge-3.0.0-1.i386
). This rpm requires that the following packages should already be present in your system... - Requires: glite-yaim = 3.0.0-34
- Requires: sge = V60u7_1-2 ( sge-V60u7_1-2)
- Requires: sge-daemons = V60u7_1-2 sge-daemons-V60u7_1-2)
- Requires: sge-docs = V60u7_1-2 ( sge-docs-V60u7_1-2)
- Requires: sge-utils = V60u7_1-2 ( sge-utils-V60u7_1-2)
- Requires: edg-sge-utils = 1.0.2-1( edg-sge-utils-1.0.2-1)
- /opt/glite/yaim/scripts/node-info-sge.def: File which defines a new node, called WN_sge, and the corresponding functions associated to that node. This file is copied to /opt/glite/yaim/scripts/node-info.def after the rpm instalation.
[root@sgetest ~]# cat /opt/glite/yaim/scripts/node-info-sge.def | grep WN_sge
WN_sge_FUNCTIONS="${WN_FUNCTIONS} config_sge_client"
- /opt/glite/yaim/functions/config_sge_client: This is the function which configures the SGE WN. It builds a configuration file /opt/glite/yaim/scripts/execd.conf used as input to the perl script opt/glite/yaim/scripts/configure_sgeclient.pm. Most variables within this configuration file are static since they depend on the SGE instalation paths defined in the rpms excepting 3 ones which have to be defined in the site-info.def file:
- SGE_QMASTER: Machines which will be working has the SGE QMASTER;
- DEFAULT_DOMAIN: lip.pt for lip case;
- ADMIN_MAIL: your email;
[root@sgetest ~]# cat /opt/glite/yaim/functions/config_sge_client
config_sge_client(){
requires CE_HOST SGE_QMASTER DEFAULT_DOMAIN ADMIN_MAIL
se_host="${SE_LIST%% *}"
cat <<EOF > /opt/glite/yaim/scripts/execd.conf
SGE_ROOT="/usr/local/sge/pro"
SGE_QMASTER="$SGE_QMASTER"
SGE_QMASTER_PORT="536"
SGE_EXECD_PORT="537"
SGE_CELL_NAME="default"
EXEC_HOST_LIST="$HOSTNAME"
EXECD_SPOOL_DIR_LOCAL="/usr/local/sge/pro/default/spool"
HOSTNAME_RESOLVING="true"
DEFAULT_DOMAIN="$DEFAULT_DOMAIN"
SET_FILE_PERMS="true"
ADMIN_USER="none"
ADMIN_MAIL="$ADMIN_MAIL"
ADD_TO_RC="true"
EOF
ln -s /usr/local/sge/V60u7_1 /usr/local/sge/pro
/opt/glite/yaim/scripts/configure_sgeclient.pm /opt/glite/yaim/scripts/execd.conf
chmod 0755 /etc/init.d/sgeexecd
chkconfig --level 2345 sgeexecd on
/etc/init.d/sgeexecd start
source /usr/local/sge/pro/default/common/settings.sh
cat <<EOF > /etc/ssh/ssh_config
Host *
Protocol 2,1
RhostsAuthentication yes
RhostsRSAAuthentication yes
RSAAuthentication yes
PasswordAuthentication yes
EnableSSHKeysign yes
HostbasedAuthentication yes
EOF
cat << EOF > /opt/edg/etc/edg-sge-knownhosts.conf
NODES = $CE_HOST $se_host
SGEBIN = /usr/local/sge/pro/bin
KEYTYPES = rsa1,rsa,dsa
KNOWNHOSTS = /etc/ssh/ssh_known_hosts
EOF
# workaround for duplicate key entries (Savannah bug 5530)
for hostname in $CE_HOST $se_host; do
if [ -f /etc/ssh/ssh_known_hosts ];then
grep -v $hostname /etc/ssh/ssh_known_hosts > /etc/ssh/ssh_known_hosts.tmp
/usr/bin/ssh-keyscan -t rsa $hostname >> /etc/ssh/ssh_known_hosts.tmp 2>/dev/null
if [ $? = 0 ]; then
mv /etc/ssh/ssh_known_hosts.tmp /etc/ssh/ssh_known_hosts
fi
fi
done
/opt/edg/sbin/edg-sge-knownhosts
cron_job edg-sge-knownhosts root "03 1,7,13,19 * * * /opt/edg/sbin/edg-sge-knownhosts"
return 0
}
- /opt/glite/yaim/scripts/configure_sgeclient.pm: This is the perl script which sets the proper environment, checks the configuration files, configures the sge ports and builds/starts the sge daemons.
[root@sgetest ~]# /opt/glite/yaim/scripts/configure_node /root/site-cfg/site-info-egee.def WN_sgeFor a sucessful configuration, the machine has to be already declared in the SGE qmaster as an administrative and exec host and should be already added to a given queue. You should not forget that some SGE related variables will have to be defined in your site-info-egee.def file. For LIP case, they are:
- SGE_QMASTER="sge01.lip.pt"
- DEFAULT_DOMAIN="lip.pt"
- ADMIN_MAIL="goncalo@lip.pt"
(...) Configuring config_sge_client ln: `/usr/local/sge/pro/V60u7_1': File exists /usr/local/sge/pro/default directory does not exist! Creating /usr/local/sge/pro/default ... /usr/local/sge/pro/default/common directory does not exist! Creating /usr/local/sge/pro/default/common ... /usr/local/sge/pro/default/common/act_qmaster file does not exist! Creating /usr/local/sge/pro/default/common/act_qmaster ... /usr/local/sge/pro/default/common/bootstrap file does not exist! Creating /usr/local/sge/pro/default/common/bootstrap ... /usr/local/sge/pro/default/common/settings.sh file does not exist! Creating /usr/local/sge/pro/default/common/settings.sh ... starting sge_execd Configuration CompleteIt simply reports the building of files and directories needed by SGE. The sge_execd daemon should be running after the WN configuration...
[root@sgetest ~]# ps xua | grep sge_execd root 25009 0.0 0.2 6108 1536 ? S 19:38 0:00 /usr/local/sge/pro/bin/lx26-x86/sge_execdand the machine should be recognized as an execution host in SGE QMASTER:
[root@sge01 ~]# qhost HOSTNAME ARCH NCPU LOAD MEMTOT MEMUSE SWAPTO SWAPUS -------------------------------------------------------------------------------------------------------------- sgetest lx26-x86 1 0.29 503.1M 50.8M 1019.7M 208.0K
NOTES:
- The packages have dependencies with libdb-4.2:
# rpm -ihv sge-V60u7_1-2.i386.rpm sge-utils-V60u7_1-2.i386.rpm sge-daemons-V60u7_1-2.i386.rpm sge-qmon-V60u7_1-2.i386.rpm sge-ckpt-V60u7_1-2.i386.rpm sge-parallel-V60u7_1-2.i386.rpm sge-docs-V60u7_1-2.i386.rpm
error: Failed dependencies:
libdb-4.2.so is needed by sge-V60u7_1-2
libdb-4.2.so is needed by sge-utils-V60u7_1-2 install them with the options ' --force ' and ' --nodeps '. - In the CE configuration node-info.def is not overwritten by the one that the package provided. Maybe this instruction is missing. In the WN it works.
- After running "configure_node site-info.def CE_sge BDII_Site' the gatekeeper is not launched, because the file lcgsge.pm is not found (only the file lcgsge.conf).
- In order to install perl_XML_Simple we had to download it by using CPAN:
perl -MCPAN -e 'install XML::Simple' - According to the document, a previous requisite is to have a basic installation with LCG CE and WN. We think this is not necessary, because the configuration with CE_sge and WN_sge calls to the CE and WN functions.
- Opened a bug ( https://savannah.cern.ch/bugs/index.php?23638) related to the obligation of using the parameter TORQUE_SERVER, even when it is not needed. Have a look to the functions config_gip (line 318) and config_gip_scheduler_pluging (line 3).
LIP SGE implementation
DISCLAIMER: PART OF THE WORK DESCRIBED IN THESE PAGES WAS DEVELOPED BY LIP STAFF AND IT IS BASED ON EXISTING WORK IMPLEMENTED BY OTHER INSTITUTES. IT MAY BE NOT FULLY OPTIMIZED OR CORRECT AND THEREFORE, IT SHOULD BE CONSIDERED AS EXPERIMENTAL.LIP SGE jobmanager
The standard LCG CE middleware is distributed with a standard jobmanager perl script which allows to submit and query job status using PBS batch system. Obviously, if local administrators wish to use a different scheduler, the jobmanager script has to be adapted to it. LIP is testing SGE scheduler and the corresponding jobmanager implementation was built by Juan Fontan@CESGA ( CESGA SGE jobmanager). CESGA jobmanager should be implemented for non-shared home directories and basicaly derives from the standard PBS script.Introduction
LIP SGE lcgsge.pm file ( LIP SGE jobmanager) is found under the CE /opt/globus/lib/perl/Globus/GRAM/JobManager directory. Very small changes were made with respect to the original CESGA implementation. We will give a very short explanation of the lcgsge.pm workflow since a more detailed description will be reported by CESGA staff.
The lcgsge.pm workflow
The lcgsge.pm script is divided in many different sections and subroutines. It starts with a section defining all relevant inputs which allow a clean SGE interaction, such as SGE binaries paths and environment variables:
BEGIN
{
###
# [GBorges]
# Define SGE_ROOT enviroment variables
$SGE_ROOT = '/usr/local/sge/V60u7_1';
$SGE_CELL = 'default';
$SGE_RELEASE = '6.0u7_1';
$ENV{'SGE_ROOT'} = $SGE_ROOT;
$ENV{'SGE_CELL'} = $SGE_CELL;
###
# [GBorges]
# Define SGE commands
$qsub = '/usr/local/sge/V60u7_1/bin/lx26-x86/qsub';
$qstat = '/usr/local/sge/V60u7_1/bin/lx26-x86/qstat';
$qdel = '/usr/local/sge/V60u7_1/bin/lx26-x86/qdel';
$qconf = '/usr/local/sge/V60u7_1/bin/lx26-x86/qconf';
###
# [GBorges]
# Define supported jobs
$mpirun = 'no';
$sge_mpirun = 'no';
if (($mpirun eq "no") && ($sge_mpirun eq "no"))
{
$supported_job_types = "(single|multiple)";
}
else
{
$supported_job_types = "(mpi|single|multiple)";
}
$cluster = 0;
$cpu_per_node = 0;
$remote_shell = '/usr/bin/ssh';
}
Afterwards, it defines different subroutines which are called by Globus package scripts and allows to interact with SGE batch system:
- subroutine submit: Checks if the RSL arguments transmitted by Globus package are valid and supported. If the RSL arguments are not supported, then the corresponding globus error code should be activated;
sub submit
{
my $self = shift;
my ($cpu_time,$wall_time);
my $description = $self->{JobDescription};
local $arguments = $description->arguments();
local $count = $description->count();
local $directory = $description->directory();
local $email_address = $description->email_address();
local $emailonabort = $description->emailonabort();
local $emailonexecution = $description->emailonexecution();
local $emailonsuspend = $description->emailonsuspend();
local $emailontermination = $description->emailontermination();
local $executable = $description->executable();
local $hostcount = $description->host_count();
local $jobtype = $description->jobtype();
local $logfile = $description->logfile();
local $max_cpu_time = $description->max_cpu_time();
local $max_memory = $description->max_memory();
local $max_time = $description->max_time();
local $max_wall_time = $description->max_wall_time();
local $parallel_environment = $description->parallel_environment();
local $project = $description->project();
local $queue = $description->queue();
local $stderr = $description->stderr();
local $stdin = $description->stdin();
local $stdout = $description->stdout();
###
# [GBorges]
# Debug file in /tmp/JobManager-lcgsge.log
chop($date=`date`);
open FILELOG,'>>/tmp/JobManager-lcgsge.log';
print FILELOG "ARGUMENTS = ",$arguments,"\n";
print FILELOG "COUNT = ",$count,"\n";
print FILELOG "DIRECTORY = ",$directory,"\n";
print FILELOG "EMAIL ADRESS = ",$email_address,"\n";
print FILELOG "EMAIL ON ABORT = ",$emailonabort,"\n";
print FILELOG "EMAIL ON EXECUTION = ",$emailonexecution,"\n";
print FILELOG "EMAIL ON SUSPEND = ",$emailonsuspend,"\n";
print FILELOG "EMAIL ON TERMINATION = ",$emailontermination,"\n";
print FILELOG "EXECUTABLE = ",$executable,"\n";
print FILELOG "HOST COUNT = ",$hostcount,"\n";
print FILELOG "JOBTYPE = ",$jobtype,"\n";
print FILELOG "LOGFILE = ",$logfile,"\n";
print FILELOG "MAX CPU TIME = ",$max_cpu_time,"\n";
print FILELOG "MAX MEMORY = ",$max_memory,"\n";
print FILELOG "MAX TIME = ",$max_time,"\n";
print FILELOG "MAX_WALL_TIME = ",$max_wall_time,"\n";
print FILELOG "PARALLEL ENVIROMENT = ",$parallel_environment,"\n";
print FILELOG "PROJECT = ",$project,"\n";
print FILELOG "QUEUE = ",$queue,"\n";
print FILELOG "STDERR = ",$stderr,"\n";
print FILELOG "STDIN = ",$stdin,"\n";
print FILELOG "STDOUT = ",$stdout,"\n";
close FILELOG;
$self->log("Entering sge submit");
#####
# check jobtype
if (defined($jobtype))
{
if ($jobtype !~ /^$supported_job_types$/)
{
return Globus::GRAM::Error::JOBTYPE_NOT_SUPPORTED;
}
}
#####
# check directory
if ( !defined $directory || $directory eq "")
{
return Globus::GRAM::Error::RSL_DIRECTORY();
}
#####
# check executable
if ( !defined $executable || $executable eq "")
{
return Globus::GRAM::Error::RSL_EXECUTABLE();
}
elsif ( !defined $stdin || $stdin eq "")
{
return Globus::GRAM::Error::RSL_STDIN;
}
#####
# Determining job max time cpu from job description
$self->log("Determining job max time cpu from job description");
if (defined($description->max_cpu_time()))
{ $cpu_time = $description->max_cpu_time();
$self->log(" using maxcputime of $cpu_time");
}
elsif (! $cluster && defined($description->max_time()))
{ $cpu_time = $description->max_time();
$self->log(" using maxtime of $cpu_time");
}
else
{ $cpu_time = 0;
$self->log(' using queue default');
}
#####
# Determining job max wall time from job description
$self->log("Determining job max wall time limit from job description");
if (defined($description->max_wall_time()))
{ $wall_time = $description->max_wall_time();
$self->log(" using maxwalltime of $wall_time");
}
elsif ($cluster && defined($description->max_time()))
{ $wall_time = $description->max_time();
$self->log(" using maxtime of $wall_time");
}
else
{ $wall_time = 0;
$self->log(' using queue default');
}
foreach ($description->environment())
{ if(!ref($_) || scalar(@$_) != 2)
{ return Globus::GRAM::Error::RSL_ENVIRONMENT();
}
}
foreach($description->arguments())
{ if(ref($_))
{ return Globus::GRAM::Error::RSL_ARGUMENTS;
}
}
my $job_id = $self->queue_submit("lcgsge",$cpu_time."|".$wall_time);
$self->log("Leaving sge submit");
return
{ JOB_ID => $job_id,
JOB_STATE => Globus::GRAM::JobState::PENDING
} if defined $job_id;
return Globus::GRAM::Error::NO_RESOURCES;
}
* subroutine poll_batch_system: Allows to know the status of jobs running in the site cluster parsing the output of the qstat SGE command.
sub poll_batch_system
{
###
# [GBorges]
# Debug outputs
chop($date=`date`);
open FILELOG,'>>/tmp/JobManager-lcgsge.log';
print FILELOG "POLL_BATCH_SYSTEM subroutine: Entering on $date \n";
my $self = shift;
# @_ is the parameter array for subroutines
my ($data_ref,$time_ref) = @_;
my $good_query = 0;
do
{ @$data_ref = ();
$$time_ref = time();
local(*JQ);
if (open(JQ,"export SGE_ROOT=/usr/local/sge/V60u7_1 ; $qstat 2>/dev/null |"))
{ my $jid;
while(<JQ>)
{ chomp(my $line = $_);
####
# [GBorges]
# Try to understand the regular expression
# "/ /" = Search $line variable for a given pattern
# "^" = Matches the beguining of the target
# " *" = Matches the space character zero or more times
# $1 = "(\d+)" = Matches digit one or more times
# "\d\.\d+" = Matches one digit followed by a dot followed by one or more digits
# "[^ ]*" = Matches anything except the space character zero or more times
# $2 = "(\w+)" = matches alphanumeric one or more times
#
if ($line =~ /^ *(\d+) +\d\.\d+ +[^ ]* +[^ ]* +(\w+)/)
{ my $st = $2;
$jid = $1;
###
# GBorges
# Stores jobid and its status
push(@$data_ref,$jid." ".$st);
print FILELOG "---> Parsing QSTAT output: Job ",$jid," status is ",$st,"\n";
}
}
close(JQ);
$good_query = 1 if $? == 0;
sleep 30 if !$good_query;
}
else
{ ###
# [GBorges]
# Debug outputs
print FILELOG "---> QSTAT output not available \n";
$good_query = -1;
}
} while($good_query != 1);
###
# [GBorges]
# Debug outputs
chop($date=`date`);
print FILELOG "POLL_BATCH_SYSTEM subroutine: Leaving on $date \n";
close FILELOG;
}
- subroutine poll: Allows to link the present status of jobs running in the site cluster with the correct Globus messages which have to generated.
sub poll
{
###
# [GBorges]
# Debug outputs
chop($date=`date`);
open FILELOG,'>>/tmp/JobManager-lcgsge.log';
print FILELOG "POLL subroutine: Entering on $date \n";
my $self = shift;
my $description = $self->{JobDescription};
my $job_id = $description->job_id();
my $state;
my $status_line;
my $job_out = $description->stdout();
my $job_err = $description->stderr();
my $internal_id = $description->jobid();
my ($batch_id,$job_submit_time);
$self->lookup_or_submit(\$batch_id,\$job_submit_time,\$state);
$self->log("polling job $batch_id") if defined $batch_id;
###
# [GBorges]
# The "make_a_poll_query" function belongs to the Helper.pm and will call the "pool_batch_system" function inside this
# jobmanager. A list of jobs identifiers and their status (filled in the "pool_batch_system" function) is available through the @data array
my @data;
my $query_ret = $self->make_a_poll_query(".lcgjm","sgequeue.cache",$job_submit_time,\@data);
print FILELOG "---> QUERY_RET ",$query_ret,"\n";
print FILELOG "---> STATE ",$state,"\n";
if ( !defined $state )
{ my $exit_code = 153;
my $status_line;
foreach my $line (@data)
{ my $jid;
print FILELOG "---> LINE ",$line,"\n";
###
# [GBorges]
# Regular expression
# "^" = Matches the beguining of the target
# $1 = "(\S+)" = Matches no whitespaces one or more times
# "\s+" = Matches whitespaces one or more times
# $2 = "(\S+)" = Matches no whitespaces one or more times
# "$" = End of string
if ($line =~ /^(\S+)\s+(\S+)$/)
{ ($jid,$status_line) = ($1,$2);
###
# [GBorges]
# Current job id matches one of the few job ids stored in the @data array
if ($jid eq $batch_id)
{ print FILELOG "---> Job ",$jid," found in the batch system \n";
$self->log(" Job found: " . $jid . ' | ' . $status_line );
$exit_code = 0;
last;
}
}
}
###
# return code 153 = "Unknown Job Id". Verifying that the job is no longer there.
if ($exit_code == 153)
{ if ($query_ret)
{ ###
# [GBorges]
# Debug Outputs
print FILELOG "---> Job is DONE with exit_code 153 \n";
$self->log("qstat rc is 153 == Unknown Job ID == DONE");
$state = Globus::GRAM::JobState::DONE;
}
else
{ ###
# [GBorges]
# Debug Outputs
print FILELOG "---> Job is PENDING with exit_code 153 \n";
$self->log("Job not found, assuming it is PENDING");
$state = Globus::GRAM::JobState::PENDING;
}
}
else
{ $_ = $status_line;
###
# [GBorges]
# Check if the last char of variable $_ matches any of the following chars
if(/[EqhwtT]$/)
{ if (/[E]$/)
{ ###
# [GBorges]
# Debug Outputs
print FILELOG "---> Job has FAILED \n";
$self->cancel();
$state = Globus::GRAM::JobState::FAILED;
}
else
{ ###
# [GBorges]
# Debug Outputs
print FILELOG "---> Job is PENDING \n";
$state = Globus::GRAM::JobState::PENDING;
}
}
elsif(/[sS]$/)
{ ###
# [GBorges]
# Debug Outputs
print FILELOG "---> Job is SUSPENDED \n";
$state = Globus::GRAM::JobState::SUSPENDED
}
elsif(/[rR]$/)
{ ###
# [GBorges]
# Debug Outputs
print FILELOG "---> Job is RUNNING \n";
$state = Globus::GRAM::JobState::ACTIVE;
}
else
{ ###
# This else is reached by an unknown response from SGE. It could be that SGE was temporarily unavailable, but it can
# recover and the submitted job is fine. So, we want the JM to ignore this poll and keep the same state as the previous state.
# Returning an empty hash below will tell the JM to ignore the respose.
$self->log("qstat returned an unknown response. Telling JM to ignore this poll");
return {};
}
}
}
###
# [GBorges]
# Debug Outputs
chop($date=`date`);
print FILELOG "POLL subroutine: Leaving on $date \n";
close FILELOG;
$self->helper_cache_import($internal_id,$batch_id,$job_submit_time,\$state,"batch.out","batch.err");
return { JOB_STATE => $state};
}
- subroutine cancel_in_batch_system: Cancels jobs in the local cluster using fork
sub cancel_in_batch_system
{ ###
# [GBorges]
# Debug output
chop($date=`date`);
open FILELOG,'>>/tmp/JobManager-lcgsge.log';
print FILELOG "CANCEL_IN_BATCH_SYSTEM subroutine: Entering on $date \n";
my $self = shift;
my ($batch_id) = @_;
my $description = $self->{JobDescription};
###
# [GBorges]
# Debug output
print FILELOG "Canceling Job ID $batch_id with $qdel cmd on $date \n";
$self->log("cancel job $batch_id");
$self->cd_fork_and_exec_cmd(undef,0,0,$qdel,$batch_id);
###
# [GBorges]
# Debug output
chop($date=`date`);
print FILELOG "CANCEL_IN_BATCH_SYSTEM subroutine: Leaving on $date \n";
close FILELOG;
if($? == 0 || $? == 153)
{ return { JOB_STATE => Globus::GRAM::JobState::FAILED };
}
return Globus::GRAM::Error::JOB_CANCEL_FAILED();
}
- submit_to_batch_system: Allows to submit jobs to the batch system. From the variables filled with the RSL arguments, this subroutine starts to build the script which will latter be submitted to the local SGE batch system. The main difference with respect to CESGA jobmanager script concerns about a "local hack" used to run mpi jobs with mpich2 using SGE parallel environments.
sub submit_to_batch_system
{ ###
# [GBorges]
# Debug Output
chop($date=`date`);
open FILELOG,'>>/tmp/JobManager-lcgsge.log';
print FILELOG "SUBMIT_TO_BATCH_SYSTEM subroutine: Entering on $date \n";
my $self = shift;
my ($submit_arg) = @_;
my ($cpu_time,$wall_time) = split('\|',$submit_arg);
my $description = $self->{JobDescription};
my $tag = $description->cache_tag() || $ENV{GLOBUS_GRAM_JOB_CONTACT};
my $cache_pgm = "$Globus::Core::Paths::bindir/globus-gass-cache";
print FILELOG "---> Cpu time = ",$cpu_time,"\n";
print FILELOG "---> Wall time = ",$wall_time,"\n";
###
# [JFontan]
# Define real and fake stdout/stderr
my $real_stdout;
my $real_stderr;
my $fake_stdout;
my $fake_stderr;
my $script_url = "$tag/sge_job_script";
$self->cd_fork_and_exec_cmd(undef,0,0,$cache_pgm,"-add","-t",$tag,"-n",$script_url,"file:/dev/null");
my $sge_job_script_name = `$cache_pgm -query -t $tag $script_url`;
chomp($sge_job_script_name);
if($sge_job_script_name eq "")
{ return "FAILED";
}
###
# [GBorges]
# Start to build SGE script: Writting script header
my $sge_job_script = new IO::File($sge_job_script_name, '>');
$sge_job_script->print("#!/bin/sh\n");
$sge_job_script->print("# SGE batch job script built by Globus job manager\n");
$sge_job_script->print("#\$ -S /bin/sh\n");
$sge_job_script->print("#\$ -l h_fsize=5G\n");
###
# [GBorges]
# Define to whom and when send email. I don't find the necessary jdl instructions to implement email notification.
if (defined $description->email_address() && $description->email_address() ne '')
{ print FILELOG "---> Monitoring job emailing to ",$description->email_address(),"\n";
$self->log("Monitoring job emailing to " . $description->email_address() );
$sge_job_script->print("#\$ -M " . $description->email_address() . "\n");
}
if(defined $description->emailonabort() && $description->emailonabort() eq 'yes')
{ print FILELOG "---> Email when job is aborted \n";
$self->log("Email when job is aborted");
$email_when .= 'a';
}
if(defined $description->emailonexecution() && $description->emailonexecution() eq 'yes')
{ print FILELOG "---> Email at the beginning of job \n";
$self->log("Email at the beginning of job");
$email_when .= 'b';
}
if(defined $description->emailontermination() && $description->emailontermination() eq 'yes')
{ print FILELOG "---> Email at the end of job \n";
$self->log("Email at the end of job");
$email_when .= 'e';
}
if(defined $description->emailonsuspend() && $description->emailonsuspend() eq 'yes')
{ print FILELOG "---> Email when job is suspended \n";
$self->log("Email when job is suspended");
$email_when .= 's';
}
# Matches one of the chars inside square brackets one or more times
if($email_when =~ /[abes]+/ )
{ $sge_job_script->print("#\$ -m $email_when\n");
}
else
{ print FILELOG "---> Do not send email(s) \n";
$self->log("Do not send email(s)");
}
###
# [GBorges]
# Submit to correct queue
if (defined $description->queue() && $description->queue() ne '')
{ $sge_job_script->print("#\$ -q ". $description->queue() . "\n");
}
###
# [GBorges]
# Some important SGE definitions
# s_cpu : The per-process CPU time limit in seconds.
# s_core : The per-process maximum core file size in bytes.
# s_data : The per-process maximum memory limit in bytes.
# s_vmem : The same as s_data (if both are set the minimum is used).
# h_cpu : The per-job CPU time limit in seconds.
# h_data : The per-job maximum memory limit in bytes.
# h_vmem : The same as h_data (if both are set the minimum is used).
# h_fsize : The total number of disk blocks that this job can create.
# s_rt and h_rt define the "real time" or also called "elapsed" or
# "wall clock" time having passed since the start of the job. If h_rt is
# exceeded by a job running in the queue, it is aborted via the SIGKILL
# signal (see kill(1)). If s_rt is exceeded, the job is first "warned"
# via the SIGUSR1 signal (which can be caught by the job) and finally
# aborted after the notification time defined in the queue configuration
# parameter notify (see above) has passed.
###
# [GBorges]
# Cpu time and Wall time are passed as arguments (array @_) to this subroutine. All values are in minutes and one had
# to compute the appropriate SGE format [hh_mm_ss]
if($cpu_time != 0)
{ my $total_cpu_time;
if($description->jobtype() eq 'multiple')
{ $total_cpu_time = $cpu_time * $description->count();
}
else
{ $total_cpu_time = $cpu_time;
}
###
# [GBorges]
# Put in proper SGE format
my $total_cpu_time_m = $total_cpu_time % 60;
my $total_cpu_time_h = ($total_cpu_time - $total_cpu_time_m)/60;
# $sge_job_script->print("#\$ -l h_cpu=${total_cpu_time_h}:${total_cpu_time_m}:00\n");
print FILELOG "---> Max cpu time defined = ",${total_cpu_time_h},":",${total_cpu_time_m},":00\n";
}
else
{ print FILELOG "---> No max cpu time defined. Use a default value of 10 hours \n";
$self->log("No max cpu time defined. Use a default value of 10 hours");
# $sge_job_script->print("#\$ -l h_cpu=10:00:00\n");
}
if($wall_time != 0)
{ my $total_wall_time;
if($description->jobtype() eq 'multiple')
{ $total_wall_time = $wall_time * $description->count();
}
else
{ $total_wall_time = $wall_time;
}
###
# [GBorges]
# Put in proper SGE format
my $total_wall_time_m = $total_wall_time % 60;
my $total_wall_time_h = ($total_wall_time - $total_wall_time_m)/60;
$sge_job_script->print("#\$ -l h_rt=${total_wall_time_h}:${total_wal_time_m}:00\n");
print FILELOG "---> Max wall time defined = ",${total_wall_time_h},":",${total_wall_time_m},":00\n";
}
else
{ print FILELOG "---> No max wall time defined. Use a default value of 20 hours \n";
$self->log("No max wall time defined. Use a default value of 20 hours");
# $sge_job_script->print("#\$ -l h_rt=20:00:00\n");
}
###
# [GBorges]
# Define max memory to run job
if(defined $description->max_memory() && $description->max_memory() != 0)
{ my $max_memory;
if($description->jobtype() eq 'multiple')
{ $max_memory = $description->max_memory() * $description->count;
}
else
{ $max_memory = $description->max_memory();
}
# $sge_job_script->print("#\$ -l s_vmem=${max_memory}M\n");
}
else
{ # $sge_job_script->print("#\$ -l h_vmem=512M\n");
}
chomp(my $my_hostname = `hostname -f`);
mkdir '.lcgjm', 0700;
chomp(my $pwd=`pwd`);
chomp(my $cache_export_dir = `mktemp -d $pwd/.lcgjm/globus-cache-export.XXXXXX`);
$self->helper_init_cache_export_url($cache_export_dir);
###
# [JFontan]
# Deal with stdout/stderr
# make .out and .err unique names
my $r_number=int(rand(65536));
$real_stdout=$cache_export_dir."/batch.out";
$real_stderr=$cache_export_dir."/batch.err";
$fake_stdout=$pwd."/.out.".$r_number;
$fake_stderr=$pwd."/.err.".$r_number;
$sge_job_script->print("#\$ -o " . $fake_stdout . "\n");
$sge_job_script->print("#\$ -e " . $fake_stderr . "\n");
###
# GBorges
# Code is not rerunable
$sge_job_script->print("#\$ -r n\n");
my @tmp_list = split("/",$cache_export_dir);
my $gpg_file = pop(@tmp_list);
$gpg_file .= ".gpg";
###
# [GBorges]
# It seems there is no use to this
# [JFontan]
# stagein is not implemented in SGE, have to deal with that other way
# $sge_job_script->print("#PBS -W stagein=".$gpg_file."@".$my_hostname.":".$cache_export_dir."/".$gpg_file."\n");
###
# GBorges
# Get user environment variables
# X509_USER_PROXY, GLOBUS_REMOTE_IO_URL, GLOBUS_TCP_PORT_RANGE,
# GLOBUS_LOCATION, GLOBUS_GRAM_JOB_CONTACT, GLOBUS_GRAM_MYJOB_CONTACT,
# SCRATCH_DIRECTORY, HOME, LOGNAME, EDG_WL_JOBID
my @user_env;
foreach my $tuple ($description->environment())
{ $tuple->[0] =~ s/"/\\\"/g;
$tuple->[1] =~ s/"/\\\"/g;
$self->helper_armour(\$tuple->[0]);
$self->helper_armour(\$tuple->[1]);
push(@user_env, $tuple->[0] . "=" . '"' . $tuple->[1] . '"');
}
###
# [GBorges]
# This is a very tricky part !!!
# We pretend to run mpi jobs without using mpirun. These jobs are
# treated as jobtype="single" but with count() > 1. In this case,
# we have to initialize the parallel environment and define the number
# of slots needed to run the job, which in general can be different from
# the number of cpus.
my $userlog;
my $userdir;
if (defined $description->count() && $description->count() > 1 )
{ ###
# Search for grid user HOME and LOGNAME environment variables
#
foreach my $env_line (@user_env)
{ # split string in array
@env_strings=split(/=/,$env_line);
if (@env_strings[0] eq "HOME")
{ $userdir=@env_strings[1];
# regular expression: replace all occurances of pattern "
$userdir=~s/"//g;
}
if (@env_strings[0] eq "LOGNAME")
{ $userlog=@env_strings[1];
# regular expression: replace all occurances of pattern "
$userlog=~s/"//g;
}
}
###
# [GBorges]
# Check if old .smpd file exists and delete it
my $smpdfile = "$userdir/.smpd";
my $smpdfilesize = -s $smpdfile;
if ($smpdfilesize >= 0)
{ $self->cd_fork_and_exec_cmd(undef,0,0,"/bin/rm","-f",$smpdfile); }
###
# [GBorges]
# Create .smpd file in the grid user home directory
# Change permissions and ownership of the .smpd file
my $pass_number=int(rand(65536));
open(SPMD, "> $smpdfile");
print SPMD "phrase=",$pass_number,"\n";
close SPMD;
# change file owner
($login,$pass,$uid,$gid)=getpwnam($userlog);
chown $uid, $gid, $smpdfile;
# change file permissions
my $mode = 0600;
chmod $mode, $smpdfile;
###
# [GBorges]
# Get the parallel environment parsing though the
# queue configuration output given by "qconf -sq <queue>"
my $queue = $description->queue();
open(QCONF, "$qconf -sq $queue |") ||
die "Unable to lookup queue parallel environment with qconf: $!";
foreach (<QCONF>)
{ # If line contains only whitespace, skip.
if (/^\s*$/) { next; }
# parse the key and value from the output
my ($key, $value) = split;
if ($key eq "pe_list")
{ chomp $value;
my $sge_pe = $value;
# Set parallel environment with the number of slots
$sge_job_script->print("#\$ -pe $sge_pe " .$description->count(). "\n");
}
}
close QCONF;
}
my @library_vars=('LD_LIBRARY_PATH');
if($Config::Config{osname} eq 'irix')
{ push(@library_vars,'LD_LIBRARYN32_PATH');
push(@library_vars,'LD_LIBRARY64_PATH');
}
###
# [GBorges]
# Fill environment variables in a single array
my $rsh_env = "";
my $local_x509 = '-';
my @new_env;
foreach my $tuple ($description->environment())
{ $tuple->[0] =~ s/"/\\\"/g;
$tuple->[1] =~ s/"/\\\"/g;
$self->helper_armour(\$tuple->[0]);
$self->helper_armour(\$tuple->[1]);
push(@new_env, $tuple->[0] . "=" . '"' . $tuple->[1] . '"');
$local_x509 = $tuple->[1] if $tuple->[0] eq 'X509_USER_PROXY';
$rsh_env .= $tuple->[0] . "=\"" . $tuple->[1] . "\"\n"
. "export " . $tuple->[0] . "\n";
}
###
# [GBorges]
# Add environment variable needed for mpi jobs
# MPIEXEC_RSH must be set for mpirun to use ssh
# PBS_NODEFILE must be set because it is the default machine
# file used in the RB wrapper
my $queue = $description->queue();
my $machinefile = "/tmp/\$JOB_ID.1.$queue/machines";
push(@new_env,"MPIEXEC_RSH=" . '"' . "ssh_sge_mpich2" . '"');
push(@new_env,"PBS_NODEFILE=" . '"' . $machinefile . '"');
###
# [JFontan]
# Add environment directly in the script
foreach my $env_line (@new_env)
{ $sge_job_script->print("export " . $env_line . "\n");
}
if (defined $description->library_path() && $description->library_path() ne '')
{ my @library_path;
if (ref $description->library_path())
{ foreach my $tuple ($description->library_path())
{ push(@library_path,@$tuple);
}
}
else
{ @library_path = ($description->library_path());
}
my $library_path = join(":",@library_path);
foreach my $lib_var (@library_vars)
{ ###
# [JFontan]
# Changed EOF by ""
$sge_job_script->print("
if test \"X\${$lib_var}\" != \"X\"; then
$lib_var=\"\${$lib_var}:$library_path\"
else
$lib_var=\"$library_path\"
fi
export $lib_var
");
$rsh_env .= "if test \"X\${$lib_var}\" != \"X\"; then\n";
$rsh_env .= "$lib_var=\"\${$lib_var}:$library_path\"\n";
$rsh_env .= "else\n";
$rsh_env .= "$lib_var=\"$library_path\"\n";
$rsh_env .= "fi\n";
$rsh_env .= "export $lib_var\n";
}
}
###
# [JFontan]
# Here we can have a problem if the first parameter is "0"
my $args="";
my @arguments = $description->arguments();
if($arguments[0])
{ foreach my $arg (@arguments)
{ $self->log("Transforming argument \"$arg\"\n");
$self->helper_armour(\$arg);
$self->log("Transformed to \"$arg\"\n");
$args .= '"' . $arg . '" ';
}
}
###
# [JFontan]
# Link fake stdout/stderr to the real one
$sge_job_script->print("mkdir -p $cache_export_dir\n");
$sge_job_script->print("touch $fake_stdout\n");
$sge_job_script->print("ln $fake_stdout $real_stdout\n");
$sge_job_script->print("touch $fake_stderr\n");
$sge_job_script->print("ln $fake_stderr $real_stderr\n");
@tmp_list=();
$self->helper_get_from_tmp_file("scratch",\@tmp_list);
my $gram_scratch_dir = (scalar(@tmp_list)>0) ? $tmp_list[0] : '-';
###
# [JFontan]
# Changed method to send the proxy from GPG to SELF (embeded in the script)
if(($description->jobtype() eq 'multiple' && !$cluster) || $description->jobtype() eq 'single')
{
# $self->helper_write_non_mpi_script($sge_job_script,$my_hostname,$local_x509,
# "X509GPG",$cache_export_dir,$gram_scratch_dir,"NONE",$args);
$self->helper_write_non_mpi_script($sge_job_script,$my_hostname,$local_x509,
"X509SELF",$cache_export_dir,$gram_scratch_dir,"NONE",$args);
}
elsif($description->jobtype() eq 'multiple')
{
# $self->helper_write_fake_mpi_script($sge_job_script,$rsh_env,$my_hostname,$local_x509,
# "X509GPG",$cache_export_dir,$gram_scratch_dir,"NONE",$args);
$self->helper_write_fake_mpi_script($sge_job_script,$rsh_env,$my_hostname,$local_x509,
"X509SELF",$cache_export_dir,$gram_scratch_dir,"NONE",$args);
my $count = $description->count;
# [JFontan]
# Changed EOF by ""
# [TODO]
$sge_job_script->print("
hosts=\`cat \$PBS_NODEFILE\`;
counter=0
while test \$counter -lt $count; do
for host in \$hosts; do
if test \$counter -lt $count; then
rsh_bootstrap=\`$remote_shell \$host mktemp /tmp/rsh_bootstrap.XXXXXX\`
$remote_shell \$host \"cat > \$rsh_bootstrap; chmod 700 \$rsh_bootstrap;\ \$rsh_bootstrap; rm \$rsh_bootstrap\" < \$local_bootstrap &
counter=\`expr \$counter + 1\`
else
break
fi
done
done
wait
rm \$local_bootstrap
");
}
###
# [JFontan]
# Delete cache dir and stdout/stderr
$sge_job_script->print("rm -rf ".$cache_export_dir."\n");
$sge_job_script->print("rm -f ".$fake_stdout."\n");
$sge_job_script->print("rm -f ".$fake_stderr."\n");
###
# [GBorges]
# Delete .smpd
my $smpdfile = "$userdir/.smpd";
$sge_job_script->print("rm -rf ". $smpdfile ."\n");
###
# Close SGE script
$sge_job_script->close();
my $errfile;
if ($description->logfile() ne "")
{ $errfile = "2>>" . $description->logfile();
}
$self->helper_cache_export();
$self->helper_remove_tmp_file();
return "FAILED" if ! -e $local_x509;
symlink $local_x509,$cache_export_dir."/.emergency-x509";
symlink $sge_job_script_name,$cache_export_dir."/.submit-script";
$self->cd_fork_and_exec_cmd(undef,0,0,"/bin/cp",$local_x509,$cache_export_dir."/.emergency-x509.ref");
## $MYLDPATH = '/usr/local/sge/V60u7_1/lib/lx26-x86:/opt/globus/lib:/opt/edg/lib:/usr/local/lib:/opt/glite/lib';
## $MYPATH = '/opt/glite/bin:/opt/glite/externals/bin:/opt/globus/bin:/usr/java/j2sdk1.4.2_08/bin:/usr/bin:/usr/sue/sbin:/usr/java/j2sdk1.4.2_08/bin:/usr/local/sge/V60u7_1/bin/lx26-x86:/opt/lcg/bin:/opt/lcg/sbin:/usr/kerberos/sbin:/usr/kerberos/bin:/opt/globus/bin:/opt/globus/sbin:/opt/edg/bin:/usr/local/bin:/opt/edg/sbin:/usr/local/sbin:/usr/sue/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/opt/glite/bin:/opt/glite/externals/bin:/opt/gpt/sbin:/opt/d-cache/srm/bin:/opt/d-cache/dcap/bin:/root/bin';
## $ENV{'LD_LIBRARY_PATH'} = $MYLDPATH;
## $ENV{'PATH'} = $MYPATH;
foreach $key (sort keys(%ENV)) {
print FILELOG "$key = $ENV{$key}","\n";
}
###
# Job submission
my $batch_id;
my $submit_status;
my $attempts=0;
my $tmp_file;
do
{ ###
# [JFontan]
# DEBUG: copy script to /tmp
system("cp -f $sge_job_script_name /tmp/sge_job_script");
chomp($tmp_batch_id=`$qsub < $sge_job_script_name`);
$submit_status = $?;
print FILELOG "COMMAND =",$qsub,"\n";
print FILELOG "SCRIPT =",$sge_job_script_name,"\n";
print FILELOG "TMP_BATCH_ID =",$tmp_batch_id,"\n";
print FILELOG "SUBMIT_STATUS =",$submit_status,"\n";
if ($tmp_batch_id =~ /^Your job (\d*)/) {
$batch_id = $1;
}
$self->log("Batch ID: " . $batch_id);
if ($submit_status != 0)
{ $batch_id = undef;
sleep 5;
}
$attempts++;
} while ($submit_status != 0 && $attempts<6);
if (!defined $batch_id)
{ $batch_id = "FAILED";
}
###
# [GBorges]
# Debug Output
chop($date=`date`);
print FILELOG "---> Job has been submitted with ID ",$batch_id,"\n";
print FILELOG "SUBMIT_TO_BATCH_SYSTEM subroutine: Leaving on $date \n";
close FILELOG;
return $batch_id;
}
LIP SGE infoprovider
The standard LCG CE middleware is distributed with a set of perl and python scripts which generate information regarding the actual state of resources inside a given cluster or site. This section describes the main changes implemented to these scripts, called hereafter infoprovider scripts, in order to adapt them to use Sun Grid Engine (SGE) scheduler instead of the standard PBS scheduler. All changes were performed in such a way that the final output remains the same as the one produced in the PBS case.Introduction
The information system supported by the LCG CE middleware is based on standard information stored on static files. Such static files are found under /opt/lcg/var/gip/ldif and represent the default inputs to the site information system. However, they do not represent the current working status of the cluster or site and have to be updated by dynamic scripts. Such dynamic scripts are found under /opt/lcg/var/gip/plugin and must run whenever the information system needs to provide a correct and up to date output.[root@ce02 gip]# cd /opt/lcg/var/gip [root@ce02 gip]# cd ldif/ [root@ce02 ldif]# ll total 56 -rw-r--r-- 1 root root 20118 Aug 11 16:23 static-file-CE.ldif -rw-r--r-- 1 root root 7736 Aug 11 16:23 static-file-CESEBind.ldif -rw-r--r-- 1 root root 4453 Aug 11 16:23 static-file-Cluster.ldif -rw-r--r-- 1 root root 705 Aug 11 16:23 static-file-Site.ldif [root@ce02 gip]# cd ../plugin/ [root@ce02 plugin]# ll total 16 -rwxr-xr-x 1 root root 102 Aug 21 14:49 lcg-info-dynamic-ce -rwxr-xr-x 1 root root 106 Jul 7 13:46 lcg-info-dynamic-scheduler-wrapper -rwxr-xr-x 1 root root 100 Aug 11 16:24 lcg-info-dynamic-software-wrapper
The lcg-info-dynamic-ce wrapper and the lcg-info-dynamic-sge script
The lcg-info-dynamic-ce script is one of the most important dynamical wrapper scripts and runs the following commands:[root@ce02 gip]# cat /opt/lcg/var/gip/plugin/lcg-info-dynamic-ce #!/bin/sh /opt/lcg/libexec/lcg-info-dynamic-sge /opt/lcg/var/gip/ldif/static-file-CE.ldif ce02.lip.pt/opt/lcg/libexec/lcg-info-dynamic-sge is a perl script which substitutes the standard /opt/lcg/libexec/lcg-info-dynamic-pbs script. It is based in a previous version of the SGE infoprovider script developed at London e-Science Center ( LeSC SGE official distribution
) and it can be downloaded in LIP lcg-info-dynamic-sge perl script. The basic structure of this script is the following:
- Starts by defining a set of site dependent constants: cluster queue array ( @clusterqueues), SGE environment variables ( $SGE_ROOT and $SGE_CELL) and path to important SGE binary comands ( qstat and qconf);
#####
# Name of cluster queue to query
my (@clusterqueues) = ("atlasgrid","cmsgrid","dteamgrid","edteamgrid","eelagrid","opsgrid","swetestgrid","biomedgrid","imaingrid");
#####
# Set path to root of SGE tools installation.
$ENV{"SGE_ROOT"} = "/usr/local/sge/V60u7_1";
#####
# Set name of SGE cell to use.
$ENV{"SGE_CELL"} = "default";
#####
# Path to qstat and qconf commands.
my ($qstat) = "/usr/local/sge/V60u7_1/bin/lx26-x86/qstat";
my ($qconf) = "/usr/local/sge/V60u7_1/bin/lx26-x86/qconf";
- Defines the scripts subroutines: processCommandLine, parseConfig, lookupDNs, lookupSGEVersion, lookupPolicy, lookupQueueState, calculateResponseEstimate, sgeToGlue;
- Finishes with the script "Main Program" where all subroutines are called and the final output is produced.
########################
# --- Main program --- #
########################
#####
# Lookup the path to the static file and the hostname we should use from the commandline.
my ($configpath) = processCommandLine();
#####
# Lookup the path to statically defined LDIF data file and check if we are able to open it
my ($ldifpath) = parseConfig($configpath);
#####
# Obtain a list of the DNs defined in the LDIF data file and store them iin array @dn. It will be used to produce the final output
my (@dn) = lookupDNs($ldifpath);
#####
# Build up our hash datastructure.
my (%data);
#####
# Set LRMS information.
$data{"GlueCEInfoLRMSType"} = "sge";
$data{"GlueCEInfoLRMSVersion"} = lookupSGEVersion();
#####
# Collected relevant information and produce output it in the expected form. This will be done through a loop running over all queues
my ($clusterqueue);
foreach $clusterqueue (@clusterqueues) {
#####
# Define temporary "LocalQueue" key in the data hash
$data{"GlueCELocalQueue"} = $clusterqueue;
#####
# Lookup queue policy information.
lookupPolicy(\%data);
#####
# Lookup queue state information.
lookupQueueState(\%data);
#####
# Calculate queue response time estimates.
calculateResponseEstimate(\%data);
#####
# Delete the Local Queue key from the data hash
delete $data{"GlueCELocalQueue"};
#####
# Simply regurgitate all of the collected state information for each of the defined queues.
my ($dn);
foreach $dn (@dn) {
# If the string $dn contains the substring $clusterqueue, returns true
if ($dn =~ m/lcgsge-$clusterqueue/) {
print $dn;
}
}
foreach (sort (keys %data)) {
print "$_" . ": " . $data{$_} . "\n";
}
print "\n";
}
The lcg-info-dynamic-sge script workflow
The core of the lcg-info-dynamic-sge perl script is defined by its "main program" which runs in a sequencial basis:- It starts by calling processCommandLine and parseConfig subroutines. These subroutines check the arguments format received by the perl script and if the static file (1st argument) exists and can be opened.
#####
# Process commandline. The only valid configurations are with exactly 1 or 2 arguments:
# The first argument is always the path to our configuration file.
# The second argument will be used as the FQDN SGE control host.
sub processCommandLine() {
if (scalar(@ARGV) == 0) {
print STDERR "Usage: $0 <config file>\n";
exit 1;
} else {
my ($configfile) = @ARGV;
return ($configfile);
}
}
#####
# Given the path to the local static configuration file check if we can open the file
sub parseConfig($) {
my ($configpath) = shift; # Path to the configuration file.
# Open the file.
open(CONFIG, $configpath) ||
die "Unable to open configuration file $configpath: $!";
close(CONFIG);
my ($ldif_file) = $configpath;
return $ldif_file;
}
- It parses through the static configuration file and searches for lines beguinning by dn:GlueCEUniqueIDs. This is done by subroutine lookupDNs. The different dns values are then stored in array @dn which will be later used to produce part of the final output.
#####
# Given the path to the local static LDIF information file, extract a list of DNs as defined in that file.
# The each DN will include the 'dn: GlueCEUniqueID=' prefix.
sub lookupDNs($) {
my ($ldifpath) = shift; # Path to the LDIF file.
my (@DN); # List of DNs that we will return.
###
# Open the file.
open(LDIFDATA, $ldifpath) ||
die "Unable to open static LDIF information file $ldifpath: $!";
###
# For every line:
while(<LDIFDATA>) {
# If the line contains a DN definition
if (/dn:\s+GlueCEUniqueID=/) {
push @DN, $_;
}
}
close(LDIFDATA);
return @DN;
}
- Afterwards, a hash datastructure is defined and filled with up to date * "Glue key = value" * information. Since SGE is a queue based scheduler, where different queues can have very different definitions, all the most interesting quantities are built quering the batch system for each queue configuration. This is done through a loop running over all queues * (see lcg-info-dynamic-sge "Main Program" definition)* where specific SGE commands are executed and the produced output is parsed to isolate the relevant quantities. The first called subroutine is lookupPolicy which searches for the Maximum Wall Clock Time and Maximum CPU Time queue definitions. The subroutine parses the output produced by qstat -sq < name of the queue > SGE command and searches for the h_rt and h_cpu key words. The final step is to convert the obtained SGE time values (HH:MM:SS) in the Glue format running the sgeToGlue subroutine.
#####
# Lookup global MaxWallClockTime and MaxCPUTime. Acquire this by running `qconf -sq` and looking up h_rt and h_cpu.
sub lookupPolicy($) {
my ($dataref) = shift; # Reference to $data hash.
my ($clusterqueue) = $dataref->{"GlueCELocalQueue"};
open(QCONF, "$qconf -sq $clusterqueue |") ||
die "Unable to lookup queue policy with qconf: $!";
foreach (<QCONF>) {
# If line contains only whitespace, skip.
if (/^\s*$/) { next; }
# parse the key and value from the output
my ($key, $value) = split;
if ($key eq "h_rt") {
# We've found the max wallclock time.
chomp $value;
$dataref->{"GlueCEPolicyMaxWallClockTime"} = sgeToGlue($value);
next;
}
if ($key eq "h_cpu") {
# We've found the max CPU time.
chomp $value;
$dataref->{"GlueCEPolicyMaxCPUTime"} = sgeToGlue($value);
next;
}
}
close QCONF;
}
#####
# Simply converts an SGE value into one that the Glue schema uses. At present, simply:
# - replaces "INFINITY" with "0", and
# - replaces AA:BB:CC with ((AA * 60) + BB ).
# (i. e. converts from hours:mins:seconds to minutes)
sub sgeToGlue($) {
my ($value) = shift;
$value =~ s/INFINITY/0/;
if ($value =~ /^(\d+):(\d+):(\d+)$/) {
$value = (($1 * 60) + $2);
}
return $value;
}
- The lookupQueueState subroutine is of most importance since it generates information regarding the current status of resources within the cluster. It starts by reporting the current status of the queue parsing the output generated by the $qstat -f | grep < name of the queue > SGE command. By default, all queues are able to receive and run jobs and therefore, the GlueCEStateStatus variable of the hash datastructure is filled with the Production string. However, If the queue is locally disabled, the Draining status is assigned to the GlueCEStateStatus. Other important variables such as the number of waiting jobs, number of running jobs, number of maximum running jobs, number of maximum total jobs, number of free CPUs or total number of CPUs are obtained within the same subroutine using the same previous procedures, either parsing the $qstat -s p -q < name of the queue > output or the $qstat -g c output.
sub lookupQueueState($) {
my ($dataref) = shift;
my ($clusterqueue) = $dataref->{"GlueCELocalQueue"};
#####
# Lookup the system status: "Queueing", "Production", "Closed", "Draining".
open(QSTAT, "$qstat -f | grep $clusterqueue |")
|| die "Unable to lookup state of the queue $!";
foreach (<QSTAT>) {
my ($queuename,$qtype,$used_tot,$load_avg,$arch,$states) = split;
$dataref->{"GlueCEStateStatus"} = "Production";
if ($states eq "d") {$dataref->{"GlueCEStateStatus"} = "Draining";}
}
###
# Lookup number of waiting jobs.
open(QSTAT, "$qstat -s p -q $clusterqueue |")
|| die "Unable to lookup number of waiting jobs: $!";
my ($jobcount) = 0;
foreach (<QSTAT>) {
s/^\s+//; # remove whitespaces (at the beguinning) from the $_ variable using the substitution operator
s/\s+$//; # remove whitespaces (at the end) from the $_ variable using the substitution operator
#####
# If the line begins with the string "job-ID", skip it. It's a column header.
if (/^job-ID/) { next; }
#####
# If the line begins with a number of '-'s, skip it. It's a header / data separator.
if (/^-+/) { next; }
#####
# If the line begins with a number, increment the job count. It's a job entry. (The number is the job's ID.)
if (/^\d+/) { $jobcount++ };
}
$dataref->{"GlueCEStateWaitingJobs"} = $jobcount;
#####
# Lookup the number of running jobs. If we're running on SGE 6.*, use `qstat -g c` and lookup the USED field.
my $version = $dataref->{"GlueCEInfoLRMSVersion"};
if ($version =~ /^6/) {
open(QSTAT, "$qstat -g c |")
|| die "Unable to run qstat to lookup queue load: $!";
foreach (<QSTAT>) {
if (/^$clusterqueue/) {
my ($name, $load, $used, $avail, $total) = split;
$dataref->{"GlueCEStateRunningJobs"} = $used;
$dataref->{"GlueCEPolicyMaxTotalJobs"} = $total;
$dataref->{"GlueCEPolicyMaxRunningJobs"} = $total;
}
}
close QSTAT;
}
else {
die "Unsupported LRMS version $version.";
}
###
# Lookup the number of free CPUs.
if ($version =~ /^6/) {
open(QSTAT, "$qstat -g c |")
|| die "Unable to run qstat to lookup free cpus: $!";
foreach (<QSTAT>) {
if (/^$clusterqueue/) {
my ($name, $load, $used, $avail, $total) = split;
$dataref->{"GlueCEStateFreeCPUs"} = $avail;
$dataref->{"GlueCEInfoTotalCPUs"} = $total;
}
}
}
else {
die "UnsupportedLRMS version $version.";
}
###
# Calculate the total number of jobs.
$dataref->{"GlueCEStateTotalJobs"} =
$dataref->{"GlueCEStateWaitingJobs"} +
$dataref->{"GlueCEStateRunningJobs"};
}
- Finally, the expected response time and worst response time for job execution are computed by the calculateResponseEstimate subroutine. Nevertheless, the present implemented procedures are not accurate since the worst response time is the total number of jobs multiplied by the maximum wall clock time allowed in the queue and divided by the total number of CPUs. The espected response time is estimated as half of the worst response time.
#####
# Compute the expected response time
sub calculateResponseEstimate($) {
my ($dataref) = shift;
my ($defaultworstcase) = 9 * 24 * 60 * 60; # 9 days.
my ($worstjobtime) = $dataref->{"GlueCEPolicyMaxWallClockTime"};
my ($jobcount) = $dataref->{"GlueCEStateTotalJobs"};
my ($cpucount) = $dataref->{"GlueCEInfoTotalCPUs"};
if ($worstjobtime == 0) {
#####
# There was no maximum wallclock time set. Assume the $defaultworstcase under these circumstances.
$worstjobtime = $defaultworstcase;
}
#####
# The predicted worst-case response time is if every job will run ahead of any new job, and it will take all the time available to run.
if ($cpucount == 0) {
#####
# No CPUs are available. Put in a large wait time.
$dataref->{"GlueCEStateWorstResponseTime"} = 99999999;
}
else {
#####
# Algorithm taken from PBS information reporter minus the job-time-already-used component as we don't have this information.
$dataref->{"GlueCEStateWorstResponseTime"} = int(($jobcount * $worstjobtime) / $cpucount);
}
#####
# The estimated response time is simply half of the worst-case response time.
$dataref->{"GlueCEStateEstimatedResponseTime"} = int($dataref->{"GlueCEStateWorstResponseTime"} / 2);
}
- Running the lcg-info-dynamic-sge perl script in a standalone mode, this is the kind of output which must be produced:
[root@ce02 libexec]# /opt/lcg/libexec/lcg-info-dynamic-sge /opt/lcg/var/gip/ldif/static-file-CE.ldif ce02.lip.pt dn: GlueCEUniqueID=ce02.lip.pt:2119/jobmanager-lcgsge-atlasgrid,mds-vo-name=local,o=grid GlueCEInfoLRMSType: sge GlueCEInfoLRMSVersion: 6.0u7 GlueCEInfoTotalCPUs: 2 GlueCEPolicyMaxCPUTime: 4320 GlueCEPolicyMaxRunningJobs: 2 GlueCEPolicyMaxTotalJobs: 2 GlueCEPolicyMaxWallClockTime: 8640 GlueCEStateEstimatedResponseTime: 15120 GlueCEStateFreeCPUs: 0 GlueCEStateRunningJobs: 0 GlueCEStateStatus: Draining GlueCEStateTotalJobs: 7 GlueCEStateWaitingJobs: 7 GlueCEStateWorstResponseTime: 30240 dn: GlueCEUniqueID=ce02.lip.pt:2119/jobmanager-lcgsge-cmsgrid,mds-vo-name=local,o=grid GlueCEInfoLRMSType: sge GlueCEInfoLRMSVersion: 6.0u7 GlueCEInfoTotalCPUs: 2 GlueCEPolicyMaxCPUTime: 12960 GlueCEPolicyMaxRunningJobs: 2 GlueCEPolicyMaxTotalJobs: 2 GlueCEPolicyMaxWallClockTime: 25920 GlueCEStateEstimatedResponseTime: 58320 GlueCEStateFreeCPUs: 0 GlueCEStateRunningJobs: 2 GlueCEStateStatus: Draining GlueCEStateTotalJobs: 9 GlueCEStateWaitingJobs: 7 GlueCEStateWorstResponseTime: 116640 dn: GlueCEUniqueID=ce02.lip.pt:2119/jobmanager-lcgsge-dteamgrid,mds-vo-name=local,o=grid GlueCEInfoLRMSType: sge GlueCEInfoLRMSVersion: 6.0u7 GlueCEInfoTotalCPUs: 1 GlueCEPolicyMaxCPUTime: 120 GlueCEPolicyMaxRunningJobs: 1 GlueCEPolicyMaxTotalJobs: 1 GlueCEPolicyMaxWallClockTime: 240 GlueCEStateEstimatedResponseTime: 0 GlueCEStateFreeCPUs: 1 GlueCEStateRunningJobs: 0 GlueCEStateStatus: Production GlueCEStateTotalJobs: 0 GlueCEStateWaitingJobs: 0 GlueCEStateWorstResponseTime: 0 (...)
The lcg-info-dynamic-scheduler-wrapper and the lcg-info-dynamic-scheduler-sge script
A different section of the output produced by the information system is generated by the /opt/lcg/var/gip/plugins/lcg-info-dynamic-scheduler-wrapper script. This file runs the /opt/lcg/libexec/lcg-info-dynamic-scheduler-sge python script with the /opt/lcg/etc/lcg-info-dynamic-scheduler.conf configuration file as argument.[root@ce02 libexec]# more /opt/lcg/var/gip/plugin/lcg-info-dynamic-scheduler-wrapper #!/bin/sh /opt/lcg/libexec/lcg-info-dynamic-scheduler-sge -c /opt/lcg/etc/lcg-info-dynamic-scheduler.confThe configuration file defines some standard options inputs (relevant static file, VO/queue mapping, path to relevant python files, etc ...) which must be given according to the following format:
[root@ce02 libexec]# cat /opt/lcg/etc/lcg-info-dynamic-scheduler.conf [Main] static_ldif_file: /opt/lcg/var/gip/ldif/static-file-CE.ldif vomap : atlasgrid:atlas cmsgrid:cms dteamgrid:dteam swetestgrid:swetest eelagrid:eela edteamgrid:edteam opsgrid:ops biomedgrid:biomed imaingrid:imain module_search_path : ../lrms:../ett [LRMS] lrms_backend_cmd : /opt/lcg/libexec/lrmsinfo-sge [Scheduler] cycle_time : 0 vo_max_jobs_cmd : /opt/lcg/libexec/vomaxjobs-sge
The lcg-info-dynamic-scheduler-sge workflow
The lcg-info-dynamic-scheduler-sge file ( LIP lcg-info-dynamic-scheduler-sge script) is basicaly the same as the default lcg-info-dynamic-scheduler script distributed with the LCG CE middleware. It starts by parsing the configuration file options, runs important python scripts and parses their produced output. In the following, we will describe how those python files ( /opt/lcg/libexec/vomaxjobs-sge and /opt/lcg/libexec/lrmsinfo-sge) are adapted to run SGE commands and how the desired information output is generated.
The vomaxjobs-sge python script
The /opt/lcg/libexec/vomaxjobs-sge substitutes the standard /opt/lcg/libexec/vomaxjobs-maui python scrypt distributed with LCG CE middleware. The original MAUI file was developed by J. A. Templon and it is now adapted to interact with SGE ( LIP vomaxjobs-sge script). Its main purpose it to generate a python dictionary with the maximum number of jobs which are presently allowed to run in each queue. After defining the SGE environment variables and the path to the SGE binaries, the script parses the qstat -g c SGE command output. Spliting the output in columns, it searches for specific column headers, defines the index number of each column and obtains the number of free CPUs for each queue.
!/usr/bin/python2
# vomaxjobs-sge
#
# Original script by J. A. Templon, NIKHEF/PDP 2005
#
# Last changes by Goncalo Borges <goncalo@lip.pt>
# Laboratorio de Fisica Experimental de Particulas
# Lisboa, Portugal
#
# Generate generic information on maximum job counts per VO/QUEUE.
# ------------------------------------------------------------------------
import sys
###
# Define script usage
def usage():
print "Usage: vomaxjobs-sge [-h <schedulerhost>]"
import getopt
import string
import os
try:
opts, args = getopt.getopt(sys.argv[1:], "h:",
["host="])
except getopt.GetoptError:
print sys.argv[0] + ": error parsing command line: " + string.join(sys.argv)
usage()
sys.exit(2)
schedhost = None
for o, a in opts:
if o in ("-h", "--host"):
schedhost = a
###
# Define SGE_ROOT environment variable and SGE qstat comand
# Run the SGE qstat command and store the output in "out" variable
os.environ['SGE_ROOT']='/usr/local/sge/V60u7_1'
cmd = '/usr/local/sge/V60u7_1/bin/lx26-x86/qstat -g c'
import commands
(stat, out) = commands.getstatusoutput(cmd)
if stat:
print sys.argv[0] + ': SGE \'qstat -g c\' command' + ' exited with nonzero status'
sys.exit(1)
###
# Split the qstat output command in several lines. Gather information on VOs/Queues
# Fill the pcaps dictionary with the queue name and number of free processors and print it
lines = out.split('\n')
fieldnames = lines[0].split() # Split column legend
gpos = fieldnames.index('CLUSTER') # column index number for queue name
lpos = fieldnames.index('cdsuE') # column index number for queue process cap
pcaps = {}
for line in lines[2:]: # Loop trough all lines
f = line.split() # Array with the line contents
max_asstring = f[lpos-4] # Store the available processors
pcaps[f[gpos]] = int( max_asstring )
print pcaps
Running the /opt/lcg/libexec/vomaxjobs-sge in a standalone mode, you should get as output the following python dictionary:
[root@ce02 ~]# /opt/lcg/libexec/vomaxjobs-sge
{'atlasgrid': 0, 'biomedgrid': 2, 'opsgrid': 1, 'imaingrid': 2, 'eelagrid': 2, 'cmsgrid': 0, 'swetestgrid': 2, 'lip': 4, 'dteamgrid': 1, 'edteamgrid': 1}
The lrmsinfo-sge python script
The lrmsinfo-sge python script substitutes the lrmsinfo-pbs one although it is basically the same script ( LIP lrmsinfo-sge). The main difference is that the lrmsinfo-sge script imports classes from other python functions, such as
- /opt/lcg/lib/python/sgeServer.py
- /opt/lcg/lib/python/sge_utils.py
[root@ce02 libexec]# /opt/lcg/libexec/lrmsinfo-sge
nactive 6
nfree 5
now 1156522995
schedCycle 26
{'group': 'atlas', 'name': 'STDIN', 'jobid': '2208.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'atlas131', 'maxwalltime': ''}
{'group': 'cmsgrid', 'name': 'STDIN', 'jobid': '2214.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'cms101', 'maxwalltime': ''}
{'group': 'cmsgrid', 'name': 'STDIN', 'jobid': '2212.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'cms101', 'maxwalltime': ''}
{'group': 'cmsgrid', 'name': 'STDIN', 'jobid': '2210.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'cms101', 'maxwalltime': ''}
{'group': 'cmsgrid', 'name': 'STDIN', 'jobid': '2158.ce02.lip.pt', 'queue': 'cmsgrid', 'state': 'running', 'user': 'cms180', 'maxwalltime': 1555200.0}
{'group': 'cmsgrid', 'name': 'STDIN', 'jobid': '2211.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'cms101', 'maxwalltime': ''}
{'group': 'cmsgrid', 'name': 'STDIN', 'jobid': '2159.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'cms180', 'maxwalltime': ''}
{'group': 'atlas', 'name': 'STDIN', 'jobid': '2179.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'atlas131', 'maxwalltime': ''}
{'group': 'atlas', 'name': 'STDIN', 'jobid': '2163.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'atlas190', 'maxwalltime': ''}
{'group': 'cmsgrid', 'name': 'STDIN', 'jobid': '2209.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'cms101', 'maxwalltime': ''}
{'group': 'atlas', 'name': 'STDIN', 'jobid': '2187.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'atlas131', 'maxwalltime': ''}
{'group': 'cmsgrid', 'name': 'STDIN', 'jobid': '2213.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'cms101', 'maxwalltime': ''}
{'group': 'cmsgrid', 'name': 'STDIN', 'jobid': '2157.ce02.lip.pt', 'queue': 'cmsgrid', 'state': 'running', 'user': 'cms180', 'maxwalltime': 1555200.0}
{'group': 'atlas', 'name': 'STDIN', 'jobid': '2201.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'atlas131', 'maxwalltime': ''}
{'group': 'atlas', 'name': 'STDIN', 'jobid': '2221.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'atlas131', 'maxwalltime': ''}
{'group': 'atlas', 'name': 'STDIN', 'jobid': '2170.ce02.lip.pt', 'queue': '', 'state': 'queued', 'user': 'atlas131', 'maxwalltime': ''}
The sgeServer.py script
The SgeServer.py is a complicated python scrypt where the only relevant code for our purposes is the LiveServer class ( LIP sgeServer.py python script). This class is changed in such a way that it is possible to built a similar output as the one produced running the default /opt/lcg/libexec/lrmsinfo-pbs file. It runs the qstat SGE command, and parsing the output, it obtains quantities such as the job id, the job name, the job owner, the job state, the queue where the job is running and the maximum wallclock time defined for that queue.
class LiveServer(Server):
def __init__(self,*arg,**kw):
Server.__init__(self,*arg,**kw)
cnow = time.ctime() # this hack is to get around time zone problems
from sge_utils import sgenodes
cpucount = 0
jobcount = 0
for node in sgenodes():
if node.isUp():
cpucount += node.numCpu
for cpu in range(node.numCpu):
jobcount += len(node.jobs[cpu])
self.slotsUp = cpucount
self.slotsFree = cpucount - jobcount
nowtuple = time.strptime(cnow,"%c")
self.__evtime__ = int(time.mktime(nowtuple))
cmdstr = '/usr/local/sge/V60u7_1/bin/lx26-x86/qstat'
(stat, out) = commands.getstatusoutput(cmdstr)
qstatlines = out.split('\n')
for qstatline in qstatlines[2:]:
newj = Job()
qstatlfds = qstatline.split() # Divide line fields
jobids = qstatlfds[0]+'.ce02.lip.pt' # Job id
jname = qstatlfds[2] # Job name
user = qstatlfds[3] # Job owner
jstate = qstatlfds[4] # Job state
if jstate == 'r':
queue = string.split(qstatlfds[7],'@')[0] # Get queue
cmd = '/usr/local/sge/V60u7_1/bin/lx26-x86/qconf -sq '+queue+' | grep h_rt' # Get MaxWallTime
(stat, out) = commands.getstatusoutput(cmd)
hms = out.split()[1]
t = string.split(hms,':')
mins = (int(t[1]) + 60*int(t[0])) # MaxWallTime in m
else:
queue = ''
mins = ''
newj.set('jobid',jobids)
newj.set('name',jname)
newj.set('user',user)
newj.set('queue',queue)
newj.set('maxwalltime',mins)
try:
thisgroup=pwd.getpwnam(user)[3]
groupname=grp.getgrgid(thisgroup)[0]
except:
thisgroup='unknown'
groupname='unknown'
newj.set('group',groupname)
if jstate == 'qw':
val = 'queued'
elif jstate == 'r':
val = 'running'
else:
val = 'unknown'
newj.set('state',val)
self.addjob(newj.get('jobid'),newj)
The sge_utils.py script
The SgeServer.py script imports the sgenodes function from the sge_utils.py python script ( LIP sge_utils.py python script). The sgenodes function runs the qstat SGE command and parses the output searching and storing information regarding the execution machine name, the number of processors, the operation status and state of the machine.
###
# SGE Definitions
os.environ['SGE_ROOT']='/usr/local/sge/V60u7_1'
SGENODES = "/usr/local/sge/V60u7_1/bin/lx26-x86/qhost"
QSTAT = "/usr/local/sge/V60u7_1/bin/lx26-x86/qstat"
###
# Define SGE execution nodes and build the same output as standard scripts
def sgenodes(nodes="", ignoreError=False):
if not _sgenodesOK:
raise IOError, "'%s' not found" % SGENODES
if not nodes:
nodes = [""] # meaning all nodes
else:
nodes = nodes.split(',')
#####
# Run the SGE command qhost to know which are the execution nodes
cmd = '/usr/local/sge/V60u7_1/bin/lx26-x86/qhost'
import commands
(stat, out) = commands.getstatusoutput(cmd)
if stat:
print sys.argv[0] + ': SGE \'qhost\' command' + ' exited with nonzero status'
sys.exit(1)
qhostlines = out.split('\n')
#####
# Run the command qstat to know which are the execution nodes
cmd = '/usr/local/sge/V60u7_1/bin/lx26-x86/qstat'
(stat, out) = commands.getstatusoutput(cmd)
if stat:
print sys.argv[0] + ': SGE \'qstat\' command' + ' exited with nonzero status'
sys.exit(1)
qstatlines = out.split('\n')
fieldnames = qstatlines[0].split()
if fieldnames != [] : # Chech if fieldnames is not empty (no running jobs)
qpos = fieldnames.index('queue') # output column for queue
params = [' state = ',' np = ',' ntype = ',' status = ']
paragraph = []
for qhostline in qhostlines[3:]: # Loop through all the lines of the qhost output
qhostlfds = qhostline.split() # Define qhostlinefields
execnd = qhostlfds[0]+'.lip.pt' # Define execution host
jobs = ''
if fieldnames != [] :
for qstatline in qstatlines[2:]: # Loop through all the lines of the qstat output
qstatlfds = qstatline.split() # Define the qstatlinefields
field = qstatlfds[qpos] # Get the SGE queue from the qpos column
n = field.count(execnd) # exec host appears n times in the string field
if n>0 :
jobid = qstatlfds[0]
jobuser = qstatlfds[3]
jobs = ' jobs = 0/'+jobid+'.ce02.lip.pt\n'
execnode = execnd+'\n'
state = params[0]+'free\n'
np = params[1]+qhostlfds[2]+'\n'
ntype = params[2]+'cluster\n'
status = params[3]+'opsys=linux,uname=Linux '+qhostlfds[0]+'.lip.pt'
entry = execnode+state+np+ntype+jobs+status
paragraph.append(entry)
result = []
for node in nodes:
for entry in paragraph:
result.append(SGENode(entry))
return result
The final produced information
After substituting the very different perl and python scripts, you should run the /opt/lcg/libexec/lcg-info-wrapper.[root@ce02 python]# more /opt/lcg/libexec/lcg-info-wrapper #!/bin/sh export LANG=C /opt/lcg/bin/lcg-info-generic /opt/lcg/etc/lcg-info-generic.conf [root@ce02 python]# more /opt/lcg/etc/lcg-info-generic.conf temp_dir = /opt/lcg/var/gip/tmp plugin_dir = /opt/lcg/var/gip/plugin static_dir = /opt/lcg/var/gip/ldif provider_dir = /opt/lcg/var/gip/provider dynamic_script = /opt/lcg/libexec/lcg-info-dynamic-sge freshness = 20 cache_ttl = 300 response = 5 timeout = 150After running this wrapper script, the updated information becomes available using an ldapsearch command:
[root@ce02 python]# ldapsearch -x -h ce02.lip.pt -p2135 -b "mds-vo-name=local,o=grid"
CESGA SGE Implementation
SGE integration with LCG at CESGA
Download
The LCG job manager and information provider for SGE currently being used at CESGA with LCG 2.7.0 can be downloaded from: http://www.egee.cesga.es/lcgsge/releases/
You can get an idea of to install it in the following sections taken from the README files of the job manager and information provider.
SGE LCG Job Manager
It is based in the PBS LCG job manager. At the beginning some variables are defined for an easier development and reading of the code:
# This script is based on jobmanager-lcgpbs provided by LCG. It is modified to
# work with SGE by Javier Fontan (jfontan_AT_gmail.com) from CESGA (www.cesga.es)
# Modify by Pablo Rey (prey@cesga.es) to include a Configuration file
# Comments, support and bug reports should be sent to egee-admin_AT_cesga.es
# SGE queues should have an epilog script to delete STDOUT and STDERR files
package Globus::GRAM::JobManager::lcgsge;
@Globus::GRAM::JobManager::lcgsge::ISA = qw(Globus::GRAM::JobManager::Helper);
use Globus::GRAM::Helper;
use Globus::GRAM::Error;
use Globus::GRAM::JobState;
use Globus::GRAM::JobManager;
use Globus::Core::Paths;
use IO::File;
use Config;
use POSIX;
my ($sge_base_path, $sge_bin_path, $mpirun, $qsub, $qstat, $qdel, $qmsg, $cluster, $cpu_per_node, $remote_shell);
BEGIN
{
# [prey]
# Including the config file
my $confile;
if (defined $ENV{'GLOBUS_LOCATION'}) {
$confile = $ENV{'GLOBUS_LOCATION'} . "/lib/perl/Globus/GRAM/JobManager/lcgsge.conf";
} else {
$confile = "/opt/globus/lib/perl/Globus/GRAM/JobManager/lcgsge.conf";
}
do $confile;
# [jfontan]
# Change this to sge tools
#$sge_base_path = '/opt/sge6';
#$sge_bin_path = $sge_base_path.'/bin/lx24-x86';
# [prey]
# Getting the $sge_base_path and $sge_bin_path from the config file
$sge_base_path = $SGE_BASE_PATH;
# Removing the last / if it is included
chop($sge_base_path) if ($sge_base_path =~ /\/$/);
$sge_bin_path = $SGE_BIN_PATH;
# Removing the last / if it is included
chop($sge_bin_path) if ($sge_bin_path =~ /\/$/);
$mpirun = $sge_bin_path.'/mpirun';
$qsub = $sge_bin_path.'/qsub';
$qstat = $sge_bin_path.'/qstat';
$qdel = $sge_bin_path.'/qdel';
$qmsg = $sge_bin_path.'/qmsg';
$cluster = 0;
$cpu_per_node = 0;
$remote_shell = '/usr/bin/ssh';
}
sub new
{
my $proto = shift;
my $class = ref($proto) || $proto;
my $self = $class->SUPER::new(@_);
bless $self, $class;
return $self;
}
* subroutine submit: it checks the RSL arguments. A globus error is obtained in case the arguments are not valid or there are no resources; otherwise a job_id is assigned.
sub submit
{
my $self = shift;
my $description = $self->{JobDescription};
my ($cpu_time,$wall_time);
$self->log("Entering sge submit");
# check jobtype
if(defined($description->jobtype()))
{
# if($description->jobtype !~ /^(mpi|single|multiple)$/)
if($description->jobtype !~ /^(single|multiple)$/)
{
return Globus::GRAM::Error::JOBTYPE_NOT_SUPPORTED;
}
}
else
{
return Globus::GRAM::Error::JOBTYPE_NOT_SUPPORTED;
}
if( !defined $description->directory() || $description->directory() eq "")
{
return Globus::GRAM::Error::RSL_DIRECTORY();
}
if( !defined $description->executable() || $description->executable() eq "")
{
return Globus::GRAM::Error::RSL_EXECUTABLE();
}
elsif( !defined $description->stdin() || $description->stdin() eq "")
{
return Globus::GRAM::Error::RSL_STDIN;
}
$self->log("Determining job max time cpu from job description");
if(defined($description->max_cpu_time()))
{
$cpu_time = $description->max_cpu_time();
$self->log(" using maxcputime of $cpu_time");
}
elsif(! $cluster && defined($description->max_time()))
{
$cpu_time = $description->max_time();
$self->log(" using maxtime of $cpu_time");
}
else
{
$cpu_time = 0;
$self->log(' using queue default');
}
$self->log("Determining job max wall time limit from job description");
if(defined($description->max_wall_time()))
{
$wall_time = $description->max_wall_time();
$self->log(" using maxwalltime of $wall_time");
}
elsif($cluster && defined($description->max_time()))
{
$wall_time = $description->max_time();
$self->log(" using maxtime of $wall_time");
}
else
{
$wall_time = 0;
$self->log(' using queue default');
}
foreach ($description->environment())
{
if(!ref($_) || scalar(@$_) != 2)
{
return Globus::GRAM::Error::RSL_ENVIRONMENT();
}
}
foreach($description->arguments())
{
if(ref($_))
{
return Globus::GRAM::Error::RSL_ARGUMENTS;
}
}
my $job_id = $self->queue_submit("lcgsge",$cpu_time."|".$wall_time);
$self->log("Leaving sge submit");
return
{
JOB_ID => $job_id,
JOB_STATE => Globus::GRAM::JobState::PENDING
} if defined $job_id;
return Globus::GRAM::Error::NO_RESOURCES;
}
* subroutine poll: It links the present status of jobs running in the site cluster with the Globus appropriate message.
sub poll
{
my $self = shift;
my $description = $self->{JobDescription};
my $state;
my $internal_id = $description->jobid();
my ($batch_id,$job_submit_time);
$self->lookup_or_submit(\$batch_id,\$job_submit_time,\$state);
$self->log("polling job $batch_id") if defined $batch_id;
my @data;
my $query_ret = $self->make_a_poll_query(".lcgjm","sgequeue.cache",$job_submit_time,\@data);
if ( !defined $state )
{
my $exit_code = 153;
my $status_line;
foreach my $line (@data)
{
my $jid;
if ($line =~ /^(\S+)\s+(\S+)$/)
{
($jid,$status_line) = ($1,$2);
if ($jid eq $batch_id)
{
$self->log(" Job found: " . $jid . ' | ' . $status_line );
$exit_code = 0;
last;
}
}
}
# return code 153 = "Unknown Job Id".
# verifying that the job is no longer there.
if ($exit_code == 153)
{
if ($query_ret)
{
$self->log("qstat rc is 153 == Unknown Job ID == DONE");
$state = Globus::GRAM::JobState::DONE;
}
else
{
$self->log("Job not found, assuming it is PENDING");
$state = Globus::GRAM::JobState::PENDING;
}
}
else
{
# Get 3rd field (after = )
$_ = $status_line;
if(/E|q|w|t/)
{
if (/E/)
{
$self->cancel();
$state = Globus::GRAM::JobState::FAILED;
}
else
{
$state = Globus::GRAM::JobState::PENDING;
}
}
elsif(/s/)
{
$state = Globus::GRAM::JobState::SUSPENDED
}
elsif(/r/)
{
$state = Globus::GRAM::JobState::ACTIVE;
}
else
{
# This else is reached by an unknown response from pbs.
# It could be that PBS was temporarily unavailable, but that it
# can recover and the submitted job is fine.
# So, we want the JM to ignore this poll and keep the same state
# as the previous state. Returning an empty hash below will tell
# the JM to ignore the respose.
$self->log("qstat returned an unknown response. Telling JM to ignore this poll");
return {};
}
}
}
#
# Not using pbsmsg for now.
#
# if ($state == Globus::GRAM::JobState::ACTIVE)
# {
# $self->l_send_pbsmsg($batch_id);
# }
#
# Dont append the batch.err, as we're using PBSMSG
# Not using PBSMSG for now, so allow appending of batch output
#
$self->helper_cache_import($internal_id,$batch_id,$job_submit_time,\$state,"batch.out","batch.err");
return {
JOB_STATE => $state
};
}
* subroutine poll_batch_system: Allows to know the status of jobs running in the site cluster parsing the output of the qstat SGE command.
sub poll_batch_system
{
my $self = shift;
my ($data_ref,$time_ref) = @_;
my $good_query = 0;
do
{
@$data_ref = ();
$$time_ref = time();
local(*JQ);
if (open(JQ,"export SGE_ROOT=".$sge_base_path." ; $qstat 2>/dev/null |"))
{
my $jid;
while(<JQ>)
{
chomp(my $line = $_);
# [jfontan]
# Changed regexp to match SGE qstat output
if ($line =~ /^ *(\d+) +\d\.\d+ +[^ ]* +[^ ]* +(\w+)/)
{
my $st = $2;
$jid = $1;
push(@$data_ref,$jid." ".$st);
}
}
close(JQ);
$good_query = 1 if $? == 0;
sleep 30 if !$good_query;
}
else
{
$good_query = -1;
}
} while($good_query != 1);
}
* subroutine cancel_in_batch_system: It cancels jobs in the local cluster by using fork.
sub cancel_in_batch_system
{
my $self = shift;
my ($batch_id) = @_;
my $description = $self->{JobDescription};
$self->log("cancel job $batch_id");
$self->cd_fork_and_exec_cmd(undef,0,0,$qdel,$batch_id);
if($? == 0 || $? == 153)
{
return { JOB_STATE => Globus::GRAM::JobState::FAILED }
}
return Globus::GRAM::Error::JOB_CANCEL_FAILED();
}
* subroutine submit_to_batch_system: It submits jobs to the batch system, after building the script to be submitted to the local SGE batch system, by getting the neccesary information from the variables filled with the RSL arguments.
sub submit_to_batch_system
{
my $self = shift;
my ($submit_arg) = @_;
my ($cpu_time,$wall_time) = split('\|',$submit_arg);
my $description = $self->{JobDescription};
my $tag = $description->cache_tag() || $ENV{GLOBUS_GRAM_JOB_CONTACT};
my $cache_pgm = "$Globus::Core::Paths::bindir/globus-gass-cache";
# [jfontan]
# Real and fake stdout/stderr
my $real_stdout;
my $real_stderr;
my $fake_stdout;
my $fake_stderr;
my $script_url = "$tag/sge_job_script";
$self->cd_fork_and_exec_cmd(undef,0,0,$cache_pgm,"-add","-t",$tag,"-n",$script_url,"file:/dev/null");
my $sge_job_script_name = `$cache_pgm -query -t $tag $script_url`;
chomp($sge_job_script_name);
if($sge_job_script_name eq "")
{
return "FAILED";
}
my $sge_job_script = new IO::File($sge_job_script_name, '>');
# [jfontan]
# Changed EOF style by "" and added h_fsize (required by cesga queues)
$sge_job_script->print("
#! /bin/sh
# SGE batch job script built by Globus job manager
#
#\$ -S /bin/sh
");
# [prey]
# Adding the extra parameters if it has been set in the Config file to a non-null value.
if(defined $EXTRA && $EXTRA) {
$sge_job_script->print("#\$ -l ".$EXTRA."\n");
}
if(defined $description->email_address() && $description->email_address() ne '')
{
# [jfontan]
# Mail wont be used with SGE
#$sge_job_script->print("#PBS -M " . $description->email_address() . "\n");
}
if(defined $description->emailonabort() && $description->emailonabort() eq 'yes')
{
$email_when .= 'a';
}
if(defined $description->emailonexecution() && $description->emailonexecution() eq 'yes')
{
$email_when .= 'b';
}
if(defined $description->emailontermination() && $description->emailontermination() eq 'yes')
{
$email_when .= 'e';
}
if($email_when eq '')
{
$email_when = 'n';
}
# [jfontan]
# Mail wont be used with SGE
#$sge_job_script->print("#PBS -m $email_when\n");
if(defined $description->queue() && $description->queue() ne '')
{
$sge_job_script->print("#\$ -q ". $description->queue() . "\n");
}
if(defined $description->project() && $description->project() ne '')
{
# [jfontan]
# Project wont be used with SGE
#$sge_job_script->print("#PBS -A " . $description->project() . "\n");
}
if($cpu_time != 0)
{
my $total_cpu_time;
if($description->jobtype() eq 'multiple')
{
$total_cpu_time = $cpu_time * $description->count();
}
else
{
$total_cpu_time = $cpu_time;
}
#$sge_job_script->print("#PBS -l pcput=${cpu_time}:00\n");
$sge_job_script->print("#\$ -l s_rt=${total_cpu_time}:00\n");
} else {
# [prey]
# Adding s_rt if it has been set in the Config file to a non-null value.
if(defined $S_RT && $S_RT) {
$sge_job_script->print("#\$ -l s_rt=".$S_RT."\n");
}
#$sge_job_script->print("#\$ -l s_rt=10:00:00\n");
}
if($wall_time != 0)
{
# [jfontan]
# Walltime wont be used with SGE
#$sge_job_script->print("#PBS -l walltime=${wall_time}:00\n");
}
if(defined $description->max_memory() && $description->max_memory() != 0)
{
my $max_memory;
if($description->jobtype() eq 'multiple')
{
$max_memory = $description->max_memory() * $description->count;
}
else
{
$max_memory = $description->max_memory();
}
$sge_job_script->print("#\$ -l s_vmem=${max_memory}M\n");
} else {
# [prey]
# Adding s_vmem if it has been set in the Config file to a non-null value.
if(defined $S_VMEM && $S_VMEM) {
$sge_job_script->print("#\$ -l s_vmem=".$S_VMEM."\n");
}
#$sge_job_script->print("#\$ -l s_vmem=512M\n");
}
chomp(my $my_hostname = `hostname -f`);
mkdir '.lcgjm', 0700;
chomp(my $pwd=`pwd`);
chomp(my $cache_export_dir = `mktemp -d $pwd/.lcgjm/globus-cache-export.XXXXXX`);
$self->helper_init_cache_export_url($cache_export_dir);
# [jfontan]
# Deal with stdout/stderr. SGE can not run jobs if it can not write to
# stdout/stderr before starting the job, and $cache_export_dir does not
# exist in worker nodes
my $r_number=int(rand(65536));
$real_stdout=$cache_export_dir."/batch.out";
$real_stderr=$cache_export_dir."/batch.err";
$fake_stdout=$pwd."/.out.".$r_number;
$fake_stderr=$pwd."/.err.".$r_number;
# OLD LCGPBS LINES
# $sge_job_script->print("#\$ -o " . $cache_export_dir."/batch.out" . "\n");
# $sge_job_script->print("#\$ -e " . $cache_export_dir."/batch.err" . "\n");
$sge_job_script->print("#\$ -o " . $fake_stdout . "\n");
$sge_job_script->print("#\$ -e " . $fake_stderr . "\n");
$sge_job_script->print("#\$ -r n\n");
my @tmp_list = split("/",$cache_export_dir);
my $gpg_file = pop(@tmp_list);
$gpg_file .= ".gpg";
# [jfontan]
# stagein is not implemented in SGE, have to deal with that other way (X509SELF)
#$sge_job_script->print("#PBS -W stagein=".$gpg_file."@".$my_hostname.":".$cache_export_dir."/".$gpg_file."\n");
if(defined $description->host_count() && $description->host_count() != 0)
{
$sge_job_script->print("#\$ -l num_proc=" .
$description->host_count().
"\n");
}
elsif($cluster && $cpu_per_node != 0)
{
$sge_job_script->print("#\$ -l num_proc=" .
POSIX::ceil($description->count /
$cpu_per_node).
"\n");
}
else
{
# [prey]
# Adding num_proc if it has been set in the Config file to a non-null value.
if(defined $NUM_PROC && $NUM_PROC) {
$sge_job_script->print("#\$ -l num_proc=".$NUM_PROC."\n");
}
#$sge_job_script->print("#\$ -l num_proc=1\n");
}
my @library_vars=('LD_LIBRARY_PATH');
if($Config::Config{osname} eq 'irix')
{
push(@library_vars,'LD_LIBRARYN32_PATH');
push(@library_vars,'LD_LIBRARY64_PATH');
}
my $rsh_env = "";
my $local_x509 = '-';
my @new_env;
foreach my $tuple ($description->environment())
{
$tuple->[0] =~ s/"/\\\"/g;
$tuple->[1] =~ s/"/\\\"/g;
$self->helper_armour(\$tuple->[0]);
$self->helper_armour(\$tuple->[1]);
push(@new_env, $tuple->[0] . "=" . '"' . $tuple->[1] . '"');
$local_x509 = $tuple->[1] if $tuple->[0] eq 'X509_USER_PROXY';
$rsh_env .= $tuple->[0] . "=\"" . $tuple->[1] . "\"\n"
. "export " . $tuple->[0] . "\n";
}
# [jfontan]
# Add environment directly in the script.
# Changed the method to exporting the environment variables directly in the
# script as SGE had some troubles using -v parameter with too much variables
#$sge_job_script->print("#\$ -v " . join(',', @new_env) . "\n");
foreach my $env_line (@new_env)
{
$sge_job_script->print("export " . $env_line . "\n");
}
if (defined $description->library_path() && $description->library_path() ne '')
{
my @library_path;
if (ref $description->library_path())
{
foreach my $tuple ($description->library_path())
{
push(@library_path,@$tuple);
}
}
else
{
@library_path = ($description->library_path());
}
my $library_path = join(":",@library_path);
foreach my $lib_var (@library_vars)
{
# [jfontan]
# Changed EOF by ""
$sge_job_script->print("
if test \"X\${$lib_var}\" != \"X\"; then
$lib_var=\"\${$lib_var}:$library_path\"
else
$lib_var=\"$library_path\"
fi
export $lib_var
");
$rsh_env .= "if test \"X\${$lib_var}\" != \"X\"; then\n";
$rsh_env .= "$lib_var=\"\${$lib_var}:$library_path\"\n";
$rsh_env .= "else\n";
$rsh_env .= "$lib_var=\"$library_path\"\n";
$rsh_env .= "fi\n";
$rsh_env .= "export $lib_var\n";
}
}
# [jfontan]
# Here we can have a problem if the first parameter is "0"
# [TODO] fix it
my $args="";
my @arguments = $description->arguments();
if($arguments[0])
{
foreach my $arg (@arguments)
{
$self->log("Transforming argument \"$arg\"\n");
$self->helper_armour(\$arg);
$self->log("Transformed to \"$arg\"\n");
$args .= '"' . $arg . '" ';
}
}
# if($description->jobtype() eq "mpi")
# {
# $sge_job_script->print("\n#Change to directory requested by user\n");
# $sge_job_script->print('cd ' . $description->directory() . "\n");
#
# $sge_job_script->print("$mpirun -np " . $description->count() . " ");
#
# if($cluster)
# {
# $sge_job_script->print(" -machinefile \$PBS_NODEFILE ");
# }
# $sge_job_script->print($description->executable()
# . " $args < "
# . $description->stdin() . "\n");
# }
# elsif...
# [jfontan]
# Link fake stdout/stderr to the real one so the script can send back the results
$sge_job_script->print("mkdir -p $cache_export_dir\n");
$sge_job_script->print("touch $fake_stdout\n");
$sge_job_script->print("ln $fake_stdout $real_stdout\n");
$sge_job_script->print("touch $fake_stderr\n");
$sge_job_script->print("ln $fake_stderr $real_stderr\n");
# [jfontan]
# Add grid environment. This is needed in our cluster because WN are not
# installed the standard way. This is not needed for standard LCG WN.
# $sge_job_script->print(". /opt/cesga/lcg/etc/profile.d/grid_env.sh\n");
# [prey]
# Adding the grid enviroment if it has been set in the Config file to a non-null value.
if(defined $GRID_ENV && $GRID_ENV) {
$sge_job_script->print(". ".$GRID_ENV."\n");
}
@tmp_list=();
$self->helper_get_from_tmp_file("scratch",\@tmp_list);
my $gram_scratch_dir = (scalar(@tmp_list)>0) ? $tmp_list[0] : '-';
# [jfontan]
# Changed method to send the proxy from GPG to SELF (embeded in the script)
if(($description->jobtype() eq 'multiple' && !$cluster) || $description->jobtype() eq 'single')
{
# $self->helper_write_non_mpi_script($sge_job_script,$my_hostname,$local_x509,
# "X509GPG",$cache_export_dir,$gram_scratch_dir,"NONE",$args);
$self->helper_write_non_mpi_script($sge_job_script,$my_hostname,$local_x509,
"X509SELF",$cache_export_dir,$gram_scratch_dir,"NONE",$args);
}
elsif($description->jobtype() eq 'multiple')
{
# $self->helper_write_fake_mpi_script($sge_job_script,$rsh_env,$my_hostname,$local_x509,
# "X509GPG",$cache_export_dir,$gram_scratch_dir,"NONE",$args);
$self->helper_write_fake_mpi_script($sge_job_script,$rsh_env,$my_hostname,$local_x509,
"X509SELF",$cache_export_dir,$gram_scratch_dir,"NONE",$args);
my $count = $description->count;
# [jfontan]
# Changed EOF by ""
# [TODO] This wont work but multiple jobs are not a priority
$sge_job_script->print("
hosts=\`cat \$PBS_NODEFILE\`;
counter=0
while test \$counter -lt $count; do
for host in \$hosts; do
if test \$counter -lt $count; then
rsh_bootstrap=\`$remote_shell \$host mktemp /tmp/rsh_bootstrap.XXXXXX\`
$remote_shell \$host \"cat > \$rsh_bootstrap; chmod 700 \$rsh_bootstrap;\ \$rsh_bootstrap; rm \$rsh_bootstrap\" < \$local_bootstrap &
counter=\`expr \$counter + 1\`
else
break
fi
done
done
wait
rm \$local_bootstrap
");
}
# [jfontan]
# Delete cache dir and stdout/stderr
# After the job completes stdout/stderr files are not deleted so $cache_export_dir
# will remain in the home diretory.
$sge_job_script->print("rm -rf ".$cache_export_dir."\n");
# [jfontan]
# Could not delete this files until the job finishes :(
# ...this is a job for... epilog!
# This files are referenced by SGE_STDOUT_PATH and SGE_STDERR_PATH
#$sge_job_script->print("rm -f ".$fake_stdout."\n");
#$sge_job_script->print("rm -f ".$fake_stderr."\n");
$sge_job_script->close();
my $errfile;
if($description->logfile() ne "")
{
$errfile = "2>>" . $description->logfile();
}
$self->helper_cache_export();
$self->helper_remove_tmp_file();
return "FAILED" if ! -e $local_x509;
symlink $local_x509,$cache_export_dir."/.emergency-x509";
symlink $sge_job_script_name,$cache_export_dir."/.submit-script";
$self->cd_fork_and_exec_cmd(undef,0,0,"/bin/cp",$local_x509,$cache_export_dir."/.emergency-x509.ref");
my $batch_id;
my $submit_status;
my $attempts=0;
do
{
#chomp($batch_id = `$qsub < $sge_job_script_name 2>&1 > $errfile`);
# [jfontan]
# DEBUG: copy script to /tmp
#system("cp -f $sge_job_script_name /tmp/sge_job_script");
chomp($tmp_batch_id = `export SGE_ROOT=$sge_base_path ;$qsub < $sge_job_script_name`);
$submit_status = $?;
# [jfontan]
# The way SGE qsub tells the job number is different to PBS
if($tmp_batch_id =~ /^Your job (\d*)/) {
$batch_id = $1;
}
$self->log("Batch ID: " . $batch_id);
if ($submit_status != 0)
{
$batch_id = undef;
sleep 5;
}
$attempts++;
} while($submit_status != 0 && $attempts<6);
if (!defined $batch_id)
{
$batch_id = "FAILED";
}
return $batch_id;
}
1;
PREREQUISITES
- The SGE client tools ( qsub, qstat, etc) must be available in the CE
- The home directories should have the same path in the CE and in the WN
- The Job Manager use the XML::Simple.pm perl module. It can be installed using the following command:
perl -MCPAN -e 'install XML::Simple'
INSTALLATION
- Copy JobManager/lcgsge.pm and JobManager/lcgsge.conf to /opt/globus/lib/perl/Globus/GRAM/JobManager/
- Edit lcgsge.conf to best fit your needs. This is the content of lcgsge.conf:
# SGE paths $SGE_BASE_PATH = '/opt/sge6'; $SGE_BIN_PATH = '/opt/sge6/bin/lx24-x86'; # Default values for SGE required complex values # In case SGE forces to specify a given set of parameters you can # specify the default values in this section # If you don't need to define some parameter you should to set it # to an empty string or to 0. For example: #$S_VMEM = ''; #$NUM_PROC = 0'; # Parameters that could be availables in the jdl file # These values are only use in case a value is not specified # in the jdl file #max cpu time #$S_RT = '10:00:00'; $S_RT = ''; #max memory #$S_VMEM = '512M'; $S_VMEM = ''; #number of processors #$NUM_PROC = 1; $NUM_PROC = 0; # Extra parameters not available in the jdl file. #$EXTRA = 'h_fsize=5G,s_cpu=0:10:0'; $EXTRA = ''; # Add grid environment. This is needed if the middleware is not # installed in the standard location in the WNs. # This is not needed for standard WN. #$GRID_ENV = '/opt/cesga/lcg/etc/profile.d/grid_env.sh'; $GRID_ENV = '';
- Edit /etc/globus.conf and add the following lines:
[gatekeeper/lcgsge] type=lcgsgeAnd restart globus-gatekeeper:
service globus-gatekeeper restartIn this way globus will add automatically the SGE jobmanager service to /opt/globus/etc/grid-services
- Copy the file conf/lcgsge.rvf to /opt/globus/share/globus_gram_job_manager/lcgsge.rvf. This file contains the queues where the jobmanager can submit.
- Edit lcgsge.rvf and adjust the queue values ( CHANGEME) to your current SGE configuration
- Configure the SGE queues to use the epilog file available in conf/epilog.sh so that home directories are cleaned after the job finishes
TESTING IT
Check the installation with:globus-job-run <CE_HOST>:2119/jobmanager-lcgsge -q <QUEUE> /bin/hostname edg-job-submit -r <CE_HOST>:2119/jobmanager-lcgsge-<SGE_QUEUE> job.jdl
SUPPORT
For further details about 'SGE LCG Job Manager' check: SGE_integration_with_LCG_at_CESGASGE LCG Information Provider
This is the SGE LCG information provider currently being used at CESGA with LCG 2.7.0. It is based in the SGE LCG information provider developed by David McBride from Imperial College.PREREQUISITES
- The SGE client tools ( qsub, qstat, etc) must be available in the CE
INSTALLATION
- Copy gip/plugin/lcg-info-dynamic-sge to /opt/lcg/var/gip/plugin/
- Copy gip/ldif/static-file-sge.ldif to /opt/lcg/var/gip/ldif/
- Edit /opt/lcg/var/gip/ldif/static-file-sge.ldif and replace <CE_HOST>, <SE_HOST> and <SGE_QUEUE> with the corresponding values for your site
- Copy the directory gip/sge/ to /opt/lcg/var/gip/
- Copy lcg-info-dynamic-sge to /opt/lcg/libexec/
- Edit /opt/lcg/libexec/lcg-info-dynamic-sge to best fit your needs:
- Adjust the paths in the beginning of the file
- Replace each occurrence of "GRID" with the name of the SGE queue that will used to run grid jobs
- In the line
$jobentry->{"JB_owner"} !~ /^cesga\d\d\d$/ ) {replace cesga with the name of the pool accounts you are using to run grid jobs (if you are using several pool accounts you can use (pool1|pool2|...))
- Create an empty sge-jobmanager.conf file
touch /etc/sge-jobmanager.conf
TESTING IT
Check the output of:ldapsearch -x -H ldap://<CE_HOST>:2135 -b mds-vo-name=local,o=grid
SUPPORT
In case of problems contact egee-admin@cesgaNOSPAMPLEASE.esSGE and Apel
Introduction
The Apel software is composed of two components: The Log Parser and Publisher. The Log Parser interprets log files to extract job information and publishes it using R-GMA. Specifically, it processes the LCG gatekeeper logs, the system message logs and the batch system (PBS, LSF, SGE, ...) event logs. Extracted data is then stored within a MySQL database. The Apel Log Parser also makes LDAP queries of the Computing Element to obtain the CPU performance figures for the worker node clusters and sub-clusters. The Publisher is used to generate accounting records derived from the parsed logging data. The accounting records are then published into R-GMA where they are then collected by a central accounting server which, aggregates records from all sites. You can get more information about Apel in the Apel User Guide and the Apel Schema which can be download from http://goc.grid-support.ac.uk/gridsite/accounting/index.html.
Publisher
The Publisher is used to piece together accounting records derived from data parsed from gate keeper, system message and event log files. The generated data is stored locally within a MySQL database and is also published into R-GMA. The published data will then be stored by R-GMA onto the central accounting server. The Publisher is deployed on the same host that runs the MySQL server, normally the MON Box. The Publisher is independent of the Log Parser used. You can get more information about the Publisher in the Apel User Guide.Log Parser
The Log Parser is used to parse gate keeper, system message and event logs produced by a site running a batch processing system. Currently, the Log Parser comes in several different flavours: PBS, LSF, SGE, Condor, .... The Log Parser you choose will depend upon the batch processing system used by the site. However, the deployment and configuration are both equivalent. In this case we will speak about the SGE flavour. The Log Parser can be deployed in a variety of ways depending upon the setup of your site. An overview of some of the typical deployments are described in the Apel User Guide. We use the Combined GK/CE option. In this setup the Log Parser is configured to process both the gate keeper logs and event logs but on the same host. At this moment the Log Parser for PBS and LSF comes with its own rpm package included in the installation of the CE. It requires the Apel Core module to be installed (included also in the installation of the CE). The Log Parser for SGE has to be installed manually. You can get the corresponding rpm from http://goc.grid-support.ac.uk/gridsite/accounting/latestBuild.html.
The rpm installs the following components (using the SGE Log Parser as an example): - /opt/glite/bin/apel-sge-log-parser the script used to run the Log Parser.
- /opt/glite/etc/glite-apel-sge/parser-config.xml contains an example config file used by the Log Parser.
25 06 * * * root env RGMA_HOME=/opt/glite APEL_HOME=/opt/glite /opt/glite/bin/apel-sge-log-parser -f /opt/glite/etc/glite-apel-sge/parser-config-yaim.xml >> /var/log/apel.log 2>&1The Log Parser is setup using a configuration file encoded in an XML format. The configuration file is composed of a list of processors. Each processor carries out a unit of functionality. When the Log Parser is started, the program will find any processors defined within the config file and will attempt to schedule each one consecutively. This is the config file used in our site:
<?xml version="1.0" encoding="UTF-8"?>
<ApelConfiguration enableDebugLogging="yes">
<SiteName>CESGA-EGEE</SiteName>
<DBURL>jdbc:mysql://mon.egee.cesga.es:3306/accounting</DBURL>
<DBUsername>***********</DBUsername>
<DBPassword>***********</DBPassword>
<CPUProcessor>
<GIIS>mon.egee.cesga.es</GIIS>
</CPUProcessor>
<EventLogProcessor>
<Logs searchSubDirs="yes" reprocess="no">
<Dir>/var/log/sge</Dir>
</Logs>
<Timezone>UTC</Timezone>
</EventLogProcessor>
<GKLogProcessor>
<SubmitHost>ce2.egee.cesga.es</SubmitHost>
<Logs searchSubDirs="yes" reprocess="no">
<GKLogs>
<Dir>/var/log</Dir>
</GKLogs>
<MessageLogs>
<Dir>/var/log</Dir>
</MessageLogs>
</Logs>
</GKLogProcessor>
</ApelConfiguration>
The SGE accounting log file
The SGE batch log file has a simple format using : as a field separator. These are the fields that you can find in the accounting log file:qname:hostname:group:owner:jobname:jobnumber:account:priority:qsub_time:start_time: end_time:failed:exit_status:ru_wallclock:ru_utime:ru_stime:ru_maxrss:ru_ixrss:ru_ismrss: ru_idrss:ru_isrss:ru_minflt:ru_majflt:ru_nswap:ru_inblock:ru_oublock:ru_msgsnd:ru_msgrcv: ru_nsignals:ru_nvcsw:ru_nivcsw:project:department:granted_pe:slots:UNKNOWN:cpu:mem: UNKNOWN:command_line_arguments:UNKNOWN:UNKNOWN:maxvmem_bytesBelow you can find an real example:
GRID:compute-1-25.local:cesga:cesga013:STDIN:865666:sge:0:1149045197:1149045325: 1149045327:0:0:2:0:0:0.000000:0:0:0:0:18439:0:0:0.000000:0:0:0:0:2935:240:NONE: defaultdepartment:NONE:1:0:0.010000:0.000020:0.000000:-U cesgaGRID_solocesga, cesgaGRID -q GRID -l h_fsize=5G,num_proc=1,s_rt=36000,s_vmem=512M:0.000000: NONE:10375168.000000The accounting file format is documented in the SGE man 5 page "accounting" (http://gridengine.sunsource.net/nonav/source/browse/~checkout~/gridengine/doc/htmlman/htmlman5/accounting.html
).
Normally, the SGE server ( qmaster) is located in the CE machine but in our case it is located in other machine. So we have to copy the SGE batch log files from this machine to the CE.
In the SGE server we have setup a cron entry which is in charge of copy daily the SGE batch log file from this machine to the CE. This is the script used to do this job:
#!/bin/sh # To take into account the change in month TZ=MET+24 export TZ DIA=`date "+%d"` MES=`date "+%m"` ANHO=`date "+%Y"` grep ^GRID /home/cesga/casperez/accounting/$ANHO$MES$DIA | ssh sge@ce2.egee.cesga.es 'cat - >> /var/log/sge/accounting'This script search the grid jobs in the SGE batch log file corresponding to the day before the current date and copy the output to a file in the CE. We need to configure the access without password from the SGE server to the CE using the ssh-keygen command and the authorized_keys file.
The Gatekeeper log file
Apel used the the JMA records listed in the Gatekeeper log file. All the records in the GK log contain the GATEKEEPER_JM_ID field. The GRAM_SCRIPT_JOB_ID and the DN are in different GK log records and this field permits them to be matched up. It serves no other purpose and does not propagate further. This is an example:JMA 2006/05/31 04:43:25 GATEKEEPER_JM_ID 2006-05-31.04:42:03.0000002096.0000052290 for /C=ES/O=DATAGRID-ES/O=CESGA/CN=Jose Carlos Mourino Gallego on 193.144.34.236 JMA 2006/05/31 04:43:31 GATEKEEPER_JM_ID 2006-05-31.04:42:03.0000002096.0000052290 has GRAM_SCRIPT_JOB_ID 1149043405:lcgsge:internal_1053670411:4710.1149043396 manager type lcgsge
The System Message log file
The MessageRecords table is built from data written to the system messages log files when the job manager is launched and when the batch job has completed. This is an example:May 31 05:13:18 ce2 gridinfo: [31767-11715] Submitted job 1149043405:lcgsge:internal_1053670411: 4710.1149043396 to batch system lcgsge with ID 865666 May 31 05:33:29 ce2 gridinfo: [31767-31767] Job 1149043405:lcgsge:internal_1053670411: 4710.1149043396 (ID 865666) has finished
Example of Accounting Record (LcgRecords)
Using the previous examples of event, gatekeeper and system message logs this the final accounting record which is stored in the LcgRecords table:| Field | Value |
|---|---|
| RecordIdentity | 2006-05-31 03:15:27 865666 ce2.egee.cesga.es CESGA-EGEE |
| ExecutingSite | CESGA-EGEE |
| LocalJobID | 865666 |
| LCGJobID | NULL |
| LocalUserID | cesga013 |
| LCGUserID | /C=ES/O=DATAGRID-ES/O=CESGA/CN=Jose Carlos Mourino Gallego |
| LCGUserVO | cesga |
| ElapsedTime | P2S |
| BaseCpuTime | P0S |
| ElapsedTimeSeconds | 2 |
| BaseCpuTimeSeconds | 0 |
| StartTime | 2006-05-31T03:15:25Z |
| StopTime | 2006-05-31T03:15:27Z |
| StartTimeUTC | 2006-05-31T03:15:25Z |
| StopTimeUTC | 2006-05-31T03:15:27Z |
| StartTimeEpoch | 1149045325 |
| StopTimeEpoch | 1149045327 |
| ExecutingCE | ce2.egee.cesga.es |
| MemoryReal | NULL |
| MemoryVirtual | NULL |
| SpecInt2000 | 381 |
| SpecFloat2000 | 0 |
| EventDate | 2006-05-31 |
| EventTime | 03:15:27 |
| MeasurementDate | 2006-06-02 |
| MeasurementTime | 05:17:06 |
Imperial SGE implementation
For all the details see http://www.gridpp.ac.uk/wiki/LCG-on-SGE#Explanation:_The_Information_Reporter
SA3 SGE TESTBED
SGE Testbed and Stress testsTopic revision: r33 - 2011-06-21 - AndresAeschlimann
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