Change Details

= First Time Setup = Create environment `virtualenv --system-site-packages -p python3 env-biop-tf2` == Activate environment == source env-biop-tf2/bin/activate == Install TF == ``` module load python gcc/8.4.0-cuda mvapich2/2.3.4-cuda py-tensorflow pip install ipython tensorboard ``` == Test == ipython import tensorflow as tf = Run on the Cluster = Request time as ptbiop user ``` salloc -t 2:0:0 -A ptbiop --exclusive squeue -u $USER ssh NAME OF ALLOCATED NODE module load python gcc/8.4.0-cuda mvapich2/2.3.4-cuda py-tensorflow source env-biop-tf2/bin/activate ``` Now you can run stuff NOTE: Nicola will update on the Jupyter Notebook setup = YAPIC Setup = NOTE: We need to work with TF 1.15 in YAPIC in order to be able to export YAPIC models to the ModelZoo structure for reuse in Fiji. == First time setup == module load gcc/8.4.0-cuda cuda/10.2.89 cudnn/7.6.5.32-10.2-linux-x64 virtualenv -p python3 --system-site-packages yapic-tf-1.15 source yapic-tf-1.15/bin/activate pip install tensorflow-gpu==1.15 cd yapic-tf-1.15/lib64 ln -s $CUDA_ROOT/lib64/libcudart.so libcudart.so.10.0 ln -s $CUDA_ROOT/lib64/libcublas.so libcublas.so.10.0 ln -s $CUDA_ROOT/lib64/libcufft.so libcufft.so.10.0 ln -s $CUDA_ROOT/lib64/libcurand.so libcurand.so.10.0 ln -s $CUDA_ROOT/lib64/libcusolver.so libcusolver.so.10.0 ln -s $CUDA_ROOT/lib64/libcusparse.so libcusparse.so.10.0 export LD_LIBRARY_PATH=$PWD:$LD_LIBRARY_PATH Then we can start using YAPIC Instructions to follow

= First Time Setup = Create environment `virtualenv --system-site-packages -p python3 env-biop-tf2` == Activate environment == source env-biop-tf2/bin/activate == Install TF == ``` module load python gcc/8.4.0-cuda mvapich2/2.3.4-cuda py-tensorflow pip install ipython tensorboard ``` == Test == ipython import tensorflow as tf = Run on the Cluster = Request time as ptbiop user ``` salloc -t 2:0:0 -A ptbiop --exclusive squeue -u $USER ssh NAME OF ALLOCATED NODE module load python gcc/8.4.0-cuda mvapich2/2.3.4-cuda py-tensorflow source env-biop-tf2/bin/activate ``` Now you can run stuff NOTE: Nicola will update on the Jupyter Notebook setup = YAPIC Setup = NOTE: We need to work with TF 1.15 in YAPIC in order to be able to export YAPIC models to the ModelZoo structure for reuse in Fiji. == First time setup == You should do this from the GPU node ``` salloc -t 2:0:0 -A ptbiop --exclusive squeue -u $USER ssh NAME OF ALLOCATED NODE ``` Then here we can install and setup Python with TF 1.15 ``` module load gcc/8.4.0-cuda cuda/10.2.89 cudnn/7.6.5.32-10.2-linux-x64 python virtualenv -p python3 --system-site-packages yapic-tf-1.15 source yapic-tf-1.15/bin/activate pip install tensorflow-gpu==1.15 yapic cd yapic-tf-1.15/lib64 ln -s $CUDA_ROOT/lib64/libcudart.so libcudart.so.10.0 ln -s $CUDA_ROOT/lib64/libcublas.so libcublas.so.10.0 ln -s $CUDA_ROOT/lib64/libcufft.so libcufft.so.10.0 ln -s $CUDA_ROOT/lib64/libcurand.so libcurand.so.10.0 ln -s $CUDA_ROOT/lib64/libcusolver.so libcusolver.so.10.0 ln -s $CUDA_ROOT/lib64/libcusparse.so libcusparse.so.10.0 export LD_LIBRARY_PATH=$PWD:$LD_LIBRARY_PATH ``` Then we can start using YAPIC Instructions to follow

= First Time Setup = Create environment `virtualenv --system-site-packages -p python3 env-biop-tf2` == Activate environment == source env-biop-tf2/bin/activate == Install TF == ``` module load python gcc/8.4.0-cuda mvapich2/2.3.4-cuda py-tensorflow pip install ipython tensorboard ``` == Test == ipython import tensorflow as tf = Run on the Cluster = Request time as ptbiop user ``` salloc -t 2:0:0 -A ptbiop --exclusive squeue -u $USER ssh NAME OF ALLOCATED NODE module load python gcc/8.4.0-cuda mvapich2/2.3.4-cuda py-tensorflow source env-biop-tf2/bin/activate ``` Now you can run stuff NOTE: Nicola will update on the Jupyter Notebook setup = YAPIC Setup = NOTE: We need to work with TF 1.15 in YAPIC in order to be able to export YAPIC models to the ModelZoo structure for reuse in Fiji. == First time setup == You should do this from the GPU node ``` salloc -t 2:0:0 -A ptbiop --exclusive squeue -u $USER ssh NAME OF ALLOCATED NODE ``` Then here we can install and setup Python with TF 1.15 ``` module load gcc/8.4.0-cuda cuda/10.2.89 cudnn/7.6.5.32-10.2-linux-x64 python virtualenv -p python3 --system-site-packages yapic-tf-1.15 source yapic-tf-1.15/bin/activate pip install tensorflow-gpu==1.15 yapic cd yapic-tf-1.15/lib64 ln -s $CUDA_ROOT/lib64/libcudart.so libcudart.so.10.0 ln -s $CUDA_ROOT/lib64/libcublas.so libcublas.so.10.0 ln -s $CUDA_ROOT/lib64/libcufft.so libcufft.so.10.0 ln -s $CUDA_ROOT/lib64/libcurand.so libcurand.so.10.0 ln -s $CUDA_ROOT/lib64/libcusolver.so libcusolver.so.10.0 ln -s $CUDA_ROOT/lib64/libcusparse.so libcusparse.so.10.0 export LD_LIBRARY_PATH=$PWD:$LD_LIBRARY_PATH ``` Then we can start using YAPIC Instructions to follow