HPC_issues

Connor H Knight & Faraz Khan

11/08/2021

Incorrect gcc version

In some instances old versions are automatically stored in your user bin. If you recieve the following error you may have an older version of gcc loaded.

g++: error: unrecognized command line option ‘-fno-plt’
g++: error: unrecognized command line option ‘-fno-semantic-interposition’

If you see this you can use the following to see which version you have loaded:

find gcc 
{paste previous output here} -- version

If you are in a HPC environemnt then you must load the correct version >=7 using the HPC infastructure or compile the correct version yourself.

ImageMagick for celda

ImageMagick version inside a HPC is commonly known to create issues. For IBRAP this affects the installation of celda. A known way to fix this is to compile a specific version of ImageMagick and to supply the pathways.

step 1: Get ImageMagick from the following link by doing:

curl -L -O https://download.imagemagick.org/ImageMagick/download/releases/ImageMagick-6.9.10-86.tar.xz

step 2: cd into the downloaded directory containing ImageMagick. Then execute the following command:

tar -xf ImageMagick-6.9.10-86.tar.xz 
cd ImageMagick-6.9.10-86
./configure
make
make install

step 3: now we must export the LD_LIBRARY_PATH and pkgconfig path to the library location of ImageMagick package. For example:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/magick/ImageMagick-6.9.10-86/lib
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/magick/ImageMagick-6.9.10-86/Magick++/lib
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/path/to/magick/ImageMagick-6.9.10-86/lib/pkgconfig

This should allow R tofind the correct imagemagick librarys and allow celda to install. However, take now that every HPC environment is different and different troubleshooting may be required on a case-by-case basis.

If you have any more isses/solutions please post them on our issues section in our github.