OSError: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory

[nosound2]

🐛 Bug

I tried to update torch-xla-nightly but broke it, getting an error
OSError: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory

To Reproduce

Steps to reproduce the behavior:

Updating torch-xla-nightly finishes in an error

/usr/share/torch-xla-nightly/pytorch/xla$ ./scripts/update_nightly_torch_wheels.sh

Cloning into 'vision'...
fatal: Remote branch v0.5.0a0+07cbb46 not found in upstream origin

Then I tried to update torch vision with just

git clone https://github.com/pytorch/vision.git 
cd vision/
python setup.py install

but then get an error

OSError: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory

I get the same error when I try to run something of my models.

Appreciate any advice, thank you

[AVancans]

I had the same issue. Not sure if the way I solved it correct but it worked.
pip install mkl
Find where it installed the library (.user, env or system) and add the library to the following env var
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/library/

[nosound2]

Cool, it worked, thank you @AVancans .

In my case the path was
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/anaconda3/envs/torch-xla-nightly/lib

[dlibenzi]

I think this came up a few weeks ago but was supposed to have been fixed @jysohn23

[chris-clem]

I have the same issue and cannot resolve it with the above mentioned method.

[jysohn23]

Hi @nosound2 @chris-clem, this issue had been fixed and you should be able to pickup that fix if you recreate your GCE VM. The fix was baked into the GCE VM Image.

[chris-clem]

Hi @nosound2 @chris-clem, this issue had been fixed and you should be able to pickup that fix if you recreate your GCE VM. The fix was baked into the GCE VM Image.

I just recreated the VM and it is still there.

[jysohn23]

@chris-clem Did you just create a fresh GCE VM with our GCE Images and then re-install the latest nightly? Mind explaining what you did?

[chris-clem]

Sure:

1. Create new GCE VM with the XLA image
2. ssh onto VM with gcloud
3. cd into /usr/share/torch-xla-nightly/pytorch/xla to run
   . ./scripts/update_nightly_torch_wheels.sh

Then the connection closes:

++ '[' '' '!=' torch-xla-nightly ']'
++ conda activate torch-xla-nightly
++ '[' 2 -lt 1 ']'
++ local cmd=activate
++ shift
++ case "$cmd" in
++ _conda_activate torch-xla-nightly
++ '[' -n '' ']'
++ local ask_conda
+++ PS1='\[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
+++ /anaconda3/bin/conda shell.posix activate torch-xla-nightly
++ ask_conda='PS1='\''(torch-xla-nightly) \[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '\''
\export CONDA_DEFAULT_ENV='\''torch-xla-nightly'\''
\export CONDA_EXE='\''/anaconda3/bin/conda'\''
\export CONDA_PREFIX='\''/anaconda3/envs/torch-xla-nightly'\''
\export CONDA_PROMPT_MODIFIER='\''(torch-xla-nightly) '\''
\export CONDA_PYTHON_EXE='\''/anaconda3/bin/python'\''
\export CONDA_SHLVL='\''1'\''
\export PATH='\''/anaconda3/envs/torch-xla-nightly/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games'\''
\. "/anaconda3/envs/torch-xla-nightly/etc/conda/activate.d/env_vars.sh"'
++ eval 'PS1='\''(torch-xla-nightly) \[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '\''
\export CONDA_DEFAULT_ENV='\''torch-xla-nightly'\''
\export CONDA_EXE='\''/anaconda3/bin/conda'\''
\export CONDA_PREFIX='\''/anaconda3/envs/torch-xla-nightly'\''
\export CONDA_PROMPT_MODIFIER='\''(torch-xla-nightly) '\''
\export CONDA_PYTHON_EXE='\''/anaconda3/bin/python'\''
\export CONDA_SHLVL='\''1'\''
\export PATH='\''/anaconda3/envs/torch-xla-nightly/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games'\''
\. "/anaconda3/envs/torch-xla-nightly/etc/conda/activate.d/env_vars.sh"'
+++ PS1='(torch-xla-nightly) \[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
+++ export CONDA_DEFAULT_ENV=torch-xla-nightly
+++ CONDA_DEFAULT_ENV=torch-xla-nightly
+++ export CONDA_EXE=/anaconda3/bin/conda
+++ CONDA_EXE=/anaconda3/bin/conda
+++ export CONDA_PREFIX=/anaconda3/envs/torch-xla-nightly
+++ CONDA_PREFIX=/anaconda3/envs/torch-xla-nightly
+++ export 'CONDA_PROMPT_MODIFIER=(torch-xla-nightly) '
+++ CONDA_PROMPT_MODIFIER='(torch-xla-nightly) '
+++ export CONDA_PYTHON_EXE=/anaconda3/bin/python
+++ CONDA_PYTHON_EXE=/anaconda3/bin/python
+++ export CONDA_SHLVL=1
+++ CONDA_SHLVL=1
+++ export PATH=/anaconda3/envs/torch-xla-nightly/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
+++ PATH=/anaconda3/envs/torch-xla-nightly/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
+++ . /anaconda3/envs/torch-xla-nightly/etc/conda/activate.d/env_vars.sh
++++ export LD_LIBRARY_PATH=/anaconda3/envs/torch-xla-nightly/lib/
++++ LD_LIBRARY_PATH=/anaconda3/envs/torch-xla-nightly/lib/
++ _conda_hashr
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
+++ dirname -bash
dirname: invalid option -- 'b'
Try 'dirname --help' for more information.
++ /update_torch_wheels.sh
-bash: /update_torch_wheels.sh: No such file or directory
Connection to 34.90.143.84 closed.

[jysohn23]

@chris-clem I'll try reproduce this, but in the meantime could you use a nightly GCE VM since that should have all the latest bits?

[chris-clem]

@jysohn23 How do I create a nightly VM?

I see the following options for the images and I choose the last one (PyTorch/XLA):

[jysohn23]

Yeah that one and then just use the conda environment torch-xla-nightly.

[chris-clem]

Yeah that one and then just use the conda environment torch-xla-nightly.

I use it and still get the error:

Traceback (most recent call last):
  File "/tmp/pycharm_project_164/deepfake_detection_challenge/lightning/train.py", line 7, in <module>
    import torch
  File "/anaconda3/envs/torch-xla-nightly/lib/python3.6/site-packages/torch/__init__.py", line 124, in <module>
    _load_global_deps()
  File "/anaconda3/envs/torch-xla-nightly/lib/python3.6/site-packages/torch/__init__.py", line 82, in _load_global_deps
    ctypes.CDLL(lib_path, mode=ctypes.RTLD_GLOBAL)
  File "/anaconda3/envs/torch-xla-nightly/lib/python3.6/ctypes/__init__.py", line 348, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory

[jysohn23]

Yeah but that's only after you try update the wheels right (I just created one fresh which works fine without updating anything after creating)? You shouldn't need to if you're already using torch-xla-nightly. That issue I'll separately look into, but use the nightly environment without updating for now. That should already have latest bits.

[jysohn23]

Once above PR is merged, that script should make its way into tomorrow' GCE VM images so you can use it from there. Alternatively just git pull from /usr/share/torch-xla-nightly/pytorch/xla.

[chris-clem]

The problem could also have been PyCharm Remote Deployement. If I run my script on the VM directly, I do not get the OSError.

[julien-c]

Same here with VSCode remote debugger (but workaround above worked)

[YuxianMeng]

The problem could also have been PyCharm Remote Deployement. If I run my script on the VM directly, I do not get the OSError.

Hi, I encountered the same issue, did you solve it?

[Borda]

similar issue solving in Lightning-AI/pytorch-lightning#2460

[ShoufaChen]

pip install mkl

solved my issue.

update:
I encounter this problem when I install custom build pytorch dist using pip.
conda install numpy ninja pyyaml mkl mkl-include setuptools cmake cffi typing_extensions future six requests dataclasses works