[BUG] lmp command doesn't start lammps (pip install) 2.2.0b0

[luukasnik]

Bug summary

I installed deepmd kit with the following command:

pip install deepmd-kit[gpu,lmp]==2.2.0b0
on an existing install of tensorflow 2.11.

The command dp works well, but when i try to run the lmp command, lammps does not start. No relevant error message is shown.

input command

lmp -h

DeePMD-kit Version

2.2.0b0

TensorFlow Version

2.11

How did you download the software?

pip

Input Files, Running Commands, Error Log, etc.

$lmp -h
2023-02-09 16:35:29.935085: 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.
2023-02-09 16:35:30.146605: 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.
2023-02-09 16:35:32.755988: 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/cuda/lib64/:/usr/mpi/gcc/openmpi-4.1.2rc2/lib64::/.singularity.d/libs
2023-02-09 16:35:32.756269: 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/cuda/lib64/:/usr/mpi/gcc/openmpi-4.1.2rc2/lib64::/.singularity.d/libs
2023-02-09 16:35:32.756291: 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.
WARNING:tensorflow:From /users/luukasni/.local/lib/python3.9/site-packages/tensorflow/python/compat/v2_compat.py:107: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
WARNING:root:To get the best performance, it is recommended to adjust the number of threads by setting the environment variables OMP_NUM_THREADS, TF_INTRA_OP_PARALLELISM_THREADS, and TF_INTER_OP_PARALLELISM_THREADS.

Steps to Reproduce

pip install deepmd-kit[gpu,lmp]==2.2.0b0

lmp -h

Further Information, Files, and Links

No response

[njzjz]

Hi, I tried to reproduce the issue in a new kaggle notebook. However, everything looks fine: https://www.kaggle.com/jinzhezeng/test-lmp-h

[luukasnik]

Hello,

Is there a command to run lmp in debug mode so i could trace to where the problem lies? The tensorflow installation is inside of a singularity container due to HPC reasons.

[njzjz]

Perhaps you could share the container, and I can take a look.

[njzjz]

I reproduced this issue on an HPC. The reason needs to be investigated.

[njzjz]

Fixed in njzjz/lammps-wheel#24 by bumping patchelf to 0.17.2.

The root reason might be NixOS/patchelf#446.