Installation issue on Ubuntu 22.04

[pcg108]

Hello,

I am trying to install and run ILLIXR on a machine running Ubuntu 22.04. I run
./install_deps.sh
and then run
./runner.sh configs/headless.yaml

Resulting in the following error:

*Warning* Installation log for conda not found at '.cache/deps/miniconda3.sh'.
Checking in '/opt/ILLIXR/miniconda3'.
./runner.sh: line 43: /opt/ILLIXR/miniconda3/etc/profile.d/conda.sh: No such file or directory

CommandNotFoundError: Your shell has not been properly configured to use 'conda deactivate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.



CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.


Traceback (most recent call last):
  File "/home/eecs/prashanthcganesh108/ILLIXR/runner/runner/main.py", line 404, in <module>
    main()
  File "/home/eecs/prashanthcganesh108/anaconda3/lib/python3.9/site-packages/click/core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "/home/eecs/prashanthcganesh108/anaconda3/lib/python3.9/site-packages/click/core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "/home/eecs/prashanthcganesh108/anaconda3/lib/python3.9/site-packages/click/core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/eecs/prashanthcganesh108/anaconda3/lib/python3.9/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "/home/eecs/prashanthcganesh108/ILLIXR/runner/runner/main.py", line 402, in main
    run_config(Path(config_path))
  File "/home/eecs/prashanthcganesh108/ILLIXR/runner/runner/main.py", line 394, in run_config
    actions[action](config)
  File "/home/eecs/prashanthcganesh108/ILLIXR/runner/runner/main.py", line 100, in load_native
    runtime_exe_path = build_runtime(config, "exe")
  File "/home/eecs/prashanthcganesh108/ILLIXR/runner/runner/main.py", line 95, in build_runtime
    make(runtime_path, targets, runtime_config, env_override=env_override)
  File "/home/eecs/prashanthcganesh108/ILLIXR/runner/runner/util.py", line 520, in make
    subprocess_run(
  File "/home/eecs/prashanthcganesh108/ILLIXR/runner/runner/util.py", line 171, in subprocess_run
    raise CalledProcessError(
util.CalledProcessError: Command returned non-zero exit status 2
command: env ILLIXR_INTEGRATION=ON make -j 16 -C runtime main.opt.exe
stdout:
  make: Entering directory '/home/eecs/prashanthcganesh108/ILLIXR/runtime'
  clang++-10        -std=c++17  -DGLSL_VERSION='"330 core"'  -O3 -DNDEBUG  -Wall -Wextra -Werror \
  -o main.opt.exe main.cpp  -ggdb -ldl -pthread -lstdc++fs -L/usr/lib64 -lGLEW -lGL -lX11 -lGLU -lsqlite3 -lX11
  make: Leaving directory '/home/eecs/prashanthcganesh108/ILLIXR/runtime'

stderr:
  make: clang++-10: No such file or directory
  make: *** [common/common.mk:54: main.opt.exe] Error 127

I have tried to install clang-10 locally using the ILLIXR install_clang.sh script, but that still does not fix the issue. Any help would be greatly appreciated

[charmoniumQ]

Did you select "Y" to installing Conda in ./install_deps.sh?

P.S. It will be easier for us to know what's going on if you three backticks (under the escape key on American keyboards) around the error messages, so we know what's part of the message.

```
like this
```

[pcg108]

Hi,

Yes, I selected Yes to all the ./install_deps.sh prompts. When I run ./scripts/install_conda.sh, I get:

Found conda installation. Exiting installation script.

Fixed the formatting, thanks for the tip.

[pcg108]

I removed my existing conda installation and used the ILLIXR script to install conda in /opt/ILLIXR/miniconda3. So the conda errors are gone now but still seeing the following:

DETECT [dep <- 'miniconda3', dir <- '/opt/ILLIXR/miniconda3']
Traceback (most recent call last):
  File "runner/runner/main.py", line 404, in <module>
    main()
  File "/opt/ILLIXR/miniconda3/envs/illixr-runner/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/opt/ILLIXR/miniconda3/envs/illixr-runner/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/opt/ILLIXR/miniconda3/envs/illixr-runner/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/ILLIXR/miniconda3/envs/illixr-runner/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "runner/runner/main.py", line 402, in main
    run_config(Path(config_path))
  File "runner/runner/main.py", line 394, in run_config
    actions[action](config)
  File "runner/runner/main.py", line 100, in load_native
    runtime_exe_path = build_runtime(config, "exe")
  File "runner/runner/main.py", line 95, in build_runtime
    make(runtime_path, targets, runtime_config, env_override=env_override)
  File "/home/eecs/prashanthcganesh108/ILLIXR/runner/runner/util.py", line 520, in make
    subprocess_run(
  File "/home/eecs/prashanthcganesh108/ILLIXR/runner/runner/util.py", line 171, in subprocess_run
    raise CalledProcessError(
util.CalledProcessError: Command returned non-zero exit status 2
command: env ILLIXR_INTEGRATION=ON make -j 16 -C runtime main.opt.exe
stdout:
  make: Entering directory '/home/eecs/prashanthcganesh108/ILLIXR/runtime'
  clang++-10        -std=c++17  -DGLSL_VERSION='"330 core"'  -O3 -DNDEBUG  -Wall -Wextra -Werror \
  -o main.opt.exe main.cpp  -ggdb -ldl -pthread -lstdc++fs -L/usr/lib64 -lGLEW -lGL -lX11 -lGLU -lsqlite3 -lX11
  make: Leaving directory '/home/eecs/prashanthcganesh108/ILLIXR/runtime'

stderr:
  make: clang++-10: No such file or directory
  make: *** [common/common.mk:54: main.opt.exe] Error 127

[charmoniumQ]

Yeah, installation is not atomic, so it is possible that install_deps.sh thinks some package is already installed, but actually trying to use that package fails (imagine the package is "half"-installed). In this case, deleting and running install_deps.sh should help.

As for clang, do you have clang++-10 installed through the install script? Can you run clang++-10?

[pcg108]

I removed my system clang installations and installed clang to /opt/ILLIXR. I am able to run clang-10 (it is found at /opt/ILLIXR/clang) but not clang++-10. Is there a separate installation?

[pcg108]

Update: I mananged to the run the install_clang.sh script and seem to have clang-10 and clang++-10 installed. However, when I go to install opencv using ./scripts/install_opencv.h, I see the following error:

[ 16%] Building CXX object 3rdparty/protobuf/CMakeFiles/libprotobuf.dir/src/google/protobuf/arena.cc.o
In file included from /opt/ILLIXR/opencv/3rdparty/protobuf/src/google/protobuf/arena.cc:31:
/opt/ILLIXR/opencv/3rdparty/protobuf/src/google/protobuf/arena.h:36:10: fatal error: 'limits' file not found
#include <limits>
         ^~~~~~~~
1 error generated.
make[2]: *** [3rdparty/protobuf/CMakeFiles/libprotobuf.dir/build.make:76: 3rdparty/protobuf/CMakeFiles/libprotobuf.dir/src/google/protobuf/arena.cc.o] Error 1
make[2]: Leaving directory '/opt/ILLIXR/opencv/build'
make[1]: *** [CMakeFiles/Makefile2:2816: 3rdparty/protobuf/CMakeFiles/libprotobuf.dir/all] Error 2
make[1]: Leaving directory '/opt/ILLIXR/opencv/build'
make: *** [Makefile:166: all] Error 2
make: Leaving directory '/opt/ILLIXR/opencv/build'

It appears as though the locally built clang isn't finding the standard c++ headers? Any ideas here?

[charmoniumQ]

They should be installed by a package called libstdc++ or something like that.

[charmoniumQ]

What version of Ubuntu are you using?

[pcg108]

I have libstdc++ but I think perhaps the locally build clang++ isn't able to find it? I am using Ubuntu 22.04. Has the ILLIXR installation been tested with this?

[pcg108]

I solved this issue (I think) by setting my C++ and C compilers to G++ and GCC for the installation of OpenCV.
Now there appears to be a backwards compatibility issue with TBB when installing GTSam (./scripts/install_gtsam):

-- GTSAM_SOURCE_ROOT_DIR: [/opt/ILLIXR/gtsam]
CMake Error at cmake/FindTBB.cmake:187 (file):
  file failed to open for reading (No such file or directory):

    /usr/include/tbb/tbb_stddef.h
Call Stack (most recent call first):
  CMakeLists.txt:198 (find_package)


-- Could NOT find TBB: Found unsuitable version ".", but required is at least "4.4" (found /usr/include, )

I see that GTSAM_WITH_TBB=OFF is set, leading me to believe that this should not occur. Is there any workaround for this?

EDIT: To solve this, I uncommented line 198 in /opt/ILLIXR/gtsam/CMakeLists.txt (find_packages for TBB).

Additionally, there was an additional Boost error from the using the deb version (1.74 I believe), so I had to install version 1.73 from source.

[astro-friedel]

The upcoming release will address this issue. The build system has been completely rewritten to be CMake based which will streamline the build process.