hannorein / rebound

💫 An open-source multi-purpose N-body code.
https://rebound.readthedocs.io/
GNU General Public License v3.0
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Getting error when running makefile on Mac #663

Closed JonathanHammer2 closed 1 year ago

JonathanHammer2 commented 1 year ago

Hello, I'm having trouble when it tries to link. Please help.

I tried installing Xcode; this is the version I get:

Apple clang version 14.0.0 (clang-1400.0.29.202) Target: x86_64-apple-darwin21.6.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

This is the error I get:

(base) cycloastro@Lindas-MBP simplest % make
Compiling shared library librebound.so ... /Applications/Xcode.app/Contents/Developer/usr/bin/make -C ../../src/

Linking share library librebound.so ... cc -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -Wno-unknown-pragmas -fPIC -DLIBREBOUND -shared rebound.o tree.o particle.o gravity.o integrator.o integrator_whfast.o integrator_saba.o integrator_ias15.o integrator_sei.o integrator_bs.o integrator_leapfrog.o integrator_mercurius.o integrator_eos.o integrator_tes.o boundary.o input.o binarydiff.o output.o collision.o communication_mpi.o display.o tools.o rotations.o derivatives.o simulationarchive.o glad.o integrator_janus.o transformations.o -L/usr/local/lib -o librebound.so Undefined symbols for architecture x86_64: "_reb_display_init", referenced from: _reb_integrate in rebound.o (maybe you meant: _reb_display_init_data) ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: [librebound.so] Error 1 make: [librebound] Error 2

hannorein commented 1 year ago

Could you try running

make clean
make
JonathanHammer2 commented 1 year ago

That seemed to work.

Thank you.

From: Hanno Rein @.> Date: Wednesday, March 1, 2023 at 10:57 AM To: hannorein/rebound @.> Cc: Jonathan Hammer @.>, Author @.> Subject: Re: [hannorein/rebound] Getting error when running makefile on Mac (Issue #663)

Could you try running

make clean

make

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hannorein commented 1 year ago

Glad it worked. This error occurred because you probably tried some example with OpenGL Visualizations turned on and some with them turned off.

JonathanHammer2 commented 1 year ago

Hello again,

Simplest worked fine, but I tried making the solar system example and it crashed. I tried “make clear” again and it still crashed.

Also I’m curious as to what units are being used for position and velocity in the solar system C file? They don’t look anything like what I see on NASA’s Horizon. Thanks very much.

Here’s the output:

Compiling problem file ...

cc -I../../src/ -Wl,-rpath,./ -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 problem.c -L. -lrebound -L/usr/local/lib -lglfw -framework Cocoa -framework OpenGL -framework IOKit -framework CoreVideo -o rebound

ld: warning: directory not found for option '-L/opt/homebrew/lib'

ld: library not found for -lglfw

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make: *** [all] Error 1

(base) @.*** solar_system % make clean

Cleaning up shared library librebound.so ...

/Applications/Xcode.app/Contents/Developer/usr/bin/make -C ../../src/ clean

Removing object files *.o ...

Removing shared library librebound.so ...

Removing coverage files ...

Cleaning up local directory ...

(base) @.*** solar_system % ls

Makefile problem.c

(base) @.*** solar_system % make

Compiling shared library librebound.so ...

/Applications/Xcode.app/Contents/Developer/usr/bin/make -C ../../src/

fatal: not a git repository (or any of the parent directories): .git

Compiling source file rebound.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o rebound.o rebound.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file tree.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o tree.o tree.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file particle.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o particle.o particle.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file gravity.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o gravity.o gravity.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file integrator.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o integrator.o integrator.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file integrator_whfast.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o integrator_whfast.o integrator_whfast.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file integrator_saba.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o integrator_saba.o integrator_saba.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file integrator_ias15.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o integrator_ias15.o integrator_ias15.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file integrator_sei.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o integrator_sei.o integrator_sei.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file integrator_bs.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o integrator_bs.o integrator_bs.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file integrator_leapfrog.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o integrator_leapfrog.o integrator_leapfrog.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file integrator_mercurius.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o integrator_mercurius.o integrator_mercurius.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file integrator_eos.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o integrator_eos.o integrator_eos.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file integrator_tes.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o integrator_tes.o integrator_tes.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file boundary.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o boundary.o boundary.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file input.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o input.o input.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file binarydiff.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o binarydiff.o binarydiff.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file output.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o output.o output.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file collision.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o collision.o collision.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file communication_mpi.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o communication_mpi.o communication_mpi.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

fatal: not a git repository (or any of the parent directories): .git

Compiling source file display.c ...

cc -c -std=c99 -Wpointer-arith -D_GNU_SOURCE -O3 -I/usr/local/include -Wall -g -I/opt/homebrew/include -L/opt/homebrew/lib -Wno-unknown-pragmas -fPIC -DLIBREBOUND -D_APPLE -DOPENGL -DGITHASH=0000000000gitnotfound0000000000000000000 -o display.o display.c

clang: warning: argument unused during compilation: '-L/opt/homebrew/lib' [-Wunused-command-line-argument]

display.c:50:10: fatal error: 'GLFW/glfw3.h' file not found

include <GLFW/glfw3.h>

     ^~~~~~~~~~~~~~

1 error generated.

From: Hanno Rein @.> Date: Wednesday, March 1, 2023 at 11:01 AM To: hannorein/rebound @.> Cc: Jonathan Hammer @.>, Author @.> Subject: Re: [hannorein/rebound] Getting error when running makefile on Mac (Issue #663)

Glad it worked. This error occurred because you probably tried some example with OpenGL Visualizations turned on and some with them turned off.

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hannorein commented 1 year ago

This is explained in the documentation: https://rebound.readthedocs.io/en/latest/quickstart_installation/

JonathanHammer2 commented 1 year ago

I hate to seem dumb, but I guess I am. Here’s what I got when I followed the instructions at the link you sent:

(base) @.*** rebound-main % brew tap homebrew/versions

zsh: command not found: brew

(base) @.*** rebound-main % sudo apt-get install libglfw3-dev

Password:

Sorry, try again.

Password:

Sorry, try again.

Password:

sudo: 3 incorrect password attempts

I tried my password for the Mac, I guess I typed it wrong 3 times, then it seemed to work but I get another error, it can’t find apt-get:

(base) @.*** rebound-main % sudo apt-get install libglfw3-dev

Password:

sudo: apt-get: command not found

(base) @.*** rebound-main %

Thanks again for your help.

Jonathan

From: Hanno Rein @.> Date: Wednesday, March 1, 2023 at 7:52 PM To: hannorein/rebound @.> Cc: Jonathan Hammer @.>, Author @.> Subject: Re: [hannorein/rebound] Getting error when running makefile on Mac (Issue #663)

This is explained in the documentation: https://rebound.readthedocs.io/en/latest/quickstart_installation/https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frebound.readthedocs.io%2Fen%2Flatest%2Fquickstart_installation%2F&data=05%7C01%7Cjhammer2%40gmu.edu%7C95abf1856ed74dda9f4a08db1ab864e1%7C9e857255df574c47a0c00546460380cb%7C0%7C0%7C638133151510190339%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=k%2FzwYticohLiEFcm2uAzp89pSpWoUMlmnS9fZr02%2BRU%3D&reserved=0

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hannorein commented 1 year ago

I can't help you with the password issue. You can turn off OpenGL visualization in the makefile if you're not able to install the glfw library.

JonathanHammer2 commented 1 year ago

Ok. I installed homebrew, then reset glfw3 to glfw and it worked. I had tried to follow your instructions to try glfw3.

** Still have a question: can you tell me what the units are on position and velocity in the solar system example? Also, if I want to run the simulation backwards to go back in time, do I just need to reverse the initial velocities?

Thank you again.

From: Hanno Rein @.> Date: Wednesday, March 1, 2023 at 8:23 PM To: hannorein/rebound @.> Cc: Jonathan Hammer @.>, Author @.> Subject: Re: [hannorein/rebound] Getting error when running makefile on Mac (Issue #663)

I can't help you with the password issue. You can turn off OpenGL visualization in the makefile if you're not able to install the glfw library.

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hannorein commented 1 year ago

They are listed in the code. AU, day, kg.

JonathanHammer2 commented 1 year ago

Ok. Thanks

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From: Hanno Rein @.> Sent: Wednesday, March 1, 2023 8:48:42 PM To: hannorein/rebound @.> Cc: Jonathan Hammer @.>; Author @.> Subject: Re: [hannorein/rebound] Getting error when running makefile on Mac (Issue #663)

They are listed in the code. AU, day, kg.

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