[Gate-users] compilation of GATE in a cluster

Fri Nov 23 14:44:43 CET 2007

Jonathan,

Maybe you can compute time-of-flight from the data in the Root file generated by Gate. In Root file you should found position and time of each event, this way you should be able to calculate T-O-F.

Best regards,

Samuel Burg

kam kim <kimkam007 at gmail.com> a écrit : Dear Samuel,

 Thank you very much for your email. I got some information about problems on the compilation of GEANT4 using low gcc version(<3.3). Since the gcc version in my linux cluster is 3.2, I installed gcc4.2.2 in my home directory. Using this gcc, I installed  CLHEP2.0.3.1, GEANT4.9.1p02. I got an error when I installed ROOT. It seems that this error is a known bug and can be fixed. Hopefully, this time I can install GATE.

 By the way, do you have any idea about the calculation of time of flight of a gamma photon travelling from the point of the annihilation to a crystal or a detector?

 Best regards,
 Jonathan

 On 11/21/07, Samuel BURG <samuel_burg at yahoo.fr> wrote: Hi Jonathan,

I have had a look in your last Gate-log's. It realy seams that you have an issue with the compilation and link of your Gate. This has nothing to do with your macro files. 
Gate 3.1.x should compil with gcc 3.2.x. On my computer I have used gcc-4.1.2, x86_64, and on my cluster I've used gcc 3.x? (don't remember sub-version), x86.

You should have a look in the logs of your compilation about any errors. 

Good luck,

Samuel Burg  

kam kim <kimkam007 at gmail.com>  a écrit :   Dear Samuel,

 I am thinking if there is something wrong with the linux version on the cluster---Red Hat 3.2.3-58. But which can only affect the compilation of GATE. I am really getting stucky. I'm checking with the adminstrator about whether the cluster has some librarys such as openGL. Do you have any other suggestions?  
 Thank you very much.

 Best regards,
 Jonathan

 On 10/26/07, kam kim <kimkam007 at gmail.com> wrote:    Dear Samuel,

 I tried this mac and got the output of Gate in a log-file. Attached are the log-file and a file including environmental variables before I performed Gate.

 Thanks,
  Jonathan

 On 10/26/07, Samuel BURG <samuel_burg at yahoo.fr  > wrote:  All right, 

your macro files are good.

try this one ("an-other-benchmarkPET.mac  "), and copy-past the output in a log-file, so we can try to figure out what's happening with your gate. 

also show us the environment variables you set before to launch gate.

 best regards,

Samuel

kam kim <kimkam007 at gmail.com > a écrit :  
   Dear Samuel,

 I used your benchmarkPET.mac file and got almost the same problem. As you suggested, attached are a tar file including all mac files and a file named benchmarkPET.log including the output of Gate. I also attached a file including the environmental variable setup in the cluster, which is named  cluster.env. I  hope that these files will give you more information to help me figure out the problem. 

 Thank you very much.

Best regards,
 Jonathan

 On 10/26/07, Samuel BURG <samuel_burg at yahoo.fr  > wrote:  Dear Jonathan,

I have test my benchmarkPET.mac, right out-of-the box from gate-v3.1.2, and it run exactly as it should, so it seams that your  benchmarkPET.mac file has been corrupted.

Check if the command :
"/run/initialize"
is call BEFORE the command :
"/control/execute digitizer.mac"
in your benchmarkPET.mac file.

 For now, I don't see other explaination of your problem.

So,
1) can you send me all your *.mac file in a tar.gz file ?
2) try the benchmarkPET.mac file I've attached to this mail.
3) if there is error remaining copy-past all the output of Gate in a file and send it to us.  

Regards,

Samuel

kam kim <kimkam007 at gmail.com > a écrit :   Dear Samuel;

 When I run Gate benchmarkPET.mac, I got errors as follows:
 ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder> *****
and
 ***** COMMAND NOT FOUND </gate/output/ascii/setOutFileHitsFlag 0> *****

 Then I looked at GATE-USER talk. I noticed that you answered a similiar question to MJ. But in my case, the linking gate was successfully done and root version is 5.14. Could you please help me out? Thanks in advance.  

 Best regards,
 Jonathan

 On 10/18/07, Samuel BURG <samuel_burg at yahoo.fr  > wrote:  Dear Kam Kim,

I sugjest you to upgrade to version 3.1.2, as last month in a mail from one of the main developer we can read this:  

<<<<

Dear
 Gaters,

To perform correctly the compressed voxel capabilities and the gamma 
backtoback emission with the last Gate version (

3.1.2), you must use

 the 
patch which is provided
with this e-mail;
Sorry for these
 inconveniences.

All the best

Sebastien
<<<<<

in fact this patch has already been apply on the Gate  v3.1.2 available from the download area.

Second point is that g++/gcc version can matter in compilation error, but I'm not sure it will solve your specific problem. 

Hope this will help,

best regards,  

Samuel

kam kim <kimkam007 at gmail.com> a écrit :  Dear Samuel;

Thank you for your email. 

In my local linux system, I installed CLHEP1.9.2.2, root5.14, geant4.8.0.p01  and gate_v3.1.1. It seems that this comibination works well, and then I decided to install them into a linux cluster. One possibility could be that linux-gcc or linux-g++ in the cluster is different from that in my local linux system. I don't know whether this would cause any problem.  

Best regards,
Jonathan

 On 10/17/07, Samuel BURG <samuel_burg at yahoo.fr  > wrote:  Well, 

it seems you have a problem with the version of Geant4.

you should restart the install with the good versions :  

Gate 3.1.1 + Geant4 8.1p2 + Root 5.12 + clhep 1.9.2.3
or
Gate 3.1.2 + Geant4 9.0 + Root 5.14 + clhep  1.9.3.1 / 2.0.3.1

don't mix the versions.

Regards,

Samuel
kam kim <  kimkam007 at gmail.com > a écrit :         
 Dear All,
 When I tried to install gate_v3.1.1 in a linux cluster, I got an error as follows:
 src/GateCompressedVoxelOutput.cc:97: no method 'G4Material::GetMaterialTable' 
src/GateCompressedVoxelOutPut.cc:130: no method 'G4Material::GetMaterialTable'
src/GateCompressedVoxelOutput.cc:131: invalid use of undefined type 'struct G4Material'  
 make: *** Error 1
 I should point out that I successfully installed root-5.14, CLHEP1.9.2.2 and geant4.8.0.p01 in the cluster. 
 Any suggestion would be appreciated.

Best regards, 
Jonathan

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