LIGO Support Ticket 7740
Ticket Information
Number: support 7740
User: dabrown@physics.syr.edu
Email: anderson__AT__ligo.caltech.edu,carsten.aulbert__AT__aei.mpg.de,henning.fehrmann__AT__aei.mpg.de
Status: resolved
Assigned To: 0
From: Duncan Brown <dabrown__AT__physics.syr.edu>
To: condor-support response tracking system <condor-support__AT__cs.wisc.edu>
Subject: LIGO: problem with large dagman.out files on atlas
Date: Tue, 28 Oct 2008 17:49:05 -0400
CC: Stuart Anderson <anderson__AT__ligo.caltech.edu>, Carsten Aulbert
<carsten.aulbert__AT__aei.mpg.de>, Henning Fehrmann
<henning.fehrmann__AT__aei.mpg.de>
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Hi Kent,
Is condor_dagman currently limited to 32 byte file support? We have=20=20
some inspiral users who's dags are constantly starting and then=20=20
exiting repeatedly. The messages in the dagman.log file are
001 (5476704.000.000) 10/28 22:45:40 Job executing on host:=20=20
<10.20.30.2:56331>
...
004 (5476704.000.000) 10/28 22:45:40 Job was evicted.
(0) Job was not checkpointed.
Usr 0 00:00:00, Sys 0 00:00:00 - Run Remote Usage
Usr 0 00:00:00, Sys 0 00:00:00 - Run Local Usage
0 - Run Bytes Sent By Job
0 - Run Bytes Received By Job
...
001 (5476704.000.000) 10/28 22:45:50 Job executing on host:=20=20
<10.20.30.2:56331>
...
004 (5476704.000.000) 10/28 22:45:50 Job was evicted.
(0) Job was not checkpointed.
Usr 0 00:00:00, Sys 0 00:00:00 - Run Remote Usage
Usr 0 00:00:00, Sys 0 00:00:00 - Run Local Usage
0 - Run Bytes Sent By Job
0 - Run Bytes Received By Job
...
over and over again. In the ScheddLog, I see the messages:
10/28 20:08:28 (pid:2297) Starting add_shadow_birthdate(5476704.0)
10/28 20:08:28 (pid:2297) Called reschedule_negotiator()
10/28 20:08:46 (pid:2297) scheduler universe job (5476704.0) pid 6741=20=20
exited with status 44
The only thing I can see that may be causing a problem is that the=20=20
dagman.out file is over 2Gb:
[dbrown@h2 injections32]$ ls -l *dag.dagman*
-rw-r--r-- 1 marion atlas 2909132 Oct 28 22:38=20=20
injections32.GRB070714_injections32.dag.dagman.log
-rw-r--r-- 1 marion atlas 2147483700 Oct 28 05:52=20=20
injections32.GRB070714_injections32.dag.dagman.out
Is this a large file support issue? This is condor_dagman 7.1.1 on the=20=
=20
Atlas cluster. Below is the full job class ad for the dagman process.
Cheers,
Duncan.
[dbrown@h2 condor]$ condor_q -long 5476704.0
-- Submitter: h2.atlas.local : <10.20.30.2:56331> : h2.atlas.local
MyType =3D "Job"
TargetType =3D "Machine"
ClusterId =3D 5476704
QDate =3D 1225220908
CompletionDate =3D 0
Owner =3D "marion"
LocalUserCpu =3D 0.000000
LocalSysCpu =3D 0.000000
RemoteUserCpu =3D 0.000000
RemoteSysCpu =3D 0.000000
NumCkpts_RAW =3D 0
NumCkpts =3D 0
NumRestarts =3D 0
NumSystemHolds =3D 0
CommittedTime =3D 0
TotalSuspensions =3D 0
CumulativeSuspensionTime =3D 0
CondorVersion =3D "$CondorVersion: 7.0.5 Oct 22 2008 $"
CondorPlatform =3D "$CondorPlatform: X86_64-LINUX_DEBIAN40 $"
RootDir =3D "/"
Iwd =3D "/home/marion/analysis/GRB070714/injections32"
JobUniverse =3D 7
Cmd =3D "/opt/condor/bin/condor_dagman"
MinHosts =3D 1
MaxHosts =3D 1
WantRemoteSyscalls =3D FALSE
WantCheckpoint =3D FALSE
JobPrio =3D 0
User =3D "marion__AT__atlas.local"
NiceUser =3D FALSE
Env =3D "CLASSPATH=3D/usr/local/ldg-4.5-server/vdt/pegasus/lib/exist.jar:/=
=20
usr/local/ldg-4.5-server/vdt/pegasus/lib/preservcsl.jar:/usr/local/=20
ldg-4.5-server/vdt/pegasus/lib/log4j-1.2.8.jar:/usr/local/ldg-4.5-=20
server/vdt/pegasus/lib/cog-jglobus.jar:/usr/local/ldg-4.5-server/vdt/=20
pegasus/lib/pegasus.jar:/usr/local/ldg-4.5-server/vdt/pegasus/lib/=20
accessors.jar:/usr/local/ldg-4.5-server/vdt/pegasus/lib/jakarta-=20
oro.jar:/usr/local/ldg-4.5-server/vdt/pegasus/lib/xmlrpc.jar:/usr/=20
local/ldg-4.5-server/vdt/pegasus/lib/puretls.jar:/usr/local/ldg-4.5-=20
server/vdt/pegasus/lib/xercesImpl.jar:/usr/local/ldg-4.5-server/vdt/=20
pegasus/lib/globus_rls_client.jar:/usr/local/ldg-4.5-server/vdt/=20
pegasus/lib/mysql-connector-java-5.0.5-bin.jar:/usr/local/ldg-4.5-=20
server/vdt/pegasus/lib/cryptix.jar:/usr/local/ldg-4.5-server/vdt/=20
pegasus/lib/cryptix32.jar:/usr/local/ldg-4.5-server/vdt/pegasus/lib/=20
jce-jdk13-125.jar:/usr/local/ldg-4.5-server/vdt/pegasus/lib/=20
postgresql-8.1dev-400.jdbc3.jar:/usr/local/ldg-4.5-server/vdt/pegasus/=20
lib/cryptix-asn1.jar:/usr/local/ldg-4.5-server/vdt/pegasus/lib/commons-=20
pool.jar:/usr/local/ldg-4.5-server/vdt/pegasus/lib/xmldb.jar:/usr/=20
local/ldg-4.5-server/vdt/pegasus/lib/commons-logging.jar:/usr/local/=20
ldg-4.5-server/vdt/pegasus/lib/java-getopt-1.0.9.jar:/usr/local/=20
ldg-4.5-server/vdt/pegasus/lib/resolver.jar:/usr/local/ldg-4.5-server/=20
vdt/pegasus/lib/xmlParserAPIs.jar:/usr/local/ldg-4.5-server/vdt/=20
pegasus/lib/exist-optional.jar:/usr/local/ldg-4.5-server/vdt/pegasus/=20
lib/junit.jar;HOSTTYPE=3Dx86_64-linux;SHLIB_PATH=3D/usr/local/ldg-4.5-=20
server/vdt/globus/lib;LSCSOFT_LOCATION=3D/home/nvf/s5grb/=20
releases;GLOBUS_OPTIONS=3D-Xmx512M;PAC_ANCHOR=3D/usr/local/ldg-4.5-=20
server;SHLVL=3D1;PWD=3D/home/marion/analysis/GRB070714/=20
injections32;GRID_SECURITY_DIR=3D/usr/local/ldg-4.5-server/vdt/globus/=20
etc;VDT_LOCATION=3D/usr/local/ldg-4.5-server/=20
vdt;SSH_CLIENT=3D193.205.72.95 39455=20=20
22;REMOTEHOST=3Dmbta1.virgo.infn.it;VDT_POSTINSTALL_README=3D/usr/local/=20
ldg-4.5-server/vdt/post-install/README;PATH=3D/home/nvf/s5grb/releases/=20
s5_exttrig_20081003/glue/bin:/home/nvf/s5grb/releases/=20
s5_exttrig_20081011/pylal/bin:/home/nvf/s5grb/releases/=20
s5_exttrig_20081003/lalapps/bin:/home/nvf/s5grb/releases/=20
s5_exttrig_20081011/lal/bin:/opt/condor/bin:/opt/condor/sbin:/usr/=20
local/ldg-4.5-server/vdt/tcl/bin:/usr/local/ldg-4.5-server/vdt/apache/=20
bin:/usr/local/ldg-4.5-server/vdt/ant/bin:/usr/local/ldg-4.5-server/=20
vdt/glite/sbin:/usr/local/ldg-4.5-server/vdt/glite/bin:/usr/local/=20
ldg-4.5-server/vdt/pegasus/bin:/usr/local/ldg-4.5-server/vdt/pyglobus-=20
url-copy/bin:/usr/local/ldg-4.5-server/vdt/unixodbc/bin:/usr/local/=20
ldg-4.5-server/vdt/mysql/bin:/usr/local/ldg-4.5-server/vdt/edg/sbin:/=20
usr/local/ldg-4.5-server/vdt/jdk1.5/bin:/usr/local/ldg-4.5-server/vdt/=20
condor/sbin:/usr/local/ldg-4.5-server/vdt/condor/bin:/usr/local/=20
ldg-4.5-server/vdt/logrotate/sbin:/usr/local/ldg-4.5-server/vdt/gpt/=20
sbin:/usr/local/ldg-4.5-server/vdt/globus/bin:/usr/local/ldg-4.5-=20
server/vdt/globus/sbin:/usr/local/ldg-4.5-server/pacman-3.21/bin:/usr/=20
local/ldg-4.5-server/vdt/vdt/sbin:/usr/local/ldg-4.5-server/vdt/vdt/=20
bin:/usr/local/ldg-4.5-server/ldg-server/bin:/usr/bin:/bin:/usr/sbin:/=20
sbin;SASL_PATH=3D/usr/local/ldg-4.5-server/vdt/globus/lib/=20
sasl;GLITE_LOCATION_LOG=3D/usr/local/ldg-4.5-server/vdt/glite/=20
log;VDT_INSTALL_LOG=3Dvdt-install.log;DYLD_LIBRARY_PATH=3D/home/nvf/s5grb/=
=20
releases/s5_exttrig_20081003/glue/lib/python2.4/site-packages:/home/=20
nvf/s5grb/releases/s5_exttrig_20081011/pylal/lib/python2.4/site-=20
packages:/home/nvf/s5grb/releases/s5_exttrig_20081011/lal/lib:/usr/=20
local/ldg-4.5-server/vdt/globus/lib;GLOBUS_PATH=3D/usr/local/ldg-4.5-=20
server/vdt/globus;X509_CERT_DIR=3D/usr/local/ldg-4.5-server/vdt/globus/=20
TRUSTED_CA;GLOBUS_TCP_PORT_RANGE=3D40000,45000;LAL_PREFIX=3D/home/nvf/=20
s5grb/releases/s5_exttrig_20081011/lal;VENDOR=3Dunknown;VOMS_USERCONF=3D/=
=20
usr/local/ldg-4.5-server/vdt/glite/etc/=20
vomses;HOST=3Dh2;LDG_SOFTWARE_LOCATION=3Dhttp://www.ldas-sw.ligo.caltech.ed=
u/ldg_dist/ldg4.5/software;PKG_CONFIG_PATH=3D/home/nvf/s5grb/releases/s5_ex=
ttrig_20081011/lal/lib/pkgconfig;GLITE_LOCATION_TMP=3D/usr/local/ldg-4.5-se=
rver/vdt/glite/tmp;GLITE_LOCATION=3D/usr/local/ldg-4.5-server/vdt/glite;SSH=
_TTY=3D/dev/pts/4;GLITE_LOCATION_VAR=3D/usr/local/ldg-4.5-server/vdt/glite/=
var;LIBPATH=3D/usr/local/ldg-4.5-server/vdt/globus/lib:/usr/lib:/lib;SHELL=
=3D/usr/bin/tcsh;LDG_INSTALL_LOG=3D/usr/local/ldg-4.5-server/ldg-server/etc=
/ldg-install.log;MACHTYPE=3Dx86_64;LDG_DIRECTORY=3D/usr/local/ldg-4.5-serve=
r/ldg-server;MAIL=3D/var/mail/marion;_CONDOR_MAX_DAGMAN_LOG=3D0;MANPATH=3D/=
home/nvf/s5grb/releases/s5_exttrig_20081003/lalapps/share/man:/home/nvf/s5g=
rb/releases/s5_exttrig_20081011/lal/share/man:/usr/local/ldg-4.5-server/vdt=
/pegasus/man:/usr/local/ldg-4.5-server/vdt/condor/man:/usr/local/ldg-4.5-se=
rver/vdt/globus/man:/usr/local/ldg-4.5-server/vdt/vdt/man:/usr/local/ldg-4.=
5-server/vdt/perl/man:/usr/local/ldg-4.5-ser=20
ver/vdt/expat/man:/usr/local/ldg-4.5-server/vdt/logrotate/man:/usr/local/ld=
g-4.5-server/vdt/jdk1.5/man:/usr/local/ldg-4.5-server/vdt/edg/share/man:/us=
r/local/ldg-4.5-server/vdt/mysql/man:/usr/local/ldg-4.5-server/vdt/glite/sh=
are/man:/usr/local/ldg-4.5-server/vdt/apache/man:/usr/local/ldg-4.5-server/=
vdt/tcl/man;GLUE_PREFIX=3D/home/nvf/s5grb/releases/s5_exttrig_20081003/glue=
;MYSQL_UNIX_PORT=3D/usr/local/ldg-4.5-server/vdt/vdt-app-data/mysql/var/mys=
ql.sock;DISPLAY=3Dlocalhost:16.0;GLUE_LOCATION=3D/home/nvf/s5grb/releases/s=
5_exttrig_20081003/glue;PERL5LIB=3D/usr/local/ldg-4.5-server/ldg-server/lib=
:/usr/local/ldg-4.5-server/vdt/pegasus/lib/perl:/usr/local/ldg-4.5-server/v=
dt/vdt/lib:/usr/local/ldg-4.5-server/vdt/perl/lib/5.8.0:/usr/local/ldg-4.5-=
server/vdt/perl/lib/5.8.0/x86_64-linux-thread-multi:/usr/local/ldg-4.5-serv=
er/vdt/perl/lib/site_perl/5.8.0:/usr/local/ldg-4.5-server/vdt/perl/lib/site=
_perl/5.8.0/x86_64-linux-thread-multi:;ANT_HOME=3D/usr/local/ldg-4.5-server=
/vdt/ant;USER=3Dmarion;SSH_=20
CONNECTION=3D193.205.72.95 39455 130.75.116.11 22;LD_LIBRARY_PATH=3D/home/=
=20
nvf/s5grb/releases/s5_exttrig_20081003/glue/lib/python2.4/site-=20
packages:/home/nvf/s5grb/releases/s5_exttrig_20081011/pylal/lib/=20
python2.4/site-packages:/home/nvf/s5grb/releases/s5_exttrig_20081011/=20
lal/lib:/usr/local/ldg-4.5-server/vdt/tclglobus/lib:/usr/local/ldg-4.5-=20
server/vdt/tcl/lib:/usr/local/ldg-4.5-server/vdt/apache/lib:/usr/local/=20
ldg-4.5-server/vdt/glite/lib:/usr/local/ldg-4.5-server/vdt/myodbc/lib:/=20
usr/local/ldg-4.5-server/vdt/unixodbc/lib:/usr/local/ldg-4.5-server/=20
vdt/mysql/lib/mysql:/usr/local/ldg-4.5-server/vdt/jdk1.5/jre/lib/i386:/=20
usr/local/ldg-4.5-server/vdt/jdk1.5/jre/lib/i386/server:/usr/local/=20
ldg-4.5-server/vdt/jdk1.5/jre/lib/i386/client:/usr/local/ldg-4.5-=20
server/vdt/berkeley-db/lib:/usr/local/ldg-4.5-server/vdt/expat/lib:/=20
usr/local/ldg-4.5-server/vdt/globus/lib;PYTHONPATH=3D/home/nvf/s5grb/=20
releases/s5_exttrig_20081003/glue/lib/python2.4/site-packages:/home/=20
nvf/s5grb/releases/s5_exttrig_20081011/pylal/lib/python2.4/site-=20
packages:/home/nvf/s5grb/releases/s5_exttrig_20081003/lalapps/lib/=20
python2.4/site-packages:/usr/local/ldg-4.5-server/ldg-server/lib/=20
python:/usr/local/ldg-4.5-server/vdt/globus/lib64/python:/usr/local/=20
ldg-4.5-server/vdt/globus/lib/python;X509_CADIR=3D/usr/local/ldg-4.5-=20
server/vdt/globus/TRUSTED_CA;CATALINA_OPTS=3D-=20
Dorg.globus.wsrf.container.persistence.dir=3D/usr/local/ldg-4.5-server/=20
vdt/vdt-app-data/globus/persisted;ODBCINI=3D/usr/local/ldg-4.5-server/=20
vdt/unixodbc/etc/odbc.ini;LAL_LOCATION=3D/home/nvf/s5grb/releases/=20
s5_exttrig_20081011/lal;HOME=3D/home/marion;LOGNAME=3Dmarion;EDG_LOCATION=
=3D/=20
usr/local/ldg-4.5-server/vdt/edg;GPT_LOCATION=3D/usr/local/ldg-4.5-=20
server/vdt/gpt;GLOBUS_ERROR_VERBOSE=3Dtrue;GROUP=3Datlas;JAVA_HOME=3D/usr/=
=20
local/ldg-4.5-server/vdt/jdk1.5;GLOBUS_LOCATION=3D/usr/local/ldg-4.5-=20
server/vdt/globus;CONDOR_CONFIG=3D/opt/condor/etc/=20
condor_config;PYLAL_PREFIX=3D/home/marion/s5grb/releases/=20
s5_exttrig_20081011/pylal;GLOBUS_MYSQL_PATH=3D/usr/local/ldg-4.5-server/=20
vdt/mysql;PACMAN_LOCATION=3D/usr/local/ldg-4.5-server/=20
pacman-3.21;PEGASUS_HOME=3D/usr/local/ldg-4.5-server/vdt/=20
pegasus;X509_VOMS_DIR=3D/usr/local/ldg-4.5-server/vdt/glite/=20
vomsdir;CONDOR_LOCATION=3D/usr/local/ldg-4.5-server/vdt/=20
condor;PYLAL_LOCATION=3D/home/nvf/s5grb/releases/s5_exttrig_20081011/=20
pylal;LDG_LOCATION=3D/usr/local/ldg-4.5-=20
server;TERM=3Dvt100;OSTYPE=3Dlinux;LALAPPS_LOCATION=3D/home/nvf/s5grb/=20
releases/s5_exttrig_20081003/=20
lalapps=20
;_CONDOR_DAGMAN_LOG=3Dinjections32.GRB070714_injections32.dag.dagman.out"
EnvDelim =3D ";"
JobNotification =3D 2
WantRemoteIO =3D FALSE
UserLog =3D "/home/marion/analysis/GRB070714/injections32/=20
injections32.GRB070714_injections32.dag.dagman.log"
CoreSize =3D 0
KillSig =3D "SIGTERM"
RemoveKillSig =3D "SIGUSR1"
Rank =3D 0.000000
In =3D "/dev/null"
TransferIn =3D FALSE
Out =3D "injections32.GRB070714_injections32.dag.lib.out"
StreamOut =3D FALSE
Err =3D "injections32.GRB070714_injections32.dag.lib.err"
StreamErr =3D FALSE
BufferSize =3D 524288
BufferBlockSize =3D 32768
ShouldTransferFiles =3D "NO"
TransferFiles =3D "NEVER"
ImageSize_RAW =3D 5564
ImageSize =3D 7500
ExecutableSize_RAW =3D 5564
ExecutableSize =3D 7500
DiskUsage_RAW =3D 5564
DiskUsage =3D 7500
Requirements =3D (Arch =3D=3D "X86_64") && (OpSys =3D=3D "LINUX") && (Disk =
>=3D=20=20
DiskUsage) && ((Memory * 1024) >=3D ImageSize)
FileSystemDomain =3D "atlas.local"
PeriodicHold =3D FALSE
PeriodicRelease =3D FALSE
PeriodicRemove =3D FALSE
OnExitHold =3D FALSE
OnExitRemove =3D (ExitSignal =3D?=3D 11 || (ExitCode =3D!=3D UNDEFINED &&=
=20=20
ExitCode >=3D 0 && ExitCode <=3D 2))
LeaveJobInQueue =3D FALSE
Arguments =3D "-f -l . -Debug 3 -Lockfile=20=20
injections32.GRB070714_injections32.dag.lock -AutoRescue 1 -=20
DoRescueFrom 0 -Condorlog /local/marion/logs/tmp9UFyEE -Dag=20=20
injections32.GRB070714_injections32.dag -CsdVersion $CondorVersion:'=20=20
'7.1.1' 'Oct' '22' '2008' '$"
GlobalJobId =3D "h2.atlas.local#1225220908#5476704.0"
ProcId =3D 0
JobStartDate =3D 1225220908
AutoClusterId =3D 3
AutoClusterAttrs =3D=20=20
"JobUniverse=20
,LastCheckpointPlatform=20
,NumCkpts,DiskUsage,ImageSize,Requirements,NiceUser"
OrigMaxHosts =3D 1
NumJobStarts =3D 1680
JobLastStartDate =3D 1225229826
JobCurrentStartDate =3D 1225229864
JobRunCount =3D 1680
ExitStatus =3D 44
ExitBySignal =3D FALSE
ExitCode =3D 44
JobStatus =3D 1
EnteredCurrentStatus =3D 1225229864
LastSuspensionTime =3D 0
RemoteWallClockTime =3D 99.000000
LastRemoteHost =3D ""
LastPublicClaimId =3D ""
LastPublicClaimIds =3D ""
CurrentHosts =3D 0
ServerTime =3D 1225229890
--=20
Duncan Brown Room 263-1, Department of Physics,
Assistant Professor of Physics Syracuse University, NY 13244, USA
Phone: (315) 443 5993 http://www.gravity.phy.syr.edu/~duncan
--Apple-Mail-24--37273164
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--Apple-Mail-24--37273164--
===========================================================================
Date of creation: Tue Oct 28 16:49:26 2008 (1225230568)
Subject: Actions
Ticket resolved by wenger
===========================================================================
Date of actions: Wed Oct 29 8:30:30 2008 (1225287030)