diff --git a/docs/source/notes/installation.rst b/docs/source/notes/installation.rst index 460d6b2a..0e65edc6 100644 --- a/docs/source/notes/installation.rst +++ b/docs/source/notes/installation.rst @@ -9,13 +9,13 @@ The framework installation goes as follows. Preliminaries: Conda installation ---------------------------------- -.. code-block:: none +.. code-block:: wget https://repo.anaconda.com/archive/Anaconda3-2024.02-1-Linux-x86_64.sh Then execute the installer with ``bash filename.sh`` and finally set ``.condarc`` as follows ``nano .condarc`` (home directory) -.. code-block:: none +.. code-block:: channel_priority: strict channels: @@ -25,7 +25,7 @@ Then execute the installer with ``bash filename.sh`` and finally set ``.condarc` Pre-installed CUDA paths (OBSOLETE) ------------------------------------ -.. code-block:: none +.. code-block:: source /vols/software/cuda/setup.sh 11.8.0 @@ -37,7 +37,7 @@ Automated setup Remark: To avoid ``No space left on device`` problem with conda or pip, set the temporary path first -.. code-block:: none +.. code-block:: mkdir /tmp export TMPDIR=/tmp @@ -46,7 +46,7 @@ Also after activating the icenet conda environment. Execute -.. code-block:: none +.. code-block:: git clone git@github.com:mieskolainen/icenet.git && cd icenet @@ -67,7 +67,7 @@ Initialize the environment Always start with -.. code-block:: none +.. code-block:: conda activate icenet source setenv.sh @@ -78,19 +78,19 @@ Possible problems Note: One may need to steer where ``pip`` installs the packages, for example -.. code-block:: none +.. code-block:: python -m pip install --target $CONDA_PREFIX Note: If you experience ``OSError: libcusparse.so.11`` (or similar) with torch-geometric, set the system path -.. code-block:: none +.. code-block:: export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:$LD_LIBRARY_PATH" Note: If you experience ``Could not load dynamic library libcusolver.so.10`` with tensorflow, make a symbolic link -.. code-block:: none +.. code-block:: ln -s $CONDA_PREFIX/lib/libcusolver.so.11 $CONDA_PREFIX/lib/libcusolver.so.10 @@ -99,7 +99,7 @@ Note: ``$CONDA_PREFIX`` will be found after ``conda activate icenet`` Note: If you experience "Requirement already satisfied" infinite loop with pip, try removing e.g. ``tensorflow`` from requirements.txt, and install it separately with -.. code-block:: none +.. code-block:: pip install tensorflow @@ -109,7 +109,7 @@ Then if something else fails, google with the error message. Show installation paths of binaries -------------------------------------- -.. code-block:: none +.. code-block:: which -a pip which -a python @@ -120,19 +120,19 @@ GPU-support commands Show the graphics card status -.. code-block:: none +.. code-block:: nvidia-smi Show CUDA-compiler tools status -.. code-block:: none +.. code-block:: nvcc --version Show Tensorflow and Pytorch GPU support in Python -.. code-block:: none +.. code-block:: import tensorflow from tensorflow.python.client import device_lib @@ -148,7 +148,7 @@ HTCondor GPU job submission Use the following command with IC machines -.. code-block:: none +.. code-block:: condor_submit condor_rm @@ -156,10 +156,34 @@ Use the following command with IC machines condor_q condor_status --gpus +With an example job description file as + +.. code-block:: + + executable = gpu_task.sh + error = gpu.$(CLUSTER).error + output = gpu.$(CLUSTER).output + log = gpu.$(CLUSTER).log + request_gpus = 1 + request_memory = 10G + +MaxRuntime = 3600 + queue + +Where ``gpu_task.sh`` is the actual steering shell script to be run + +.. code-block:: + + source setconda.sh + conda activate icenet + python icecool.py + +where ``source setconda.sh`` has the Conda (system specific) init commands. + Conda virtual environment commands ----------------------------------- -.. code-block:: none + +.. code-block:: conda create -y --name icenet python==3.X.Y conda activate icenet @@ -178,6 +202,6 @@ Conda virtual environment commands C-library versions ----------------------------------- -.. code-block:: none +.. code-block:: ldd --version