[Gate-users] filemerger...

Wed Oct 24 06:06:00 CEST 2007

Dear Jan,

I did benchSPECT with jobsplitter...
filemerger works for it...with fastMerge option on root 5.12...
Without fastMerge option...there is same error except a message...
following is shell output...
----------------------------------------
turbo978 at MJ-GATE:~/gate_v3.1.2/benchmarks/benchmarkSPECT$
../../Cluster_Tools/filemerger/gjm -fastMerge SPECTbench.mac
turbo978 at MJ-GATE:~/gate_v3.1.2/benchmarks/benchmarkSPECT$
../../Cluster_Tools/filemerger/gjm SPECTbench.mac
Combining:
/home/turbo978/gate_v3.1.2/benchmarks/benchmarkSPECT/benchSPECT1.root
/home/turbo978/gate_v3.1.2/benchmarks/benchmarkSPECT/benchSPECT2.root ->
benchSPECT.root

 *** Break *** segmentation violation
 Generating stack trace...
 0xb6a85309 in __libc_free + 0x49 from /lib/tls/i686/cmov/libc.so.6
 0xb6c268b1 in operator delete(void*) + 0x21 from /usr/lib/libstdc++.so.6
 0x0804a3c5 in <unknown> from ../../Cluster_Tools/filemerger/gjm
 0xb6a36ea2 in __libc_start_main + 0xd2 from /lib/tls/i686/cmov/libc.so.6
 0x08049db1 in __gxx_personality_v0 + 0x6d from
../../Cluster_Tools/filemerger/gjm
Aborted
turbo978 at MJ-GATE:~/gate_v3.1.2/benchmarks/benchmarkSPECT$
----------------------------------------
The merged root file with fastMerge option is able to read in TBrowser...and
the result is find...[600s]
but root had to recover 13 keys...

I dont know how to accept this...

I guess there is some problem with output option...

I will report after I found anything...

Thanks,
MJ

//=================================================
//  Park MinJae
//  SNU BME Ph.D. Candidate
//
//  DialTo:+82-17-711-7809
//  MailTo:MJ at ToTi.us
//
//  Make the Dream True...
//================================================= 

-----Original Message-----
From: gate-users-bounces at lists.healthgrid.org
[mailto:gate-users-bounces at lists.healthgrid.org] On Behalf Of Park MinJae
Sent: Tuesday, October 23, 2007 8:10 PM
To: 'Jan De Beenhouwer'; 'Samuel BURG'
Cc: 'Users Gate'
Subject: RE: RE : RE: [Gate-users] filemerger...

Dear Jan,

1. Environment setting...
I set as following...
GC_GATE_EXE_DIR=/home/turbo978/geant4_9.0.p01/bin/Linux-g++
GC_DOT_GATE_DIR=/home/turbo978/gate_v3.1.2

but there is a strange thing...
Even though there is no entry in latest_event_id, small root files can be
merged with gjm...
[when TBrowser load the merged file, root is trying to recover 8 keys, Hits,
Singles, Gate, latest_event_ID, etc...]

2. ROOT version...
I am using 5.12 version...
Based on your mail, 5.12 version is problem, right?

3. Loading individual root files...
I can load them in TBrowser without any problem...

4. Cluster benchmark...
I just have started the benchmark with clustering as you said...

I got some problem with installing root 5.14 and 5.16...
I guess it's library problem with xpm...
I start to install 5.14 again...

and I start to use TChain...but the way to connect Singles is a little
different...
I use the following code...
TFile *f = new TFile("duals10.root");
TTree *Singles = (TTree*)gDirectory->Get("Singles");
Singles->SetBranchAddress("energy",&energy);

but when I use the following code...
TChain chain("T");
chain.Add("file1.root");
chain.Add("file2.root");
TTree *Singles = (TTree*)gDirectory->Get("Singles");

ROOT said...illegal pointer to class object Singles...at
Singles->SetBranchAddress("energy",&energy);

I guess there is another way of using TChain than TFile...

Thanks,
MJ

//=================================================
//  Park MinJae
//  SNU BME Ph.D. Candidate
//
//  DialTo:+82-17-711-7809
//  MailTo:MJ at ToTi.us
//
//  Make the Dream True...
//================================================= 

-----Original Message-----
From: gate-users-bounces at lists.healthgrid.org
[mailto:gate-users-bounces at lists.healthgrid.org] On Behalf Of Jan De
Beenhouwer
Sent: Tuesday, October 23, 2007 7:48 PM
To: Samuel BURG
Cc: Users Gate; Park MinJae
Subject: Re: RE : RE: [Gate-users] filemerger...

On Tue, 2007-10-23 at 12:08 +0200, Samuel BURG wrote:
> Dear MJ,
> 
> I have also lot of problems with gjm.
> One 'easy' solution is to do a 'fast merge' with gjm and the to use a 
> TChain under ROOT to post-process your (multiple files) data.
> 
> Pro : it works, no need to update any code Cons : files 25% bigger, 
> not very fun

This isn't the case if you only merge the tree or leaves of the tree that
you need. If you disable the Gate ntuple, then spect root files are quite
small.
The file merger should work on all root files generated by Gate, fast mode
or not.

If you experience problems then check the following:
- are your environment setting set for cluster gate ? if they are, then any
root file generated should have a latest_event_id histogram with an entry in
it. ->Park MJ: your root files have no entry in that histogram.

- are you using a recent root version ? Try root v5 at least. ->Park MJ:
merging your files with an older root version gave a segmentation fault.
With root v5.12 it displays an error about an empty latest_event_id
histogram.

- can you load the individual root files before merging ? You should be able
to open them with root and view the contents with a TBrowser.

- you can test all this with the cluster benchmark

If you are still having a problem then send a test case like Park MJ did.

Regards,

--
MScE Jan De Beenhouwer
Ghent University Hospital
IBITECH - MEDISIP
De Pintelaan 185
Block B - 5th floor
B-9000 Ghent
Tel. +32-9-240.43.26
Fax: +32-9-240.33.90
E-mail: <Jan.DeBeenhouwer at UGent.be>
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