| Table of Contents |
|---|
ILC VO
Firstly, you need to obtain a membership in the ilc Virtual Organization
...
(VO),
...
which
...
is
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sponsored
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by
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DESY.
...
This
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is
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a
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VO
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on
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the
...
...
grid.
...
Alternately,
...
you
...
can
...
become
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a
...
member
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of
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the
...
calice
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VO,
...
but
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this
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will
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only
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work
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if
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your
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institution
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is
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actually
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a
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member
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of
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this
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collaboration.
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Follow
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the
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workflow
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at
...
https://grid-voms.desy.de:8443/
...
voms/ilc/register/start.action which will require several rounds of confirmations and emails.
Setup
| Info |
|---|
The rest of the tutorial assumes that you are running from an lxplus node at CERN and using the bash shell. |
This command can be used to setup the LCG environment using tools on the DESY AFS file system.
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|---|
vomrs] which will require several rounds of confirmations and emails. {warning} Somewhat confusingly, there is another ILC VO run by Fermilab located at [https://voms.fnal.gov:8443/vomrs/ilc/vomrs] which is on the [OSG|http://www.opensciencegrid.org/] grid. The two Virtual Organizations are not interchangeable so make sure you get a membership in the DESY one to follow the instructions in this tutorial\! {warning} h2. Setup {info} The rest of the tutorial assumes that you are running from an lxplus node at CERN and using the bash shell. {info} This command can be used to setup the LCG environment using tools on the DESY AFS file system. {noformat} source /afs/desy.de/group/grid/UI/GLITE-pro/etc/profile.d/grid_env.sh {noformat} |
There
...
also
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exists
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a
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setup
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script
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maintained
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at
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CERN.
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|---|
} source /afs/cern.ch/project/gd/LCG-share/current/etc/profile.d/grid_env.sh {noformat} |
The
...
DESY
...
afs
...
script
...
seems
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to
...
work
...
the
...
best.
...
I
...
am
...
having
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trouble
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running
...
EDG
...
commands
...
with
...
the
...
CERN
...
setup
...
script.
...
VOMS
...
Server
...
At
...
the
...
beginning
...
of
...
each
...
session,
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a
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proxy
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certificate
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needs
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to
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be
...
obtained.
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|---|
} voms-proxy-init -verify -debug -voms ilc {noformat} |
This
...
command
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should
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be
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executed
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at
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the
...
start
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of
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every
...
session
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in
...
which
...
jobs
...
are
...
going
...
to
...
be
...
submitted.
...
If
...
you
...
get
...
the
...
message
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VOMS
...
Server
...
for
...
ilc
...
not
...
known
...
!
...
when
...
trying
...
to
...
run
...
this
...
command,
...
or
...
if
...
other
...
similar
...
error
...
messages
...
occur
...
when
...
running
...
other
...
grid
...
commands,
...
then
...
the
...
information
...
about
...
the
...
ILC
...
VOMS
...
server
...
is
...
missing
...
and
...
needs
...
to
...
be
...
installed
...
at
...
your
...
site.
...
The
...
ILC
...
VO
...
information
...
can
...
be
...
found
...
on
...
the
...
...
...
...
page.
...
The
...
ilc
...
VOMS
...
information
...
can
...
be
...
downloaded
...
from
...
http://grid.desy.de/etc/vomses/ilc-grid-voms.desy.de
...
.
...
The
...
contents
...
of
...
this
...
file
...
should
...
be
...
added
...
to
...
the
...
list
...
of
...
VOMS
...
configuration
...
data
...
kept
...
in
...
~/.glite/vomses
...
.
...
Alternately,
...
your
...
system
...
administrator
...
can
...
install
...
the
...
ilc
...
VO
...
information
...
into
...
a
...
central
...
config
...
file.
...
The
...
following
...
commands
...
will
...
download
...
the
...
VOMS
...
file
...
and
...
add
...
the
...
information
...
to
...
the
...
user
...
config
...
file
...
in
...
the
...
home
...
directory.
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|---|
} mkdir -p ~/.glite/vomses cd ~/.glite/vomses wget http://grid.desy.de/etc/vomses/ilc-grid-voms.desy.de {noformat} {noformat} |
Now,
...
the
...
voms-proxy-init
...
command
...
should
...
work
...
correctly.
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|---|
} voms-proxy-init -verify -debug -voms ilc {noformat} h2. LCG File System In order to use the LCG file system, the LFC_ |
LCG File System
In order to use the LCG file system, the LFC_HOST variable must be setup.
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HOST variable must be setup. {noformat} export LFC_HOST=`lcg-infosites --vo ilc lfc` {noformat} |
List
...
files
...
on
...
the
...
mass
...
storage
...
system
...
at
...
DESY.
| No Format |
|---|
} lfc-ls -l /grid {noformat} |
Put
...
a
...
file
...
into
...
DESY
...
mass
...
storage.
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|---|
} echo "test" > /tmp/test_file lcg-cr -v --vo ilc -l lfn:/grid/ilc/test/test_file file:/tmp/test_file -d srm-dcache.desy.de {noformat} |
Copy
...
a
...
file
...
from
...
mass
...
storage
...
to
...
local
...
disk.
| No Format |
|---|
} lcg-cp -v --vo calice lfn:/grid/ilc/test/test_file file:/tmp/test_file {noformat} |
Copying
...
one
...
of
...
the
...
Standard
...
Model
...
background
...
files
...
from
...
a
...
local
...
NFS
...
disk
...
to
...
the
...
DESY
...
dcache
...
system
...
and
...
registering
...
into
...
the
...
grid
...
catalog.
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|---|
} > . /afs/desy.de/group/grid/UI/GLITE/etc/profile.d/grid-env.sh > export LFC_HOST=grid-lfc.desy.de > voms-proxy-init -debug -verify -voms ilc > lcg-cr -v --vo ilc -n 10 file:/nfs/slac/g/lcd/ilc_data/ILC500/StandardModel/250fb-1_-80e-_+30e+_polarization-003.stdhep -l /grid/ilc/mc/ILC500/SM250fb-1/generated/250fb-1_-80e-_+30e+_polarization-003.stdhep -d srm://srm-dcache.desy.de/pnfs/desy.de/ilc/mc/ILC500/SM250fb-1/generated/250fb-1_-80e-_+30e+_polarization-003.stdhep {noformat} |
Listing
...
the
...
available
...
SM
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files
| No Format |
|---|
} lfc-ls -l /grid/ilc/mc/ILC500/SM250fb-1/generated/ {noformat} h2. Test Commands The GLITE UI will be used to run test jobs. It uses commands starting with "edg-" for job submission, monitoring, etc. If not running from DESY, many of the edg commands will require a config file for the ilc VO, which can be copied from a DESY afs location. In another shell on lxplus, execute the following commands. |
Fetching a Grid LCIO File to SLAC from DESY mass storage
Here is a more advanced script showing how to fetch a file to SLAC, assuming that you have an lxplus account at CERN.
| No Format |
|---|
# ssh to cern
ssh lxplus
# setup grid tools
source /afs/cern.ch/project/gd/LCG-share/current/etc/profile.d/grid_env.sh
# start a grid session
voms-proxy-init -verify -debug -voms ilc
# copy the file to temp location on lxplus (it's fast)
lcg-cp -v --vo ilc lfn:/grid/ilc/mc-2008/simulated/LDC01_05Sc/ZPole/M-6-5p2_ZPoleuds_LDC01_05Sc_LCP_Test_ZPole_0001.slcio file:/tmp//M-6-5p2_ZPoleuds_LDC01_05Sc_LCP_Test_ZPole_0001.slcio
# copy file to slac (slow...go get some coffee)
scp M-6-5p2_ZPoleuds_LDC01_05Sc_LCP_Test_ZPole_0001.slcio jeremym@iris01.slac.stanford.edu:/afs/slac/g/lcd/public_data/ILC/test/mokka/
|
The user name jeremym should be replaced above with your real SLAC account name.
Test Commands
The GLITE UI will be used to run test jobs. It uses commands starting with "edg-" for job submission, monitoring, etc.
If not running from DESY, many of the edg commands will require a config file for the ilc VO, which can be copied from a DESY afs location.
In another shell on lxplus, execute the following commands.
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|---|
{noformat} source /afs/desy.de/group/grid/UI/GLITE-pro/etc/profile.d/grid_env.sh cp $EDG_LOCATION/etc/ilc/edg_wl_ui.conf ~ {noformat} |
The
...
file
...
~edg_wl_ui.conf
...
needs
...
to
...
be
...
used
...
in
...
place
...
of
...
"--vo
...
ilc"
...
in
...
the
...
test
...
commands
...
at
...
...
.
...
Now
...
follow
...
the
...
instructions
...
for
...
submitting
...
a
...
test
...
job
...
at
...
...
under
...
"Submitting
...
jobs
...
to
...
the
...
Grid".
...
Look
...
for
...
resources
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to
...
run
...
a
...
job.
| No Format |
|---|
} edg-job-list-match --config-vo ./edg_wl_ui.conf test.jdl {noformat} |
Run
...
a
...
test
...
job.
| No Format |
|---|
} edg-job-submit --nogui --config-vo ./edg_wl_ui.conf -o test.jid test.jdl {noformat} |
Check
...
the
...
job
...
status.
| No Format |
|---|
} edg-job-status -i test.jid {noformat} |
Get
...
the
...
output.
| No Format |
|---|
} edg-job-get-output -i test.jid {noformat |
Running SLIC
Simple Shell Script
Create a shell script slic.sh.
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} h2. Running SLIC h3. Simple Shell Script Create a shell script *slic.sh*. {noformat} #!/bin/sh wget http://www.lcsim.org/dist/slic/slic_v2r3p0_geant4_v9r0_i686_linux-gnu.tar.gz tar xzf ./slic_v2r3p0_geant4_v9r0_i686_linux-gnu.tar.gz wget http://www.lcsim.org/detectors/acme0605/acme0605.lcdd printenv ./SimDist/scripts/slic.sh -g ./acme0605.lcdd -r 1 ls *.slcio {noformat} |
The
...
above
...
script
...
does
...
the
...
following.
...
- Downloads
...
- a
...
- tarball
...
- with
...
- the
...
- slic
...
- binary
...
- and
...
- untars
...
- it.
...
- Downloads
...
- a
...
- detector
...
- XML
...
- file.
...
- Prints
...
- the
...
- environment.
...
- Runs
...
- one
...
- event
...
- (single
...
- muon)
...
- on
...
- the
...
- detector
...
- file.
...
- Prints
...
- a
...
- list
...
- of
...
- LCIO
...
- files
...
- created.
...
Shell
...
Script
...
Using
...
DESY
...
Mass
...
Storage
...
Here
...
is
...
another
...
version
...
of
...
the
...
script
...
that
...
uses
...
grid
...
commands
...
to
...
fetch
...
a
...
stdhep
...
file
...
and
...
upload
...
the
...
output
...
LCIO
...
file
...
using
...
DESY
...
mass
...
storage.
...
(This
...
example
...
would
...
only
...
work
...
if
...
you
...
have
...
been
...
granted
...
access
...
to
...
DESY
...
mass
...
storage.)
| No Format |
|---|
} #!/bin/sh printenv wget http://www.lcsim.org/dist/slic/slic_v2r3p0_geant4_v9r0_i686_linux-gnu.tar.gz tar xzf ./slic_v2r3p0_geant4_v9r0_i686_linux-gnu.tar.gz wget http://www.lcsim.org/detectors/acme0605/acme0605.lcdd lcg-cp -v --vo ilc lfn:/grid/ilc/test/test.stdhep file:`pwd`/test.stdhep ./SimDist/scripts/slic.sh -g ./acme0605.lcdd -i ./test.stdhep -r 1 ls -la lcg-cr -v --vo ilc -l lfn:/grid/ilc/test/outfile.slcio file:`pwd`/outfile.slcio -d srm-dcache.desy.de lfc-ls -l /grid/ilc/test/outfile.slcio {noformat} h3. JDL File Now make a file * |
JDL File
Now make a file slic.jdl
...
.
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|---|
} Executable = "slic.sh"; StdOutput = "out"; StdError = "err"; InputSandbox = {"slic.sh"}; OutputSandbox = {"out","err","outfile.slcio"}; {noformat} The _OutputSandbox_ contains a list of files that will be cached for retrieval later, including the output LCIO file. h3. Job Submission, Monitoring, and Output Retrieval To run the SLIC test job. {noformat} |
The OutputSandbox contains a list of files that will be cached for retrieval later, including the output LCIO file.
Job Submission, Monitoring, and Output Retrieval
To run the SLIC test job.
| No Format |
|---|
edg-job-submit --nogui --config-vo ./edg_wl_ui.conf -o slic.jid slic.jdl
{noformat}
|
Check
...
the
...
job
...
status.
| No Format |
|---|
} edg-job-status -i slic.jdl {noformat} Retrieve the jid |
Retrieve the output.
...
By,
...
default
...
the
...
job
...
output
...
will
...
go
...
into
...
a
...
directory
...
in
...
/tmp
...
so
...
we
...
specify
...
the
...
current
...
directory
...
instead.
| No Format |
|---|
} edg-job-get-output --dir `pwd` -i slic.jdl {noformat} h2. Links [gLite User Guide|https://edms.cern.ch/file/722398//gLite-3-UserGuide.html] [Virtual Data Toolkit (VDT)|http://vdt.cs.wisc.edu/] [CERN AFS UI Setup|https://twiki.cern.ch/twiki/bin/view/LCG/AfsUiUserSetup] \- setup instructions on jid |
Links
gLite User Guide
Virtual Data Toolkit (VDT)
CERN AFS UI Setup - setup instructions on lxplus@cern