[gate-users] Maximum file size exceeded problem
Amarnath Srinivasan
asrinivasan at hsc.wvu.edu
Thu Sep 30 20:41:46 CEST 2004
Dear Santin,
Thanks a lot for the files. I tested the programs. Both the mask for
parameter reduction and the file splitter command worked well as expected.
I use Redhat 9.0 with gcc 3.0 on a Intel Xeon Dual processor system for
running Gate.
But when exiting Gate from idle it produces a core dump. I have attacahed
the error messsage I got form Gate.
I am not sure if it is because of the new files. Yopu might want to take a
look into this.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~
Time set to (s) 20
User simulation time (sec) := 125481
Real simulation time (sec) := 192313
System simulation time (sec) := 1061.69
Idle> exit
Graphics systems deleted.
Visualization Manager deleting...
*** Break *** segmentation violation
Generating stack trace...
/usr/bin/addr2line: Gate: No such file or directory
/usr/bin/addr2line: Gate: No such file or directory
/usr/bin/addr2line: Gate: No such file or directory
/usr/bin/addr2line: Gate: No such file or directory
/usr/bin/addr2line: Gate: No such file or directory
/usr/bin/addr2line: Gate: No such file or directory
/usr/bin/addr2line: Gate: No such file or directory
0x420734d6 in __libc_free + 0x86 from /lib/tls/libc.so.6
0x412f4983 in operator delete(void*) + 0x23 from /usr/lib/libstdc++.so.5
0x412e832e in std::basic_string<char, std::char_traits<char>,
std::allocator<char> >::_Rep::_M_destroy(std::allocator<char> const&) + 0x3e
from /usr/lib/libstdc++.so.5
0x08721c32 in G4UIparameter::~G4UIparameter [in-charge]() + 0x14c from Gate
0x08711d37 in G4UIcommand::~G4UIcommand [in-charge deleting]() + 0x57 from
Gate
0x08212fbb in GateToASCIIMessenger::~GateToASCIIMessenger [in-charge
deleting]() + 0x39 from Gate
0x0817b7df in GateToASCII::~GateToASCII [in-charge deleting]() + 0x5b from
Gate
0x08164f09 in GateOutputMgr::~GateOutputMgr [in-charge deleting]() + 0x41
from Gate
0x081529c3 in main + 0x825 from Gate
0x42015574 in __libc_start_main + 0xe4 from /lib/tls/libc.so.6
0x08151b9d in TFile::TFile[in-charge](char const*, char const*, char
const*, int) + 0x41 from Gate
Abort (core dumped)
[ray at rayraylman9 ~/benchmarkPET]$
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Thanks a lot for your help.
Amarnath Srinivasan
Research Assistant
Center for Advanced Imaging
PO Box 9235
Dept of Radiology, HSC, WVU
Morgantown, WV 26506
asrinivasan at hsc.wvu.edu
Phone Office: 304 293 6925 /Lab: 304 293 5586
----- Original Message -----
From: "Giovanni Santin" <giovanni.santin at cern.ch>
To: "GATE feedback and helpline for Users" <gate-users at lphe1pet1.epfl.ch>
Sent: Sunday, September 19, 2004 3:38 AM
Subject: Re: [gate-users] Maximum file size exceeded problem
> Dear Amarnath
>
> I was not aware of any solution to this problem via compilation flags.
> It sounds interesting.
>
> Nevertheless, in the last days I wrote a few modifications to Gate to have
> an automatic file swap when the file size exceeds a user defined limit.
>
> The old file fileCoincidences.dat is then closed and a new one
> fileCoincidences_1.dat is opened.
>
> This should work for both Coincidences and Singles.
>
> The file size limit is set to 2GB by default, and the user can set it to a
> different value, or to zero (in this case no file swap is done).
>
> In addition, there will be the possibility to choose the variables to
> include in Coincidences and Singles ASCII files, with a mask.
>
> I hope the new additions will come out soon in the next release, but we
> still need to wait for some validation feedback as usual before releasing
> the code.
>
> If the release will wait, I'll make the single modified files available
> for testing.
>
> Best regards,
> --
> Giovanni
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Giovanni Santin
> Space Environments and Effects Analysis
> ESA - ESTEC - TEC-EES
> Keplerlaan 1, 2200 AG Noordwijk, Netherlands
> e-mail: giovanni.santin at esa.int
> Tel: +31 71 565 6267
> Fax: +31 71 565 4999
>
>
> On Thu, 16 Sep 2004, Amarnath Srinivasan wrote:
>
> > Hello Zhang and Others,
> > I am using Gate in Redhat 9 for simulating a PET scanner and produce
output
> > in Ascii Format. When the output file exceeds 2Gb I get an error saying
> > "FileSize Limit Exceeded" and the program terminates. I am hitting the
2**31
> > bit limit of the datatype off_t.
> >
> > 1. I am looking for ways to fix this problem.Based on Mr.Zhang's
> > provious mail I looked for large file support in Redhat Linux. RH9
supports
> > large files. But to enable that for gate, gate should be compiled in
gcc
> > with the "large file support turned on". I would like to know if gate
> > supports
> > large files? What is the procedure to compile gate with large file
support
> > turned on? Has anyone done this before?
> >
> > 2. Will doing "gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
program.c"
> > by editing the make file for gate help? If yes what are the files that
> > should be edited ?
> > Does this have to be done for geant too?
> >
> > 3. I would also like to know if someone has produced files larger than
2GB
> > in gate in "any" platform?
> >
> > Thankyou
> > Amarnath Srinivasan
> > Research Assistant
> > Center for Advanced Imaging
> > PO Box 9235
> > Dept of Radiology, HSC, WVU
> > Morgantown, WV 26506
> > asrinivasan at hsc.wvu.edu
> > Phone Office: 304 293 6925 /Lab: 304 293 5586
> > ----- Original Message -----
> > From: "Long ZHANG" <zhanglong99 at tsinghua.org.cn>
> > To: <gate-users at lphe1pet1.epfl.ch>
> > Sent: Friday, August 27, 2004 2:46 AM
> > Subject: Re: [gate-users] Maximum file size exceeded problem
> >
> >
> > > Dear Srinivasan,
> > >
> > > There are several limits on Linux Filesystem, the one you met is
defined
> > by VFS
> > > module, that is to say, all filesystemson your kerenl have a maximus
size
> > of 2GB.
> > >
> > >
> > > So the solution is to update your kernel and use another filesystem. A
> > journal
> > > filesystem can resolve this problem (EXT2/EXT3 can't). You'd better
query
> > Linux
> > > Journal Filesystem on GOOGLE, then you can get many good solution.
> > >
> > > Hope this helps!
> > >
> > > Best regards,
> > >
> > > Long
> > >
> > > In your mail:
> > > >From:"Amarnath Srinivasan" <asrinivasan at hsc.wvu.edu>
> > > >Reply-To: GATE feedback and helpline for Users
> > <gate-users at lphe1pet1.epfl.ch>
> > > >To: "GATE feedback and helpline for Users"
<gate-users at lphe1pet1.epfl.ch>
> > > >Subject: Re: [gate-users] Maximum file size exceeded problem
> > > >
> > > >
> > > >Hello,
> > > >
> > > >We were running gate on RedHat 9 . When the output ascii file
> > > "gate_coincidence.dat" size exceeded 2GB I got an error saying
maximum
> > file size
> > > exceeded and the program terminated.
> > > >Does anybody have idea on how to fix this problem.
> > > >
> > > >
> > > >
> > > >thankyou
> > > >Amarnath Srinivasan
> > > >Research Assistant
> > > >Center for Advanced Imaging
> > > >PO Box 9235
> > > >Dept of Radiology, HSC, WVU
> > > >Morgantown, WV 26506
> > > >asrinivasan at hsc.wvu.edu
> > > > ----- Original Message -----
> > > > From: yuxuan.zhang at di.mdacc.tmc.edu
> > > > To: gate-users at lphe1pet1.epfl.ch
> > > > Sent: Tuesday, August 24, 2004 5:08 PM
> > > > Subject: [gate-users] about random coincidences
> > > >
> > > >
> > > >
> > > > hi all,
> > > >
> > > > In my simulation I noticed a strange result that I can not figure
it
> > out.
> > > > My setup is that: using cylindricalPET system with 30 rsetors, one
> > point
> > > > source at the center. The radiation activity is very high, thus
there
> > are
> > > > lots of random coincidences (accidental coincidences) in the totoal
> > > > coincidences. Now I do the statistics on these random coincidences
> > according
> > > > to the sector index, then I found that the coincidences between 2
> > opposite
> > > rsectors
> > > > (e.g. No.0 and 15, or No.5 and 20) are much more than the
coincidences
> > between
> > > other
> > > > 2 sectors ( No. 0 and 14, or No. 0 and 16 ...) Usually the
difference
> > can be
> > > 50% or 100% depend on the thickness of the detector. Is anyone else
> > noticed that?
> > >
> > > > Can you have a try in your computer to find out whether this is a
bug
> > of GATE
> > > or there
> > > > is somthing wrong with my simulation? Thank you very much.
> > > >
> > > >
> > > > Best regards,
> > > >
> > > > Yuxuan Zhang
> > > >
> > > >
> > > > Dr. Yuxuan ZHANG
> > > > Dept. Experimental Diagnostic Imaging
> > > > Univ. Texas, MD Anderson Cancer Center
> > > > 1515 Holcombe Blvd, Unit 217
> > > > Houston, TX 77030-4095
> > > >
> > > > Tel: +1-713-745-1671
> > > > Fax: +1-713-745-1672
> > > >
> > > >
> > >
> >
>---------------------------------------------------------------------------
> > ---
> > > >
> > > >
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