Difference: MakeDPDs (1 vs. 15)

Revision 15
16 Oct 2009 - Main.TomRockwell
Line: 1 to 1
Changed:
<
<
META TOPICPARENT name="Trash.Tier3WebHome"
>
>
META TOPICPARENT name="Trash.Trash/Tier3WebHome"
 

Introduction

This describes how to make the DPDs necessary for our analysis.
Revision 14
13 Oct 2009 - Main.ChipBrock
Line: 1 to 1
Changed:
<
<
META TOPICPARENT name="WebHome"
>
>
META TOPICPARENT name="Trash.Tier3WebHome"
 

Introduction

This describes how to make the DPDs necessary for our analysis.
Revision 13
18 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Introduction

Line: 129 to 129
 

IN3P3 DPD Tutorial
Added:
>
>
ATLAS Physics Workbook - Batch Jobs
 

Produce D3PDs locally

The Group Area must be setup before making the D3PD (see above). If you have not done so already,
Revision 12
12 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Introduction

Line: 224 to 224
 

Grid Setup

Before using the Grid you must have a Grid Certificate and install it properly.
Changed:
<
<
The ATLAS Workbook [[https://twiki.cern.ch/twiki/bin/view/Atlas/WorkBookStartingGrid Starting on the Grid]
>
>
The ATLAS Workbook Starting on the Grid
  page describes how to do this.

Use this Grid setup script which gives you a validity period
Line: 285 to 285
  The -r option is for remote file transfer. The AANT0 root file is the one that contains the info we are interested in analyzing.
Changed:
<
<

Run over a Single-Top Data Set

>
>

More Info

My jobs were failing on the grid. The datasets could not be found and I was getting the following errors in my log files:
11 Jun 2008 11:01:55| !!FAILED!!2999!! Missing input file(s) in xml: [AOD.017323._00013.pool.root.2, AOD.017323._00014.pool.root.1, AOD.017323._00017.pool.root.1, AOD.017323._00019.pool.root.2]
11 Jun 2008 11:01:55| Number of transferred root files    : 4
11 Jun 2008 11:01:55| Number of transferred non-root files: 1
11 Jun 2008 11:01:55| Mover get_data finished (failed)
11 Jun 2008 11:01:55| Will return fail code = 117, pilotErrorDiag = Missing input file(s) in xml: [AOD.017323._00013.pool.root.2, AOD.017323._00014.pool.root.1, AOD.017323._00017.pool.root.1, AOD.017323._00019.pool.root.2]

See the Top FDR Page for more info.
 

-- PatRyan - 30 May 2008 \ No newline at end of file
Revision 11
12 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Introduction

Line: 258 to 258
 

Check Status of Jobs on the Grid

Job status can be checked on the Panda Monitor.
Changed:
<
<
You can use the search function with the corresponding JobID and PandaID of your jobs (these are printed to STDOUT
>
>
You can use the search function with the corresponding JobID and PandaID of your jobs (these are printed to STDOUT
  when you submit the job) or check the jobs according to the status. The meaning of each status is described here.
Revision 10
10 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Introduction

Line: 279 to 279
 

The files are retrieved using the dq2_get command:
Changed:
<
<
>
>
  dq2_get -r user.PatrickRyan.test.DP3D.001 user.PatrickRyan.test.DP3D.001.AANT0._00001.root The -r option is for remote file transfer. The AANT0 root file is the one that contains the info we
Revision 9
10 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Introduction

Line: 248 to 248
 

To submit an example job to PANDA using pathena,
Changed:
<
<
$> pathena share/ElectroweakD3PD_topOptions.py --outDS user.PatrickRyan.test.DP3D.002 --site ANALY_MWT2
>
>
$> pathena -c "doStream=True" TopPhysDPDMaker/ElectroweakD3PD_topOptions.py --inDS fdr08_run1.0003077.StreamEgamma.merge.AOD.o1_r12_t1 --outDS your_name_and_job_name --site ANALY_MWT2
 
Changed:
<
<
The option --outDS specifies the output name of the Data Set. The option --site specifies the Grid Site.
>
>
The option inDS specifies the input Data Set and the option --outDS specifies the output name of the Data Set. It seems that files stored under AFS are not valid as Input Data Sets. You must specify a data set already on the Grid. The option --site specifies the Grid Site.
  A full list of Grid Sites is listed http://pandamon.usatlas.bnl.gov:25880/server/pandamon/query?dash=analysis here
Added:
>
>
The doStream=True option is specific to FDR stream files.
 

Check Status of Jobs on the Grid

Job status can be checked on the Panda Monitor.
Line: 259 to 262
  when you submit the job) or check the jobs according to the status. The meaning of each status is described here.
Added:
>
>

Get Files of the Grid

First you must check the existence of a data set (wildcards are allowed)
$>  dq2_ls user.PatrickRyan.test.DP3D.001
user.PatrickRyan.test.DP3D.001
 
Added:
>
>
Then you must check which root files are in the dataset
 
Changed:
<
<
pathena -c "doStream=True" share/ElectroweakD3PD_topOptions.py --inDS fdr08_run1.0003077.StreamEgamma.merge.AOD.o1_r12_t1 --outDS user.PatrickRyan.test.DP3D.001 --site ANALY_MWT2
>
>
$> dq2_ls -g user.PatrickRyan.test.DP3D.001 user.PatrickRyan.test.DP3D.001 Total: 3 user.PatrickRyan.test.DP3D.001.AANT0._00001.root user.PatrickRyan.test.DP3D.001.META0._00001.root user.PatrickRyan.test.DP3D.001._12453403.log.tgz
 
Added:
>
>
The files are retrieved using the dq2_get command:
The -r option is for remote file transfer.  The AANT0 root file is the one that contains the info we
are interested in analyzing.
 
Added:
>
>

Run over a Single-Top Data Set

 

-- PatRyan - 30 May 2008 \ No newline at end of file
Revision 8
10 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Introduction

Line: 136 to 136
  $> source setup.sh -tag=13.0.40,groupArea
Changed:
<
<
In order to produce an ensure that you have completed the above steps correctly, you should
>
>
In order to ensure that you have completed the above steps correctly, you should
  produce an example D3PD. Edit the file ElectroweakD3PD_topOptions.py by commenting out the line
if not "InFileNames"        in dir():      InFileNames = glob.glob("/tmp/ashibata/fdr08*")
Line: 220 to 220
  output root files must be moved to the lxplus tmp space because your AFS space will quickly be filled. A script doing this is coming shortly.
Changed:
<
<

Produce D3PDs using the GRID

>
>

Produce D3PDs on the Grid

Grid Setup

Before using the Grid you must have a Grid Certificate and install it properly. The ATLAS Workbook [[https://twiki.cern.ch/twiki/bin/view/Atlas/WorkBookStartingGrid Starting on the Grid] page describes how to do this.

Use this Grid setup script which gives you a validity period of 90 hours instead of the default 12 hours.
$> source GridSetupAndProxy.sh

Submit jobs to Grid

The Group Area must be setup before submitting jobs (see above). If you have not done so already,
$> source setup.sh -tag=13.0.40,groupArea

In order to submit jobs, you must have a directory TopPhysDPDMaker/testarea/13.0.40/InstallArea/python' in your work area. Failure to have such a directory will causes errors such as
OSError: [Errno 2] No such file or directory: '/afs/cern.ch/user/p/pryan/atlas/TopPhysDPDMaker/testarea/13.0.40/InstallArea/python'

To submit an example job to PANDA using pathena,
$> pathena   share/ElectroweakD3PD_topOptions.py   --outDS user.PatrickRyan.test.DP3D.002 --site ANALY_MWT2
The option --outDS specifies the output name of the Data Set. The option --site specifies the Grid Site. A full list of Grid Sites is listed http://pandamon.usatlas.bnl.gov:25880/server/pandamon/query?dash=analysis here

Check Status of Jobs on the Grid

Job status can be checked on the Panda Monitor. You can use the search function with the corresponding JobID and PandaID of your jobs (these are printed to STDOUT when you submit the job) or check the jobs according to the status. The meaning of each status is described here.

pathena  -c "doStream=True"  share/ElectroweakD3PD_topOptions.py  --inDS fdr08_run1.0003077.StreamEgamma.merge.AOD.o1_r12_t1  --outDS user.PatrickRyan.test.DP3D.001 --site ANALY_MWT2
 

Revision 7
06 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Introduction

Line: 129 to 129
 

IN3P3 DPD Tutorial
Changed:
<
<

Produce an Example D3PD locally

>
>

Produce D3PDs locally

  The Group Area must be setup before making the D3PD (see above). If you have not done so already,
Line: 156 to 156
  used. Earlier versions cannot handle variables stored in a vector. Open up a TBrowser in root and make sure that the variables are filled.
Changed:
<
<

Produce an Example D3PD using lxbatch

>
>

Produce D3PDs using lxbatch

Create Executable File

Put the following in a file called, for example, lxbatchSub.sh in the run directory.

#!/bin/bash
source /afs/cern.ch/user/p/pryan/atlas/TopPhysDPDMaker/cmthome/setup.sh -tag=13.0.40,groupArea
cd /afs/cern.ch/user/p/pryan/atlas/TopPhysDPDMaker/testarea/13.0.40/PhysicsAnalysis/TopPhys/TopPhysDPDMaker/
athena.py share/ElectroweakD3PD_topOptions.py

This file must be executable
$> chmod +x lxbatchSub.sh

Essential Batch System Commands

The commands necessary to submit and list jobs on the batch system are given below. For a more complete listing see the LSF Documentation.

Submit Jobs

$> bsub -q queue ExecutableFile
The valid queues are: 8nm (8 minutes), 1nh (1 hour), 8nh (8 hours), 1nd (1 day) and 1nw (1 week). The default is queue is 8nm. The n stands for normalized.

List jobs

To see what jobs are running (list unfinished jobs):
$> bjobs

To list all jobs (finished and unfinished):
$> bjobs -a
Note that after a certain time the jobs are removed from the list.

To get more info about a job:
$> bjobs -l JobID

Produce an Example D3PD

Submit the job using the batch commands
$> bsub -q 1nh lxbatchSub.sh

An email notification will be sent when your job is finished. The root file Electroweak.D3PD.aan.root should be produced in the TopPhysDPDMaker directory. In addition, a directory with a name such as LSFJOB_2896624 will be produced in the run/ directory, where the number in the directory name corresponds to the JobID in the batch system. This directory will contain a file named STDOUT which includes all the text that your job would have normally printed to the screen if run interactively.

Produce Many D3PDs

To automate the production of D3PDs with lxbatch, it is necessary to edit the job options file to correspond to each input and output file. In addition, output root files must be moved to the lxplus tmp space because your AFS space will quickly be filled. A script doing this is coming shortly.

Produce D3PDs using the GRID

 

-- PatRyan - 30 May 2008 \ No newline at end of file
Revision 6
06 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Introduction

Line: 56 to 56
  # Set the location of your preferred development area macro ATLAS_GROUP_AREA "/afs/cern.ch/atlas/groups/PAT/Tutorial/EventViewGroupArea/EVTags-13.0.40.2"
Changed:
<
<
macro ATLAS_TEST_AREA "" 12.0.7 "${HOME}/scratch0/athena/12.0.7" 13.0.40 "${HOME}/scratch0/athena/13.0.40"
>
>
macro ATLAS_TEST_AREA "" 13.0.40 "/work/jever/pryan/atlas/TopPhysDPDMaker/testarea/13.0.40/"
 

use AtlasLogin AtlasLogin-* $(ATLAS_DIST_AREA)
Changed:
<
<
Edit the line
 13.0.40 "/work/jever/pryan/atlas/TopPhysDPDMaker/testarea/13.0.40/"
>
>
Edit the line
 macro ATLAS_TEST_AREA "" 13.0.40 "/work/jever/pryan/atlas/TopPhysDPDMaker/testarea/13.0.40/"
  to correspond to the present version of the code and your directory.

Setup CMT Environment

Revision 5
06 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Introduction

Line: 18 to 18
 

Setup CMT Directory Structure

Create Directories

Changed:
<
<
You should make the following directories somewhere on your scratch space since the amount of material that will be contained in these directories is large.
>
>
The compiled code talke up about 15M of disk space and an output root file containing 1000 events takes up another 15M. If you have enough room under AFS, it is better to put the code there since this allows the code to be accessed from lxplus and therefore jobs can be submitted to lxbatch. The data disks on the MSU cluster cannot be seen from lxplus. If you do not have enough AFS space put the code on the data disk. You can still run jobs locally and submit them to the GRID.
  The current version of the code at the time this note was written was 13.0.40.
$> mkdir -p TopPhysDPDMaker/cmthome TopPhysDPDMaker/testarea/13.0.40/
Line: 127 to 131
 

IN3P3 DPD Tutorial
Changed:
<
<

Produce an Example D3PD

>
>

Produce an Example D3PD locally

  The Group Area must be setup before making the D3PD (see above). If you have not done so already,
Line: 145 to 149
 

Run athena:
Changed:
<
<
$> athena share/ElectroweakD3PD_topOptions.py
>
>
$> athena share/ElectroweakD3PD_topOptions.py &> ExampleD3PD_local.log
 

It will take approximately 6 minutes to run over the 1000 events using the machines
Line: 154 to 158
  used. Earlier versions cannot handle variables stored in a vector. Open up a TBrowser in root and make sure that the variables are filled.
Added:
>
>

Produce an Example D3PD using lxbatch

  -- PatRyan - 30 May 2008 \ No newline at end of file
Revision 4
04 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Introduction

Line: 151 to 151
  It will take approximately 6 minutes to run over the 1000 events using the machines in the MSU cluster at CERN. A root file called Electroweak.D3PD.aan.root will be produced. To open the root file using root, Version 5.19.04 or later must be
Changed:
<
<
used. Earlier versions cannot handle variables stored as vector.
>
>
used. Earlier versions cannot handle variables stored in a vector.
  Open up a TBrowser in root and make sure that the variables are filled.

-- PatRyan - 30 May 2008 \ No newline at end of file
Revision 3
04 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Introduction

Line: 7 to 7
  package. This is the successor to TopView for ATHENA versions 13 and greater. The instructions are for the MSU cluster at CERN.
Changed:
<
<
Information from this page was taken from following:
>
>

Workspace Setup

Introduction

Information for the workspace setup was taken from following:
 

Top Physics DPD Maker - Getting Started

ATLAS Workbook - Account Setup
Changed:
<
<

Setup Work Space

Create Directories

>
>

Setup CMT Directory Structure

Create Directories

  You should make the following directories somewhere on your scratch space since the amount of material that will be contained in these directories is large. The current version of the code at the time this note was written was 13.0.40.
Line: 22 to 25
  $> mkdir -p TopPhysDPDMaker/cmthome TopPhysDPDMaker/testarea/13.0.40/
Changed:
<
<

Setup CMT

>
>

Setup CMT

  Create a file called "requirements" in the cmthome directory and paste the code listed below into this file.
Line: 59 to 62
  Edit the line
 13.0.40 "/work/jever/pryan/atlas/TopPhysDPDMaker/testarea/13.0.40/"
to correspond to the present version of the code and your directory.
Changed:
<
<

Setup CMT Environment

>
>

Setup CMT Environment

  In the cmthome directory do the following to get version v1r20p20080222 of CMT. Note that this command only works on the CERN cluster.
Line: 71 to 74
  $> cmt config
Changed:
<
<

Set Group Area

>
>

Set Group Area

  This command will has to be executed in each new shell before you start working
$> source setup.sh -tag=13.0.40,groupArea
Changed:
<
<

Checkout packages

>
>

Get and Compile Packages

Checkout packages

  Go to testarea/13.0.40 directory
$> cd ../testarea/13.0.40
Line: 89 to 94
  $> cmt co -r TopPhysDPDMaker-00-00-10 PhysicsAnalysis/TopPhys/TopPhysDPDMaker
Changed:
<
<

Compile Packages

>
>

Compile Packages

The Group Area must be setup before compiling and running (see above). If you have not done so already,
$> source setup.sh -tag=13.0.40,groupArea
  For TopPhysTools
cd PhysicsAnalysis/TopPhys/TopPhysTools/cmt
Line: 104 to 115
  cmt bro make
Added:
>
>

Make D3PDs

Introduction

TopPhysDPDMaker makes D3PDs, which are flat nTuples similar to those produced previously with TopView. The information in this section was taken from the following pages:

TopPhysDPDMaker Page

D3PD Info Page

IN3P3 DPD Tutorial

Produce an Example D3PD

The Group Area must be setup before making the D3PD (see above). If you have not done so already,
$> source setup.sh -tag=13.0.40,groupArea

In order to produce an ensure that you have completed the above steps correctly, you should produce an example D3PD. Edit the file ElectroweakD3PD_topOptions.py by commenting out the line
if not "InFileNames"        in dir():      InFileNames = glob.glob("/tmp/ashibata/fdr08*")
and inserting the line
if not "InFileNames"        in dir():      InFileNames = ['/afs/cern.ch/atlas/maxidisk/d66/AOD.019335._00001.pool.root.4']

Run athena:
$> athena share/ElectroweakD3PD_topOptions.py

It will take approximately 6 minutes to run over the 1000 events using the machines in the MSU cluster at CERN. A root file called Electroweak.D3PD.aan.root will be produced. To open the root file using root, Version 5.19.04 or later must be used. Earlier versions cannot handle variables stored as vector. Open up a TBrowser in root and make sure that the variables are filled.
  -- PatRyan - 30 May 2008 \ No newline at end of file
Revision 2
02 Jun 2008 - PatRyan
Line: 1 to 1
 
META TOPICPARENT name="WebHome"
Added:
>
>

Introduction

 
Changed:
<
<
test
>
>
This describes how to make the DPDs necessary for our analysis. The DPDs are made with the TopPhysDPDMaker, which relies on the TopViewTools package. This is the successor to TopView for ATHENA versions 13 and greater. The instructions are for the MSU cluster at CERN.
 
Added:
>
>
Information from this page was taken from following:

Top Physics DPD Maker - Getting Started

ATLAS Workbook - Account Setup

Setup Work Space

Create Directories

You should make the following directories somewhere on your scratch space since the amount of material that will be contained in these directories is large. The current version of the code at the time this note was written was 13.0.40.
$> mkdir -p TopPhysDPDMaker/cmthome TopPhysDPDMaker/testarea/13.0.40/

Setup CMT

Create a file called "requirements" in the cmthome directory and paste the code listed below into this file.

$> cd TopPhysDPDMaker/cmthome
$> emacs requirements &

Code which goes into requirements (cut and paste):
set CMTSITE CERN
set SITEROOT /afs/cern.ch
macro ATLAS_DIST_AREA ${SITEROOT}/atlas/software/dist

# use optimised version by default
apply_tag  opt
apply_tag  runtime 
# simple workarea directories
apply_tag  simpleTest
apply_tag  oneTest 
apply_tag  setup
apply_tag  32

# Set the location of your preferred development area
macro ATLAS_GROUP_AREA "/afs/cern.ch/atlas/groups/PAT/Tutorial/EventViewGroupArea/EVTags-13.0.40.2"

macro ATLAS_TEST_AREA "" \
  12.0.7 "${HOME}/scratch0/athena/12.0.7" \
  13.0.40 "${HOME}/scratch0/athena/13.0.40" 

use AtlasLogin AtlasLogin-* $(ATLAS_DIST_AREA)

Edit the line
 13.0.40 "/work/jever/pryan/atlas/TopPhysDPDMaker/testarea/13.0.40/"
to correspond to the present version of the code and your directory.

Setup CMT Environment

In the cmthome directory do the following to get version v1r20p20080222 of CMT. Note that this command only works on the CERN cluster.
$> source /afs/cern.ch/sw/contrib/CMT/v1r20p20080222/mgr/setup.sh

Copy the required scripts into the cmthome directory.
$> cmt config

Set Group Area

This command will has to be executed in each new shell before you start working
$> source setup.sh -tag=13.0.40,groupArea

Checkout packages

Go to testarea/13.0.40 directory
$> cd ../testarea/13.0.40

Get packages
$> cmt co -r TopPhysTools-13-00-40-06 PhysicsAnalysis/TopPhys/TopPhysTools
$> cmt co -r TopPhysDPDMaker-00-00-10 PhysicsAnalysis/TopPhys/TopPhysDPDMaker

Compile Packages

For TopPhysTools
cd PhysicsAnalysis/TopPhys/TopPhysTools/cmt
source setup.sh
cmt bro make

For TopPhysDPDMaker
cd PhysicsAnalysis/TopPhys/TopPhysDPDMaker/cmt
source setup.sh
cmt bro make
 

-- PatRyan - 30 May 2008 \ No newline at end of file
 
This site is powered by FoswikiCopyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding Foswiki? Send feedback