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hello
I run the helixer when use the singularity, the command was "srun -p gpu-3090 /public/software/singularity-ce-3.11.3/bin/singularity run --nv helixer-docker_helixer_v0.3.3_cuda_11.8.0-cudnn8.sif Helixer.py --fasta-path /public/agis/yanjianbin_group/baishaoxing/Maidenhair_fern/GCA_014529385.2_ASM1452938v2_genomic.fna.gz --lineage land_plant --gff-output-path GCA_014529385.2_ASM1452938v2_genomic.helixer.gff3"
but its error



how could I debug , thank you

singularity run --nv /home/liux/miniconda3/envs/braker3/helixer-docker_helixer_v0.3.2_cuda_11.8.0-cudnn8.sif Helixer.py --fasta-path /home/liux/DATA/genomic/RepeatMasker/AT/TAIR10_chr_all.fa --lineage land_plant --gff-output-path /data/liux/zhushi/Arabidopsis_lyrata_chromosome8_helixer.gff3

INFO: Setting 'NVIDIA_VISIBLE_DEVICES=all' to emulate legacy GPU binding.
INFO: Setting --writable-tmpfs (required by nvidia-container-cli)
FATAL: container creation failed: exec: "/usr/bin/nvidia-container-cli": stat /usr/bin/nvidia-container-cli: no such file or directory

Hi,

Following the install procedure I've run, on a GPU node, an annotation test. But I get warnings about missing libraries : libnvinfer.so.7, libnvinfer_plugin.so.7. And when I monitor the server, the job seems to run only on CPU.

What should I do to fix this?

singularity run --nv helixer-docker_helixer_v0.3.1_cuda_11.2.0-cudnn8.sif Helixer.py --fasta-path my.fasta --lineage land_plant --gff-output-path my.gff3
2023-03-13 16:06:09.959811: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-03-13 16:06:10.359479: I tensorflow/core/util/port.cc:104] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable TF_ENABLE_ONEDNN_OPTS=0.
2023-03-13 16:06:12.183775: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/nvidia/lib:/usr/local/nvidia/lib64:/.singularity.d/libs
2023-03-13 16:06:12.187243: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/nvidia/lib:/usr/local/nvidia/lib64:/.singularity.d/libs
2023-03-13 16:06:12.187293: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.