[Gate-users] compilation of GATE in a cluster
Samuel BURG
samuel_burg at yahoo.fr
Fri Oct 26 23:49:42 CEST 2007
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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PATH=/usr/local/mpich-1.2.5..12-intel/bin:/usr/local/gm-1.6.5/bin:/usr/local/clustersuite-20040816/silver/bin:/usr/local/clustersuite-20040816/moab/bin:/usr/local/pbs-2.3.12-14/bin:/usr/local/intel-8.0-20040412/bin:/usr/local/pgi-5.1.3/linux86/5.1/bin:/usr/local/modules-env-3.1.6-6/bin:/usr/kerberos/bin:/bin:/usr/bin:/usr/local/bin:/usr/X11R6/bin:/home/zhibin/.GATE/ROOT5.14/bin:/home/zhibin/.GATE/autoconf/bin:/home/zhibin/geant4/bin/Linux-g++:.:/home/zhibin/geant4/bin/Linux-g++:/home/zhibin/.GATE/ROOT5.14/bin:/home/zhibin/.GATE/autoconf/bin:/home/zhibin/geant4/bin/Linux-g++:.:/home/zhibin/geant4/bin/Linux-g++:/home/zhibin/.GATE/gate_v3.1.2::/home/zhibin/.GATE/ROOT5.14/bin:/home/zhibin/.GATE/autoconf/bin:/home/zhibin/geant4/bin/Linux-g++::/home/zhibin/geant4/bin/Linux-g++
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