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Subject: Re: [OMPI users] Open MPI program cannot complete
From: Jack Bryan (dtustudy68_at_[hidden])
Date: 2010-10-25 17:30:10


Thanks
I have downloaded http://padb.googlecode.com/files/padb-3.2-beta1.tar.gz
and followed the instructions of INSTALL file and installed it at /mypath/padb32
But, I got:
-bash-3.2$ padb -Ormgr=pbs -Q 48279.clusterJob 48279.cluster is not active
Actually, the job was running.
I have installed bin at
/mypath/padb32/bin

libexec at/lustre/jxding/padb32/libexec
When I installed it, I used
./configure --prefix=/mypath/padb32
I got -----------------------------
checking for a BSD-compatible install... /usr/bin/install -cchecking whether build environment is sane... yeschecking for a thread-safe mkdir -p... /bin/mkdir -pchecking for gawk... gawkchecking whether make sets $(MAKE)... yeschecking for gcc... gccchecking whether the C compiler works... yeschecking for C compiler default output file name... a.outchecking for suffix of executables...checking whether we are cross compiling... nochecking for suffix of object files... ochecking whether we are using the GNU C compiler... yeschecking whether gcc accepts -g... yeschecking for gcc option to accept ISO C89... none neededchecking for style of include used by make... GNUchecking dependency style of gcc... gcc3checking whether gcc and cc understand -c and -o together... yesconfigure: creating ./config.statusconfig.status: creating Makefileconfig.status: creating src/Makefileconfig.status: executing depfiles commands
-------------------------------
-bash-3.2$ makeMaking all in srcmake[1]: Entering directory `/mypath/padb32/padb-3.2-beta1/src'gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"padb\" -DVERSION=\"3.2-beta1\" -I. -Wall -g -O2 -MT minfo-minfo.o -MD -MP -MF .deps/minfo-minfo.Tpo -c -o minfo-minfo.o `test -f 'minfo.c' || echo './'`minfo.cminfo.c: In function âfind_symâ:minfo.c:158: warning: dereferencing type-punned pointer will break strict-aliasing rulesminfo.c: In function âmainâ:minfo.c:649: warning: type-punning to incomplete type might break strict-aliasing rulesminfo.c:650: warning: type-punning to incomplete type might break strict-aliasing rulesmv -f .deps/minfo-minfo.Tpo .deps/minfo-minfo.Pogcc -Wall -g -O2 -ldl -o minfo minfo-minfo.omake[1]: Leaving directory `/mypath/padb32/padb-3.2-beta1/src'make[1]: Entering directory `/mypath/padb32/padb-3.2-beta1'make[1]: Nothing to be done for `all-am'.make[1]: Leaving directory `/mypath/padb32/padb-3.2-beta1'-------------------------------------------------
-bash-3.2$ make installMaking install in srcmake[1]: Entering directory `/mypath/padb32/padb-3.2-beta1/src'make[2]: Entering directory `/mypath/padb32/padb-3.2-beta1/src'test -z "/lustre/jxding/padb32/bin" || /bin/mkdir -p "/mypath/padb32/bin" /usr/bin/install -c padb '/lustre/jxding/padb32/bin'test -z "/lustre/jxding/padb32/libexec" || /bin/mkdir -p "/mypath/padb32/libexec" /usr/bin/install -c minfo '/lustre/jxding/padb32/libexec'make[2]: Nothing to be done for `install-data-am'.make[2]: Leaving directory `/mypath/padb32/padb-3.2-beta1/src'make[1]: Leaving directory `/mypath/padb32/padb-3.2-beta1/src'make[1]: Entering directory `/mypath/padb32/padb-3.2-beta1'make[2]: Entering directory `/mypath/padb32/padb-3.2-beta1'make[2]: Nothing to be done for `install-exec-am'.make[2]: Nothing to be done for `install-data-am'.make[2]: Leaving directory `/mypath/padb32/padb-3.2-beta1'make[1]: Leaving directory `/mypath/padb32/padb-3.2-beta1'-bash-3.2$ make installcheckMaking installcheck in srcmake[1]: Entering directory `/mypath/padb32/padb-3.2-beta1/src'make[1]: Nothing to be done for `installcheck'.make[1]: Leaving directory `/mypath/padb32/padb-3.2-beta1/src'make[1]: Entering directory `/mypath/padb32/padb-3.2-beta1'make[1]: Nothing to be done for `installcheck-am'.make[1]: Leaving directory `/mypath/padb32/padb-3.2-beta1'--------------------------------------------------
Are there something wrong with what I have done ?
Any help is appreciated.
thanks
Jack
Oct. 25 2010

> From: ashley_at_[hidden]
> Date: Mon, 25 Oct 2010 20:40:18 +0100
> To: users_at_[hidden]
> Subject: Re: [OMPI users] Open MPI program cannot complete
>
>
> On 25 Oct 2010, at 20:18, Jack Bryan wrote:
>
> > Thanks
> > I have downloaded
> > http://padb.googlecode.com/files/padb-3.0.tgz
> >
> > and compile it.
> >
> > But, no user manual, I can not use it by padb -aQ.
>
> The -a flag is a shortcut to all jobs, if you are providing a jobid (which is normally numeric) then don't set the -a flag.
>
> > Do you have use manual about how to use it ?
>
> In my previous mail I was assuming you were using orte to launch the jobs but if you are using PBS then you'll need to use the 3.2 beta as the PBS code is new, alternatively you could find the host where the PBS script itself runs and check of the "ompi-ps" command gives you any output, if it does then you could run it from there giving it the orte jobid.
>
> A bit of background about resource managers (in which I'm including orte and PBS), padb supports many resource managers and tries to automatically detect which ones you have installed on your system. If you don't specify one then it'll see what is installed, if there is more than one resource manager installed then it'll see which of them claim to have active jobs - if only one resource manager meets this criteria then it'll pick that one - hence 99% of the time it should just work. If more than one resource manager claims to have active jobs then padb will refuse to run but ask the user to specify one explicitly.
>
> You should try the following in order once you have 3.2 installed.
>
> padb -Ormgr=pbs -Q <myjob>
>
> Or - find the node where the PBS script is being executed, check that the ompi-ps command is returning the jobid and then run
>
> padb -Ormgr=orte -Q <openmpi_jobid>
>
> Ashley,
>
> --
>
> Ashley Pittman, Bath, UK.
>
> Padb - A parallel job inspection tool for cluster computing
> http://padb.pittman.org.uk
>
>
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