Test data cannot be downloaded after new installation of GATE 10

[Mariag-hub]

Hi, I am trying to install Gate but I have encountered some problems with both Gate10 and Gate9. For example, Gate10 does not find all the opengate_tests, while for Gate9 I cannot install both ECAT7 and LMF3_0. Can someone help? I am using a virtual machine with Ubuntu 24.04.

[BishopWolf]

Question: why a virtual machine?

[Mariag-hub]

Question: why a virtual machine?

I would like to install Gate on a Linux machine to use it with Slicer OpenDose3D. For now I am trying to install everything using my macos but I will later on the installation migrate the installation on a linux environment.

[BishopWolf]

I am the creator of Slicer OpenDose3D. It only accepts Gate 9 for now. We have some issues finding support to move to gate 10. It will eventually move but not for now.

Now using gate 9 and Slicer OpenDose3D, you don't need a virtual machine. You can use the recommended docker launch method for gate 9. It is described in the documentation.

[Mariag-hub]

Ok, thanks a lot for the clarification. However, as I said in the initial post, I already tried to install Gate9 with no luck because I cannot install both ECAT7 and LMF3_0, do you know how can i solve that?

[BishopWolf]

In the docker image there is everything you need. I have never installed geant nor gate9 in windows. I always use the docker way.

[nkrah]

Hey. Thanks for posting an issue. When you write "Gate10 does not find all the opengate_tests", what do you mean exactly? Can you post the terminal output with the error you receive?

Please also post the output of opengate_info.

[Mariag-hub]

In the docker image there is everything you need. I have never installed geant nor gate9 in windows. I always use the docker way.

Ok thanks, so after I did docker pull opengatecollaboration/gate this is what i see. Does it work correctly? Sorry if my questiona are stupid, I am just approaching to this world.

[BishopWolf]

This is an entirely different issue. You must be located at the root of your macro folder.
The folder must contain a mac subfolder and inside you must have a script named main.mac
It is literally in the docker line you wrote

[Mariag-hub]

Hey. Thanks for posting an issue. When you write "Gate10 does not find all the opengate_tests", what do you mean exactly? Can you post the terminal output with the error you receive?

Please also post the output of opengate_info.

I attach the screen of my terminal when I try to do opengate_tests. It basically searches for the tests but doesn't find anything.

Also this is the output of opengate_info:

`================================================================================
The opengate_core library cannot be loaded.
Error is: cannot allocate memory in static TLS block
Please use the following export lines before importing opengate:
export LD_LIBRARY_PATH=/home/pcdti1/opengate_env/lib/python3.11/site-packages/opengate_core.libs:${LD_LIBRARY_PATH}
export LD_PRELOAD=/home/pcdti1/opengate_env/lib/python3.11/site-packages/opengate_core.libs/libG4processes-d7125d28.so:/home/pcdti1/opengate_env/lib/python3.11/site-packages/opengate_core.libs/libG4geometry-cf4c216c.so
or:
export GLIBC_TUNABLES=glibc.rtld.optional_static_tls=2000000

We try to restart with :
export LD_LIBRARY_PATH=/home/pcdti1/opengate_env/lib/python3.11/site-packages/opengate_core.libs:/opt/minc/1.9.18/lib:/opt/minc/1.9.18/lib/InsightToolkit:/usr/lib/x86_64-linux-gnu::/usr/local/fsl/lib:$LD_LIBRARY_PATH
export LD_PRELOAD=/home/pcdti1/opengate_env/lib/python3.11/site-packages/opengate_core.libs/libG4geometry-cf4c216c.so:/home/pcdti1/opengate_env/lib/python3.11/site-packages/opengate_core.libs/libG4processes-d7125d28.so::$LD_PRELOAD
export GLIBC_TUNABLES=glibc.rtld.optional_static_tls=2000000

Python version 3.11.8 | packaged by conda-forge | (main, Feb 16 2024, 20:53:32) [GCC 12.3.0]
Platform linux
Site package /home/pcdti1/opengate_env/lib/python3.11/site-packages
Geant4 version geant4-11-03 [MT]
Geant4 MT True
Geant4 Qt True 5.9.7
Geant4 GDML True
Geant4 date 6-December-2024
Geant4 data /home/pcdti1/opengate_env/lib/python3.11/site-packages/opengate_core/geant4_data
ITK version 5.2.1
GATE version 10.0.2
GATE folder /home/pcdti1/opengate_env/lib/python3.11/site-packages/opengate
GATE data /home/pcdti1/opengate_env/lib/python3.11/site-packages/opengate/data
GATE tests /home/pcdti1/opengate_env/lib/python3.11/site-packages/opengate/tests/src
GATE core path /home/pcdti1/opengate_env/lib/python3.11/site-packages/opengate_core/opengate_core.cpython-311-x86_64-linux-gnu.so
GATE date 2025-03-25T16:13:28 (pypi)`

[tbaudier]

You have an old version of Gate (10.0.2). Could you try with version 10.1.0, that problem was solved

[Mariag-hub]

This is an entirely different issue. You must be located at the root of your macro folder. The folder must contain a mac subfolder and inside you must have a script named main.mac It is literally in the docker line you wrote

These are the folders inside the docker image, i cannot find the mac folder. I'm surely not understanding properly how docker works though.

PreInit> ls
Command directory path : /
Sub-directories :
/control/ UI control commands.
/units/ Available units.
/gate/ GATE detector control.
/process/ Process Table control commands.
/particle/ Particle control commands.
/tracking/ TrackingManager and SteppingManager control commands.
/geometry/ Geometry control commands.
/event/ EventManager control commands.
/cuts/ Commands for G4VUserPhysicsList.
/run/ Run control commands.
/random/ Random number status control commands.
/material/ Commands for materials
/hits/ Sensitive detectors and Hits
/digi/ DigitizerModule
/vis/ Visualization commands.
Commands :

[BishopWolf]

These are the folders inside the docker image, i cannot find the mac folder. I'm surely not understanding properly how docker works though.

You must launch docker from WITHIN the folder where your macro files are. NEVER from the gate folder.
You don't need to understand docker, just
cd /path/to/your/macro/folder

then ls must show
folder mac

and ls mac must show
file main.mac

[Mariag-hub]

I am sorry, but i cannot understand what is the macro folder. By looking at the instructions regarding the docker installation I only see the docker image but I cannot understand what else i should download (macro folder).

[BishopWolf]

I recommend you then to https://opengate.readthedocs.io/

[BishopWolf]

🧩 What is the “macro folder” in OpenGATE?

In OpenGATE, a macro is simply:

👉 A text file (usually .mac) that contains simulation commands

Examples:

define geometry
define sources
set physics
run simulation

So the “macro folder” = a directory on your machine that contains your .mac files.

📦 What you actually need (Docker case)

When using Docker, you do NOT download a special “macro folder”.

Instead, you must:

Create your own folder locally
Put your .mac files inside
Mount it into the container

🔑 Key idea (this is the confusion)

The documentation assumes you already understand that:

“macro folder” = your working directory containing simulation scripts

It is NOT something you download, unlike the Docker image.

🧠 Analogy

Think of Docker like:

OpenGATE = the engine
Macro files = the input script

👉 Without macros, OpenGATE has nothing to run.

⚠️ Common mistakes
❌ Expecting macros inside the Docker image

➡️ The image usually does NOT include your simulation files

❌ Running Gate without mounting a folder

➡️ You’ll get errors like:

file not found
nothing happens

[Mariag-hub]

so the command docker run -i --rm -v $PWD:/APP opengatecollaboration/gate mac/main.mac is not necessary to check the installation but is an example of how i can run a simulation called main.mac? Again, I'm sorry to bother you with these stupid questions

[BishopWolf]

yes, you have finally understood. And sorry, but chatGPT is immensely more pedagogical than me. That's why I paste its response

[nkrah]

For Clarity: Part of the discussion in this thread is about GATE 9, not GATE 10. GATE 10 does not use macro files!

[nkrah]

I close this because it mainly concerns GATE 9.