[gate-users] root file size
Corinne J Groiselle
corinne.groiselle at umassmed.edu
Mon Dec 13 15:34:18 CET 2004
*I don't have the 2G limit, but I am running GATE on a 64-bits machine
and it may be an explanation. But I copy/paste one of Fernando's email
from last October and it seems that the 2G limit is not a limit anymore
with the new version!
So, try to update your version of ROOT and see if it solves the problem.
Hope this helps,
Corinne
/Fernando Rannou/*/ rannou at mednet.ucla.edu
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------------------------------------------------------------------------
/Dear Gaters,
look at this ls -la command:
-rw-r--r-- 1 rannou isl 3.7G Oct 19 10:13
ptsrc_10mmLead_0.0_Large.root
Yeap, a 3.7 Giga bytes ROOT file. This file contains singles and
coincidences.
I then processed the file with a .C program to create my listmode data
and everything went smooth. The listmode file was smaller than 2Giga though.
But In theory the latest version of ROOT can read and write files larger
than 2 Gigabytes
What to do:
1) update ROOT to version v4.01.02.
2) edit the petsim/include/GateToRoot.hh file as follows:
In the class SingleOutputChannel : public VOutputChannel,
in the inline method Book, add the SetMaxTreeSize call to set the
maximum size of the Singles tree.
inline void Book()
{
m_collectionID=-1;
if (m_outputFlag) {
m_tree = new GateSingleTree(m_collectionName);
m_tree->SetMaxTreeSize(17179869184L);
m_tree->Init(m_buffer);
}
}
Do the same for
class CoincidenceOutputChannel : public VOutputChannel
inline void Book()
{
m_collectionID=-1;
if (m_outputFlag) {
m_tree = new GateCoincTree(m_collectionName);
m_tree->SetMaxTreeSize(17179869184L);
m_tree->Init(m_buffer);
}
}
3) Recompile Gate
The method TTree::SetMaxTreeSize(Long64_t maxsize) takes a 64 bits Long,
so in theory you could
go all the way to 2^64=18446744073709550000 bytes, if unsigned (I'm not
sure, maybe is only to 2^63).
Right now, the value I 'm using is 16Gb.
I got all this info from ROOT people. Who can help me test this? We
would need to decide what
max size value to use in the GATE release.
Fernando/
Nehmeh, Sadek/Medical Physics wrote:
>Theodore, I know there is 2GB limitation in the root file size. One way
>to analyze your data, and that's how I do it, is to loop over the root
>files and do you analysis on a file-by-file basis, while you update your
>output information. Another thing you may need to be careful with when
>you combine your root files into one is that some variables, like for
>example the eventID which will be incremented to cover the total number
>if events from all runs, may exceed the max number allowed for an
>integer for example. In this case, random numbers will be assigned to
>the varaible.
>
> Regards,
>
> Sadek
>
>
>----------------------------------------
> Sadek A. Nehmeh, Ph.D.
> Assistant Attending Physicist
> Medical Physics Department
> Nuclear Medicine Service
> Memorial Sloan-Kettering Cancer Center
> Tel: (212)-639-2175
> Email: nehmehs at mskcc.org
>------------------------------------------
>
>
>
>
>
>
>-----Original Message-----
>From: gate-users-bounces at lphe1pet1.epfl.ch
>[mailto:gate-users-bounces at lphe1pet1.epfl.ch] On Behalf Of Mutanga
>Theodore
>Sent: Sunday, December 12, 2004 7:28 AM
>To: gate-users at lphe1pet1.epfl.ch
>Subject: [gate-users] root file size
>
>Greetings, I am running some 100 simulations in batch mode on the
>cluster, 50 % of them succeeded and I have to collect the files together
>to get one big root file.And also the .ima , .dim and .info files.
>
>I tried to use Dirk K's Combine.C code to combine the files. The
>resulting output file is still split into other smaller files when the
>size gets to about 2G.
>
>Is there some means of not having this split , ? I don't know how to
>analyze the files with root if I have them seperated.
>
>Regards
>
>Theo
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>
>
>
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--
Corinne J. Groiselle, PhD
Instructor of Radiology
Department of Radiology / Division of Nuclear Medicine
University of Massachusetts Medical School
55 Lake Avenue North
Worcester, MA 01655
USA
_Phone_: (508)-856-6123 - FAX: (508)-856-4572
_Email_: Corinne.Groiselle at umassmed.edu _
Professional homepage_: http://users.umassmed.edu/corinne.groiselle
Official faculty page: http://www.umassmed.edu/faculty/show.cfm?faculty=731
_Personal homepage_: http://corinne.groiselle.free.fr
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