Compiling and Running the gmy tool

[amroabuzer]

Hello, I recently found out about this project and I would like to say thank you for the great work! Some background I'm currently trying to get the GPU HemeLB project going with my own stl files. I got everything setup and I'm currently trying to setup the geometry tool to convert my stl files to gmy files, but I'm stuck.

Issue:

• I tried following the steps from the geometry tool's documentation (i.e. I set up the gmy-tool environment) but when running

pip install '.[gui]'

I got the following issue:

• Since vmtk is already in my package list I just commented out the vmtk requirement in setup.py
• After compiling and running hlb-gmy-gui I get this mystical OpenGL VTK issue and segmentation fault:
• Might also be useful to say that I haven't compiled the hemelb project since I have the HemePureGPU already compiled and I'm currently only compiling the geometry tool I hope you can help me out here and thank you in advance

[rupertnash]

Is the VMTK package visible to pip? Sometimes conda installed packages do not show up there. Do a pip list to check. If it's not showing, you can bodge this with the following bash function (make_dist_info vmtk in this case)

function make_dist_info() {
    NAME=$1
    if pip list --format json | jq -e ".[] | select (.name == \"$NAME\" )" > /dev/null; then
	echo "pip already knows about $NAME"
	return 0
    fi

    VERSION=$(conda list --json $NAME | jq -r -e '.[].version')
    if [ $? -ne 0 ]; then
	echo "Couldn't get version for $NAME"
	exit 1
    fi

    SITE_PACKAGES_DIR=$(python -c 'import sysconfig; print(sysconfig.get_path("platlib"))')
    if [ ! -d $SITE_PACKAGES_DIR/$NAME ]; then
	echo "No package dir '$SITE_PACKAGES_DIR/$NAME'"
	exit 1
    fi
    distinfo=$SITE_PACKAGES_DIR/$NAME-$VERSION.dist-info
    mkdir -p $distinfo
    cat > $distinfo/METADATA <<EOF
Metadata-Version: 2.1
Name: $NAME
Version: $VERSION
EOF
}

Regarding the segfault, it looks like you are maybe missing some open gl package(s) that VTK is expecting? Was your VTK installed by conda? If so, I suggest asking there. Perhaps you can install OS packages that provide the missing modules in the error? Which OS etc are you using?

[c-denham]

Hello, Were you able to resolve the issue @amroabuzer? I am having the same error, I have tried uninstalling and reinstalling the VTK and installed the OS packages but still get the following error:

[rupertnash]

So we need to narrow down where your problems are.

First, can your VTK open a render window correctly? (compile and run any VTK program that does this)

second, can you open a render window from python? (In an interactive session, import VTK, read eg one of your STL files, create a render window, connect the output of your vtkSTLReader, and call interact a see VTK examples)

third, can vmtk open a window? (Try vmtksurfaceviewer with one of your STL files as an input)

[rupertnash]

I've had no response, so closing. Please reopen if this is an issue for you.