iCub-CRIS training 2021/06/10 #2

traversaro · 2021-06-09T16:18:40Z

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 · 2021-06-10T10:14:24Z

Training done, notes:

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
Switch to mamba for docs and presentation: the slow speed of conda is problematic for interactive presentation (Migrate conda documentation to use mamba instead of conda robotology/robotology-superbuild#847)
Document that command prompt is the suggested shell on Windows due to Gazebo and ROS problems (see On Windows Gazebo does not start in Powershell or Git Bash conda-forge/gazebo-feedstock#42 and ROS tools not found in PowerShell on Windows RoboStack/ros-noetic#21) @ste93. ( In Conda documentaton, document that the preferred shell on Windows is Command Prompt and that the environment should be as clean as possible robotology/robotology-superbuild#850 )
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. (In Conda documentaton, document that the preferred shell on Windows is Command Prompt and that the environment should be as clean as possible robotology/robotology-superbuild#850)

traversaro · 2021-06-10T10:16:41Z

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

traversaro · 2021-06-10T11:04:17Z

@Giulero feel free to report the zsh problem.

HosameldinMohamed · 2021-06-10T11:40:57Z

@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 · 2021-06-10T11:50:34Z

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 Heightmap caching of geometry / textures is not documented, indicated, or overridable gazebosim/gazebo-classic#2604)?

traversaro · 2021-06-10T11:56:05Z

@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 · 2021-06-10T11:59:49Z

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 · 2021-06-10T12:45:23Z

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

Giulero · 2021-06-10T12:55:00Z

@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 · 2021-06-10T14:43:08Z

@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!

traversaro · 2021-06-10T15:15:34Z

@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: conda-forge/gazebo-feedstock#81 . Please continue the discussion there, thanks!

traversaro · 2021-06-10T15:16:30Z

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 · 2021-06-12T14:41:50Z

@Giulero feel free to report the zsh problem.

@traversaro sure!

Thanks! This error are similar to the one experienced by @lrapetti in robotology/robotology-superbuild#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 · 2021-06-14T09:33:01Z

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 · 2021-07-30T13:31:24Z

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

traversaro · 2021-08-05T11:07:02Z

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

This will be fixed by robotology/robotology-superbuild#847 .

traversaro · 2021-08-05T12:08:08Z

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 In Conda documentaton, document that the preferred shell on Windows is Command Prompt and that the environment should be as clean as possible robotology/robotology-superbuild#850
A peculiar problem in brand-new distribution, that @HosameldinMohamed experienced. On this, the related issue is libGL error: MESA-LOADER: failed to open iris conda-forge/gazebo-feedstock#81 , and there was a change discussed in libGL error: MESA-LOADER: failed to open iris conda-forge/gazebo-feedstock#81 (comment) .

traversaro · 2021-08-05T12:13:08Z

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

Will be fixed by robotology/robotology-superbuild#850 .

traversaro changed the title ~~First instance of the training~~ iCub-CRIS training 2021/06/10 Jun 9, 2021

traversaro mentioned this issue Jun 10, 2021

libGL error: MESA-LOADER: failed to open iris conda-forge/gazebo-feedstock#81

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traversaro mentioned this issue Jun 12, 2021

Switch conda docs to use mamba robotology/robotology-superbuild#795

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traversaro mentioned this issue Jun 12, 2021

Test robotology-superbuild with zsh robotology/robotology-superbuild#779

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Migrate docs to mamba #3

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iCub-CRIS training 2021/06/10 #2

iCub-CRIS training 2021/06/10 #2

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iCub-CRIS training 2021/06/10 #2

iCub-CRIS training 2021/06/10 #2

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