iCub-CRIS training 2021/06/10

[traversaro]

A first run of the traning based on the material on this repo will be done on 2021/06/10 on IIT. The slides used will be: 2021-06-09-conda-for-scientific-robotics-software-research-and-development.pdf

[traversaro]

Training done, notes:

• [x] For the next time before the training check the network, I did the dry run on Wi-Fi and for some reason instead the wired network was way slower
• [x] Switch to mamba for docs and presentation: the slow speed of conda is problematic for interactive presentation (https://github.com/robotology/robotology-superbuild/pull/847)
• [x] Document that command prompt is the suggested shell on Windows due to Gazebo and ROS problems (see https://github.com/conda-forge/gazebo-feedstock/issues/42 and https://github.com/RoboStack/ros-noetic/issues/21) @ste93. ( https://github.com/robotology/robotology-superbuild/pull/850 )
• [x] For several users it was not possible to start Gazebo installed from conda @HosameldinMohamed @isorrentino . @GiulioRomualdi then suggested to remove the setup.sh from robotology-superbuild installed with apt, and probably we need to add this in the docs. (https://github.com/robotology/robotology-superbuild/pull/850)

[traversaro]

@HosameldinMohamed @isorrentino can you report the problems you were having?

[traversaro]

@Giulero feel free to report the zsh problem.

[HosameldinMohamed]

@HosameldinMohamed @isorrentino can you report the problems you were having?

@traversaro what we did after creating the environment and installing icub-models and gazebo-yarp-plugins is open 2 terminals, activate the environment in both run yarpserver in one of them and gazebo in the other one.

Gazebo crashes and gives this error

 >> gazebo --verbose
Gazebo multi-robot simulator, version 11.5.1
Copyright (C) 2012 Open Source Robotics Foundation.
Released under the Apache 2 License.
http://gazebosim.org

[Msg] Waiting for master.
Gazebo multi-robot simulator, version 11.5.1
Copyright (C) 2012 Open Source Robotics Foundation.
Released under the Apache 2 License.
http://gazebosim.org

[Msg] Waiting for master.
[Msg] Connected to gazebo master @ http://127.0.0.1:11345
[Msg] Publicized address: 10.240.2.33
[Err] [server_main.cc:57] Ogre Error:ItemIdentityException: Resource with the name Console already exists. in ResourceManager::add at /home/conda/feedstock_root/build_artifacts/ogre_1612037790705/work/OgreMain/src/OgreResourceManager.cpp (line 157)

But this is not producible every time I try it. After the training I've tried it many times. In some times Gazebo was starting normally.

Note: I have already Gazebo installed from the source.

[traversaro]

Thanks @HosameldinMohamed ! Two comments:

• Did you removed the sourcing of setup.sh of the robotology-superbuild compiled with apt dependencies as suggested by @GiulioRomualdi ?
• Can you try to remove the ~/.gazebo directory, as this already created problem in the past, and see if the problem disappears (see https://github.com/osrf/gazebo/issues/2604)?

[traversaro]

@drdanz reported that it would be useful to know what Miniconda and mamba is. The latter explanation will be necessary especially if we switch to use mamba in the instructions.

[traversaro]

Thinkg to add:

• Generate/consume environment files
• Generate a Docker image out of an environment file
• Generate a Singularity image out of an environment file @GiuliaPasquale

[traversaro]

Link to the video registration: https://youtu.be/DF2aZa1GhYo .

[Giulero]

@Giulero feel free to report the zsh problem.

@traversaro sure!

When I type conda activate robenv (but also with base) I get this output:

pathremove:5: bad substitution
pathremove:5: bad substitution
pathremove:5: bad substitution

If I type it again, in the same terminal (I guess it calls the reactivate command):

pathremove:5: bad substitution
pathremove:5: bad substitution
pathremove:5: bad substitution
pathappend:3: bad substitution
pathappend:3: bad substitution
pathappend:3: bad substitution

Maybe the issue comes from the lines added in the .zshrc:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/icublap127/miniconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/icublap127/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/home/icublap127/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/icublap127/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

and

conda() {
    if [ "$#" -lt 1 ]; then
        "$CONDA_EXE" $_CE_M $_CE_CONDA
    else
        \local cmd="$1"
        shift
        case "$cmd" in
            activate|deactivate)
                __conda_activate "$cmd" "$@"
                ;;
            install|update|upgrade|remove|uninstall)
                CONDA_INTERNAL_OLDPATH="${PATH}"
                __add_sys_prefix_to_path
                "$CONDA_EXE" $_CE_M $_CE_CONDA "$cmd" "$@"
                \local t1=$?
                PATH="${CONDA_INTERNAL_OLDPATH}"
                if [ $t1 = 0 ]; then
                    __conda_reactivate
                else
                    return $t1
                fi
                ;;
            *)
                CONDA_INTERNAL_OLDPATH="${PATH}"
                __add_sys_prefix_to_path
                "$CONDA_EXE" $_CE_M $_CE_CONDA "$cmd" "$@"
                \local t1=$?
                PATH="${CONDA_INTERNAL_OLDPATH}"
                return $t1
                ;;
        esac
    fi
}

present in miniconda3/etc/profile.d/conda.sh, more precisely __conda_activate and __conda_reactivate.

__conda_activate is defined as:

__conda_activate() {
    if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
        # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
        # after conda updated to >= 4.4. See issue #6173.
        PS1="$CONDA_PS1_BACKUP"
        \unset CONDA_PS1_BACKUP
    fi

    \local cmd="$1"
    shift
    \local ask_conda
    CONDA_INTERNAL_OLDPATH="${PATH}"
    __add_sys_prefix_to_path
    ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix "$cmd" "$@")" || \return $?
    rc=$?
    PATH="${CONDA_INTERNAL_OLDPATH}"
    \eval "$ask_conda"
    if [ $rc != 0 ]; then
        \export PATH
    fi
    __conda_hashr
}

[HosameldinMohamed]

@traversaro

• Did you removed the sourcing of setup.sh of the robotology-superbuild compiled with apt dependencies as suggested by @GiulioRomualdi ?

Not when i wrote this https://github.com/dic-iit/training-conda-robotics/issues/2#issuecomment-858548856.

• Can you try to remove the ~/.gazebo directory, as this already created problem in the past, and see if the problem disappears (see osrf/gazebo#2604)?

Doing both requests doesn't solve it. Again, some times Gazebo starts normally and others the error happens.

Note: I am not sure if it's relevant, but I am not using Ubuntu based OS. I am using Manjaro!

[traversaro]

@traversaro

• Did you removed the sourcing of setup.sh of the robotology-superbuild compiled with apt dependencies as suggested by @GiulioRomualdi ?

Not when i wrote this #2 (comment).

• Can you try to remove the ~/.gazebo directory, as this already created problem in the past, and see if the problem disappears (see osrf/gazebo#2604)?

Doing both requests doesn't solve it. Again, some times Gazebo starts normally and others the error happens.

Note: I am not sure if it's relevant, but I am not using Ubuntu based OS. I am using Manjaro!

Ok, this bug officially graduated to its own discussion: https://github.com/conda-forge/gazebo-feedstock/issues/81 . Please continue the discussion there, thanks!

[traversaro]

Just to clarify, if this @HosameldinMohamed problem was not fixed by removing the superbuild's setup.sh, probably it is a problem different from the problem of @isorrentino or @GiulioRomualdi ?

[traversaro]

@Giulero feel free to report the zsh problem.

@traversaro sure!

Thanks! This error are similar to the one experienced by @lrapetti in https://github.com/robotology/robotology-superbuild/issues/779, let's continue the discussion there. My the way, there is any reason why you install miniconda instead of miniforge as suggested in the docs in this repo and in the robotology-superbuild documentation?

[Giulero]

there is any reason why you install miniconda instead of miniforge as suggested in the docs in this repo

Not really. I was just using miniconda before the training. It's time for a change!

[traversaro]

I just tested zsh after the fixes in https://github.com/robotology/robotology-superbuild/pull/810 and everything seems to work, no pathremove:5: bad substitution error anymore. I just fixed a bit the installation guide in https://github.com/robotology/robotology-superbuild/pull/839, zsh users feel free to review it @lrapetti @Giulero .

[traversaro]

Switch to mamba for docs and presentation: the slow speed of conda is problematic for interactive presentation

This will be fixed by https://github.com/robotology/robotology-superbuild/pull/847 .

[traversaro]

For several users it was not possible to start Gazebo installed from conda @HosameldinMohamed @isorrentino . @GiulioRomualdi then suggested to remove the setup.sh from robotology-superbuild installed with apt, and probably we need to add this in the docs.

This are actually two distinct problem:

• Clarify that it is better to remove any apt-based setup.sh from the environment if you are using conda, that will be fixed in https://github.com/robotology/robotology-superbuild/pull/850
• A peculiar problem in brand-new distribution, that @HosameldinMohamed experienced. On this, the related issue is https://github.com/conda-forge/gazebo-feedstock/issues/81 , and there was a change discussed in https://github.com/conda-forge/gazebo-feedstock/issues/81#issuecomment-893402590 .

[traversaro]

* Document that command prompt is the suggested shell on Windows due to Gazebo and ROS problems

Will be fixed by https://github.com/robotology/robotology-superbuild/pull/850 .