Libvips library yggdrasil

HPC Support HPC issues
1

Hello @support !

Primary informations

Username: humeau
Cluster: Yggdrasil

Description

I want to use a python script requiring the pyvips library. To use this library I need libvips which is the original library, pyvips is only a binding.

I tried to find the module with spider, but it was not successful. Is it possible to find this library via another module?

Actual Result

OSError: cannot load library ‘libvips.so.42’: libvips.so.42: cannot open shared object file: No such file or directory. Additionally, ctypes.util.find_library() did not manage to locate a library called ‘libvips.so.42’

Any help would be greatly appreciated, thank you !

Maxime

2

Hi @Maxime.Humeau

To find out more:

Did you install pyvips in your home, with the Python version you use ?

Could you give me a small code to reproduce the issue (code + sbatch) ?

3

Thanks you for your support !

for sbatch

#!/bin/env bash

#SBATCH --partition=debug-gpu
#SBATCH --time=00:15:00
#SBATCH --output=journal-%j.out
#SBATCH --mem=8000
#SBATCH --gres=gpu:1,VramPerGpu:20GB
#SBATCH --cpus-per-task=10
module load cuDNN/8.6.0.163-CUDA-11.8.0 GCCcore/10.3.0 Python/3.9.5 OpenSSL/1.1.1q

echo "I: CUDA_VISIBLE_DEVICES: ${CUDA_VISIBLE_DEVICES}"

echo "====="

srun nvidia-smi

echo "====="


#srun python3  -m venv yaltaienv
source yaltaienv/bin/activate

#wget https://github.com/FoNDUE-HTR/Documentation/releases/download/v.0.9/fondue_emmental.mlmodel -O htr_model.mlmodel
wget https://zenodo.org/records/10972956/files/CapricciosaX.pt?download=1 -O seg_model.pt

pip install -r requirements.txt
pip install yaltai~=1.0.0 --extra-index-url https://download.pytorch.org/whl/cu118

srun python3 run.py

I’m installing pyvips with requirements.txt

For the code, i’m reusing this (GitHub - PonteIneptique/rtk at a9902aa1d21b4c57cd28fba71f81e1023ffeb14a) in same environment. I don’t separate yaltai and kraken

4

You don’t pull the git repository to make this instruction works, it’s this one ? :

5

I’m using an older version at the moment. But in any case, the new version still uses libvips via pipvips binding. I download in zip and i transfert with ssh.

6

Hi,

libvips isn’t provided by easybuild (module). Did you tried to install libvips in you home by following the doc: libvips => Building libvips from source ?