egs++ compiling issue: Undefined symbols for architecture arm64 #996

walleludvig · 2023-05-21T12:03:27Z

walleludvig
May 21, 2023

Hi EGSnrc community,

I am trying to implement a modified version of egs_application with egs++, but get a linking error at compilation. The issue arises when attempting to compile the original egs_application.cpp too (source code as distributed with EGSnrc install https://nrc-cnrc.github.io/EGSnrc/doc/pirs898/egs__application_8cpp.html).

The error is:

Undefined symbols for architecture arm64:
  "_main", referenced from:
     implicit entry/start for main executable
ld: symbol(s) not found for architecture arm64

This error does not arise at compilation of any other applications (e.g., egs_cavity, egs_app, etc.).

Has anyone else experienced a similar issue? Anyone got some suggestions as to how I can resolve this?

I have gcc-13 compilers installed through home-brew and running on MacOS Ventura 13.4 (M1 chip).

ftessier · 2023-05-22T23:30:43Z

ftessier
May 22, 2023
Maintainer

Well you cannot compile egs_applicaton.cpp directly, this is just a c++ library to build an application (so there is no __main symbol in the object code). If you want to modify egs_application.cpp and compile an application that uses your modified EGS_Application class. In that case, go into $HEN_HOUSE/egs++ and issue the command make. This will rebuild the library object and place it in egs++/dso/.../ so that it is in your path.

Better yet, keep the original egs_application.cpp and create your own copy of it under different .cpp and .h names under egs++/. Adjust the Makefile accordingly so that your new library object is included when you issue make.

Note: to compile a file as a library object (without requiring a __main symbol), you need to use the gcc flag -c. But in this case, you would then have to move it to the right location etc. Better use make!

0 replies

walleludvig · 2023-05-23T22:01:07Z

walleludvig
May 23, 2023
Author

Hi @ftessier, thank you for the response.

Compiling in egs++ did indeed work fine, however I am unsure of how I can manage to include the modified version of egs_application. When I issues make after moving the modified egs_application and its header file over to egs++ and modifying the Makefile I keep getting some errors like *** make error: no rules to make target egs_my_app.h needed ** when I add the header file to the same lists that I found egs_application in. However, I also attempted to exclude it in some of these and only mention it in the egspp_files and a line to generate the DSO1 object. I still then get an error about no rules to make target ... needed by egs_my_app.o. I believe an object file (egs_my_app.o) was created in the egs++/dso/.../ directory regardless and I thought this file is what I am after all looking for?

What I don't understand is how I can generate information/"rules" on how to make the target for the modified version of egs_application. Apologies for my lack of knowledge, but your help and expertise is greatly appreciated. Thank you!

1 reply

ftessier May 24, 2023
Maintainer

Yes, makefiles can be convoluted! To add egs_my_app.cpp, you have to:

1. Add `egs_my_app` in the `egspp_files` variable:

EGSnrc/HEN_HOUSE/egs++/Makefile

Lines 40 to 46 in 5c98134

 egspp_files = egs_input egs_base_geometry egs_library egs_transformations \ 

 egs_rndm egs_shapes egs_geometry_tester egs_timer egs_polygon \ 

 egs_projectors egs_alias_table egs_object_factory egs_spectra \ 

 egs_base_source egs_functions egs_application egs_run_control \ 

 egs_scoring egs_interpolator egs_atomic_relaxations \ 

 egs_ausgab_object egs_particle_track egs_fortran_geometry \ 

 egs_ensdf

2. Create a rule to make `egs_my_app.o`, similar to what is done for `egs_application`:

EGSnrc/HEN_HOUSE/egs++/Makefile

Line 142 in 5c98134

$(DSO1)egs_application.$(obje): egs_application.cpp egs_application.h

3. Add `egs_my_app.h` where `egs_application.h` is included in the Makefile:

EGSnrc/HEN_HOUSE/egs++/Makefile

Lines 85 to 86 in 5c98134

 $(DSO1)egspp.$(obje): egspp.cpp egs_application.h egs_base_geometry.h egs_vector.h \ 

 egs_math.h egs_library.h $(config1h)

EGSnrc/HEN_HOUSE/egs++/Makefile

Lines 146 to 148 in 5c98134

 $(DSO1)egs_atomic_relaxations.$(obje): egs_atomic_relaxations.cpp egs_atomic_relaxations.h \ 

 $(config1h) egs_simple_container.h egs_rndm.h egs_math.h egs_application.h \ 

 egs_base_geometry.h egs_vector.h

EGSnrc/HEN_HOUSE/egs++/Makefile

Lines 150 to 152 in 5c98134

 $(DSO1)egs_ausgab_object.$(obje): egs_ausgab_object.cpp egs_ausgab_object.h \ 

 $(config1h) egs_application.h egs_base_geometry.h egs_vector.h egs_math.h \ 

 egs_object_factory.h egs_input.h

4. Modify the class name

However, for all of this to work, you must rename the class in your new files (to EGS_Myapp, for example), otherwise the EGS_Application symbol will be multiply defined. So perhaps it is easier to just modify egs_application.* in the end? 🤔

rtownson · 2023-05-25T14:11:24Z

rtownson
May 25, 2023
Maintainer

What are you actually trying to do? Are you sure that you need to modify egs_application, and it can't be done in your new application instead?

4 replies

ftessier May 25, 2023
Maintainer

Good point! Normally one would indeed derive the EGS_Application class and add features there.

walleludvig May 27, 2023
Author

I am trying to compile an egs++ application code written by Jonas Lippuner in 2011 called Epp. He provided the source code and a user manual at this link: https://jonaslippuner.com/research/epp/.

While the instructions for installation indicates that all that is needed is to cd into the installed directory and do make. This failed for me and so I am trying to make it work step by step instead. I also suspect that since the user code is from 2011 it may be a bit outdated and need modifications along the way.

rtownson May 29, 2023
Maintainer

I'd just like to point out that we've discussed solving the epp compatibility with modern EGSnrc before: #746

walleludvig Jun 1, 2023
Author

Interesting! Thanks for pointing that out @rtownson. I guess I am currently making my own attempt at making it work with modern EGSnrc at the moment and while it seems like I have got it compiled I am still struggling a bit to make it run a simulation. As I am only learning about C++ on the fly here I've got doubts in my implementation of it and assume that the errors I am getting got to do with the way I managed to get it to "compile".

I will let you know if I get any success.

walleludvig · 2023-05-27T07:31:11Z

walleludvig
May 27, 2023
Author

Thank you so much for the descriptive instructions for help @ftessier. Really appreciate your assistance!

I ended up modifying egs_application directly instead (but with clear comments to identify where about). These modifications seem to have compiled fine.

However when I try to compile the actual egs++ application which uses this modified version of egs_application, I am still getting some linking errors with a list of duplicate symbol... (total of 47 duplicate symbols between Epp_macosx.o and egs_advanced_application_macosx.o) It is also followed by the following error ld: 47 duplicate symbols for architecture arm64 collect2: error: ld returned 1 exit status.

Any chance you happen to know why this is happening as well?

3 replies

walleludvig May 28, 2023
Author

I think I've actually managed to fix this issue by changing one of the #include egs_advanced_application.cpp to #include egs_advanced_application.h. Epp seems to have compiled successfully now but when running one of the examples I get an error saying:

You must turn ON Compton binding corrections when using
a detailed atomic relaxation (eadl_relax=true) since 
binding energies taken from incoh.data below 1 keV!

Which I found to be a result of eadl_relax & photon_xsections = 'xcom' returning True in egsnrc.mortran. While I doubt this is an instance of something like incorrect compilation I cannot be sure as I do not understand enough of all this.
Furthermore I do not really understand how to resolve the issue. I've tried changing multiple of the MC Transport parameters such as Photon cross sections to others than xcom but I just end up with a segmentation fault.

Apologies for constantly asking, but any suggestions on how to fix this Compton binding corrections issue? How can I do as the error message suggest and turn ON Compton binding corrections?

rtownson May 29, 2023
Maintainer

In the input file, you could remove the transport parameters to just use the defaults, or set Bound Compton scattering=On. At least this is the solution for other egs++ applications..

walleludvig Jun 1, 2023
Author

@rtownson

Setting Bound Compton Scattering=On does not change results and I receive the same error.

Setting all the MC Transport parameters to default values (Jonas' code requires that a block of MC transport parameters is included in input file) results in a segmentation fault.

I will keep trying to make this work, but any suggestions are greatly appreciated!

walleludvig · 2023-06-04T11:51:35Z

walleludvig
Jun 4, 2023
Author

Hi @rtownson and @ftessier,

Just writing here to ask if either of you may know why the following issue I am having might be occurring:

While Epp seems to have compiled fine for me know, when I try to run a simulation with it (Example_1.egsinp or Example_2.egsinp provided by Jonas) I keep getting a segmentation fault error.

I have noticed that when running a simulation a new input file (with filename eg Example_1.egsinp.egsinp) is created in my directory and this file just contains the MC transport parameters. I therefore suspect that I am getting a segmentation fault because the simulation starts reading from this file at runtime instead. However I am unsure as the creation of geometries, sources, media etc seems to have been successful during compilation of the input file (i.e., the output to terminal is as expected and the error only occurs when trying to execute the first batch).

Have you encountered or seen any similar behaviour before?

Thanks for all your help so far!

17 replies

mchamberland Aug 17, 2023

@walleludvig After adding the relevant media definitions and Epp-specific output options, the input file runs fine. So, feel free to give my version of Epp a shot.

walleludvig Aug 24, 2023
Author

Amazing! Thank you so much for providing this @mchamberland. I will test out your new version of Epp and I am sure it will a very helpful tool for my needs!

walleludvig Sep 3, 2023
Author

Hi @mchamberland,

I have successfully trialed your new version of Epp for the example input files and it is working very well with output detector images produced as expected. Thank you again for doing this!

However when I try with my own simulation setup I cannot seem to get the expected output images produced and I am only getting empty images as output. I believe there may be some issues with how I am setting up the sources and that ultimately the photons aren't reaching the detector. For this purpose I have been trying to use ptracks in ausgab object definition but it seems that Epp does not support this. I have tried using it for Example_1.egsinp but no tracks are stored in the output Example_1.ptracks file.

Do you happen to know if use of ptracks is compatible with this version of Epp, or if there may be some simple solution to making it work?

mchamberland Sep 5, 2023

@walleludvig Tracks should be supported out of the box. I was able to generate some right now (though I have not visualized them).

Maybe double-check your input file?

walleludvig Sep 10, 2023
Author

@mchamberland Okay, would have to be something I am getting wrong then. However I did use the exact same code in egs_chamber and got the tracks are visualised just fine. I will look more into the output .ptracks file to see if the issue is with visualisation in egs_view or writing to the .ptracks file.

Thanks for checking.

morfius84 · 2023-06-05T20:27:08Z

morfius84
Jun 5, 2023

I have a problem when compiling dosrznrc input

Error: Symbol 'git_hash' at (1) has no IMPLICIT type
mingw32-make[1]: *** [D:\EGSnrc\EGSnrc-master\HEN_HOUSE\makefiles\standard_makefile:90: D:\EGSnrc\EGSnrc-master\third-party\bin\win3264\dosrznrc.exe] Error 1
mingw32-make: *** [D:\EGSnrc\EGSnrc-master\HEN_HOUSE\makefiles\standard_makefile:189: opt] Error 2

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egs++ compiling issue: Undefined symbols for architecture arm64 #996

walleludvig May 21, 2023

Replies: 6 comments · 25 replies

ftessier May 22, 2023 Maintainer

walleludvig May 23, 2023 Author

ftessier May 24, 2023 Maintainer

1. Add egs_my_app in the egspp_files variable:

2. Create a rule to make egs_my_app.o, similar to what is done for egs_application:

3. Add egs_my_app.h where egs_application.h is included in the Makefile:

4. Modify the class name

rtownson May 25, 2023 Maintainer

ftessier May 25, 2023 Maintainer

walleludvig May 27, 2023 Author

rtownson May 29, 2023 Maintainer

walleludvig Jun 1, 2023 Author

walleludvig May 27, 2023 Author

walleludvig May 28, 2023 Author

rtownson May 29, 2023 Maintainer

walleludvig Jun 1, 2023 Author

walleludvig Jun 4, 2023 Author

mchamberland Aug 17, 2023

walleludvig Aug 24, 2023 Author

walleludvig Sep 3, 2023 Author

mchamberland Sep 5, 2023

walleludvig Sep 10, 2023 Author

morfius84 Jun 5, 2023

walleludvig
May 21, 2023

Replies: 6 comments 25 replies

ftessier
May 22, 2023
Maintainer

walleludvig
May 23, 2023
Author

ftessier May 24, 2023
Maintainer

1. Add `egs_my_app` in the `egspp_files` variable:

2. Create a rule to make `egs_my_app.o`, similar to what is done for `egs_application`:

3. Add `egs_my_app.h` where `egs_application.h` is included in the Makefile:

rtownson
May 25, 2023
Maintainer

ftessier May 25, 2023
Maintainer

walleludvig May 27, 2023
Author

rtownson May 29, 2023
Maintainer

walleludvig Jun 1, 2023
Author

walleludvig
May 27, 2023
Author

walleludvig May 28, 2023
Author

rtownson May 29, 2023
Maintainer

walleludvig Jun 1, 2023
Author

walleludvig
Jun 4, 2023
Author

walleludvig Aug 24, 2023
Author

walleludvig Sep 3, 2023
Author

walleludvig Sep 10, 2023
Author

morfius84
Jun 5, 2023