Merge pull request #70 from programmah/jupyter_lab_resolve

Jupyter lab update and file link resolved

ai/DeepStream/Dockerfile

@@ -11,4 +11,4 @@ WORKDIR /opt/nvidia/deepstream/deepstream-5.0
 RUN pip3 install jupyterlab
 COPY English /opt/nvidia/deepstream/deepstream-5.0
 
-CMD jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8889 --NotebookApp.token="" --notebook-dir=/opt/nvidia/deepstream/deepstream-5.0/python
+CMD jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8889 --NotebookApp.token="" --notebook-dir=/opt/nvidia/deepstream/deepstream-5.0/python

ai/DeepStream/README.md

@@ -36,10 +36,10 @@ For instance:
 and to run the container, run:
 `sudo docker run --rm -it --gpus=all --network=host -p 8888:8888 myimage:1.0`
 
-Once inside the container launch the jupyter notebook by typing the following command
-`jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/opt/nvidia/deepstream/deepstream-5.0/python`
+Once inside the container launch the jupyter lab by typing the following command
+`jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/opt/nvidia/deepstream/deepstream-5.0/python`
 
-Then, open the jupyter notebook in browser: http://localhost:8888
+Then, open the jupyter lab in browser: http://localhost:8888
 Start working on the lab by clicking on the `Start_Here.ipynb` notebook.
 
 ### Singularity Container
@@ -52,9 +52,9 @@ and copy the files to your local machine to make sure changes are stored locally
 
 
 Then, run the container:
-`singularity run --nv --writable <image_name>.simg jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=~/workspace/python`
+`singularity run --nv --writable <image_name>.simg jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=~/workspace/python`
 
-Then, open the jupyter notebook in browser: http://localhost:8888
+Then, open the jupyter lab in browser: http://localhost:8888
 Start working on the lab by clicking on the `Start_Here.ipynb` notebook.
 
 ## Known issues

ai/DeepStream_Perf_Lab/Dockerfile

@@ -34,5 +34,5 @@ RUN ls -l
 RUN unzip deepstream_dataset.zip
 WORKDIR /opt/nvidia/deepstream/deepstream-5.0
 ## Uncomment this line to run Jupyter notebook by default
-CMD jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8889 --NotebookApp.token="" --notebook-dir=/opt/nvidia/deepstream/deepstream-5.0/python
+CMD jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8889 --NotebookApp.token="" --notebook-dir=/opt/nvidia/deepstream/deepstream-5.0/python
 

ai/DeepStream_Perf_Lab/README.md

@@ -37,13 +37,13 @@ For instance:
 and to run the container, run:
 `sudo docker run --rm -it --gpus=all --network=host -p 8888:8888 myimage:1.0`
 
-The container launches jupyter notebook and runs on port 8888
-`jupyter notebook --ip 0.0.0.0 --port 8888 --no-browser --allow-root`
+The container launches jupyter lab and runs on port 8888
+`jupyter-lab --ip 0.0.0.0 --port 8888 --no-browser --allow-root`
 
-Once inside the container launch the jupyter notebook by typing the following command
-`jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/opt/nvidia/deepstream/deepstream-5.0/python`
+Once inside the container launch the jupyter lab by typing the following command
+`jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/opt/nvidia/deepstream/deepstream-5.0/python`
 
-Then, open the jupyter notebook in browser: http://localhost:8888
+Then, open the jupyter lab in browser: http://localhost:8888
 Start working on the lab by clicking on the `Start_Here.ipynb` notebook.
 
 ### Singularity Container
@@ -56,9 +56,9 @@ and copy the files to your local machine to make sure changes are stored locally
 
 
 Then, run the container:
-`singularity run --nv --writable <image_name>.simg jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=~/workspace/python`
+`singularity run --nv --writable <image_name>.simg jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=~/workspace/python`
 
-Then, open the jupyter notebook in browser: http://localhost:8888
+Then, open the jupyter lab in browser: http://localhost:8888
 Start working on the lab by clicking on the `Start_Here.ipynb` notebook.
 
 ## Known issues

ai/RAPIDS/README.MD

@@ -35,7 +35,7 @@ For instance:
 and to run the container, run:
 `sudo docker run --rm -it --gpus=all --network=host -p 8888:8888 myimage:1.0`
 
-Then, open the jupyter notebook in browser: http://localhost:8888
+Then, open the jupyter lab in browser: http://localhost:8888
 Start working on the lab by clicking on the `Start_Here.ipynb` notebook.
 
 ### Singularity Container
@@ -49,7 +49,7 @@ and copy the files to your local machine to make sure changes are stored locally
 Then, run the container:
 `singularity run --nv --writable <image_name>.simg /opt/conda/envs/rapids/bin/jupyter lab --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/workspace/jupyter_notebook`
 
-Then, open the jupyter notebook in browser: http://localhost:8888
+Then, open the jupyter lab in browser: http://localhost:8888
 Start working on the lab by clicking on the `Start_Here.ipynb` notebook.
 
 ## Troubleshooting

hpc/miniprofiler/Dockerfile

@@ -18,8 +18,11 @@ RUN apt-get update -y && \
 RUN apt-get update 
 RUN apt-get install --no-install-recommends -y python3
 RUN pip3 install --upgrade pip
-
-RUN pip3 install --no-cache-dir jupyter
+RUN apt-get update -y        
+RUN apt-get install -y git nvidia-modprobe
+RUN pip3 install jupyterlab
+# Install required python packages
+RUN pip3 install ipywidgets
 RUN pip3 install netcdf4
 
 # NVIDIA nsight-systems-2020.2.1 
@@ -49,4 +52,4 @@ ENV PATH="/opt/nvidia/nsight-systems/2020.2.1/bin:$PATH"
 
 ADD English/ /labs
 WORKDIR /labs
-CMD service nginx start && jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/labs
+CMD jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/labs

hpc/miniprofiler/English/C/jupyter_notebook/profiling-c-lab2.ipynb

@@ -37,7 +37,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "From the top menu, click on *File*, and *Open* `miniWeather_openacc.cpp` and `Makefile` from the current directory at `C/source_code/lab2` directory and inspect the code before running below cells. We have already added OpenACC compute directives (`#pragma acc parallel`) around the expensive routines (loops) in the code.\n",
+    "Click on the <b>[miniWeather_openacc.cpp](../source_code/lab2/miniWeather_openacc.cpp)</b> and <b>[Makefile](../source_code/lab2/Makefile)</b> and inspect the code before running below cells. We have already added OpenACC compute directives (`#pragma acc parallel`) around the expensive routines (loops) in the code.\n",
     "\n",
     "Once done, compile the code with `make`. View the PGI compiler feedback (enabled by adding `-Minfo=accel` flag) and investigate the compiler feedback for the OpenACC code. The compiler feedback provides useful information about applied optimizations."
    ]
@@ -176,7 +176,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/miniprofiler/English/C/jupyter_notebook/profiling-c-lab3.ipynb

@@ -85,7 +85,7 @@
     "\n",
     "Now, add `collapse` clause to the code and make necessary changes to the loop directives. Once done, save the file, re-compile via `make`, and profile it again. \n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `miniWeather_openacc.cpp` and `Makefile` from the current directory at `C/source_code/lab3` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Click on the <b>[miniWeather_openacc.cpp](../source_code/lab3/miniWeather_openacc.cpp)</b> and <b>[Makefile](../source_code/lab3/Makefile)</b> links and modify `miniWeather_openacc.cpp` and `Makefile`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -241,7 +241,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/miniprofiler/English/C/jupyter_notebook/profiling-c-lab4.ipynb

@@ -54,7 +54,7 @@
     "\n",
     "Now, add `data` directives to the code, save the file, re-compile via `make`, and profile it again.\n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `miniWeather_openacc.cpp` and `Makefile` from the current directory at `C/source_code/lab4` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Click on the <b>[miniWeather_openacc.cpp](../source_code/lab4/miniWeather_openacc.cpp)</b> and <b>[Makefile](../source_code/lab4/Makefile)</b> links and modify `miniWeather_openacc.cpp` and `Makefile`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -179,7 +179,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/miniprofiler/English/C/jupyter_notebook/profiling-c.ipynb

@@ -219,7 +219,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/miniprofiler/English/Fortran/jupyter_notebook/profiling-fortran-lab2.ipynb

@@ -37,7 +37,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "From the top menu, click on *File*, and *Open* `miniWeather_openacc.f90` and `Makefile` from the current directory at `Fortran/source_code/lab2` directory and inspect the code before running below cells.We have already added OpenACC compute directives (`!$acc parallel loop`) around the expensive routines (loops) in the code.\n",
+    "Click on the <b>[miniWeather_openacc.f90](../source_code/lab2/miniWeather_openacc.f90)</b> and <b>[Makefile](../source_code/lab2/Makefile)</b> and inspect the code before running below cells. We have already added OpenACC compute directives (`!$acc parallel loop`) around the expensive routines (loops) in the code.\n",
     "\n",
     "Once done, compile the code with `make`. View the PGI compiler feedback (enabled by adding `-Minfo=accel` flag) and investigate the compiler feedback for the OpenACC code. The compiler feedback provides useful information about applied optimizations."
    ]
@@ -172,7 +172,7 @@
     "\n",
     "## Licensing \n",
     "\n",
-    "This material is released by NVIDIA Corporation under the Creative Commons Attribution 4.0 International (CC BY 4.0). "
+    "This material is released by OpenACC-Standard.org, in collaboration with NVIDIA Corporation, under the Creative Commons Attribution 4.0 International (CC BY 4.0). "
    ]
   }
  ],
@@ -193,7 +193,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/miniprofiler/English/Fortran/jupyter_notebook/profiling-fortran-lab3.ipynb

@@ -79,7 +79,7 @@
     "\n",
     "Now, add `collapse` clause to the code and make necessary changes to the loop directives. Once done, save the file, re-compile via `make`, and profile it again. \n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `miniWeather_openacc.f90` and `Makefile` from the current directory at `Fortran/source_code/lab3` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Click on the <b>[miniWeather_openacc.f90](../source_code/lab3/miniWeather_openacc.f90)</b> and <b>[Makefile](../source_code/lab3/Makefile)</b> links and modify `miniWeather_openacc.f90` and `Makefile`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -229,7 +229,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/miniprofiler/English/Fortran/jupyter_notebook/profiling-fortran-lab4.ipynb

@@ -55,7 +55,7 @@
     "Now, add `data` directives to the code, save the file, re-compile via `make`, and profile it again.\n",
     "\n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `miniWeather_openacc.f90` and `Makefile` from the current directory at `Fortran/source_code/lab4` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Click on the <b>[miniWeather_openacc.f90](../source_code/lab4/miniWeather_openacc.f90)</b> and <b>[Makefile](../source_code/lab4/Makefile)</b> links and modify `miniWeather_openacc.f90` and `Makefile`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -180,7 +180,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/miniprofiler/English/Fortran/jupyter_notebook/profiling-fortran.ipynb

@@ -230,7 +230,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/miniprofiler/English/profiling_start.ipynb

@@ -93,7 +93,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/miniprofiler/Singularity

@@ -22,7 +22,10 @@ FROM: nvcr.io/nvidia/nvhpc:20.9-devel-ubuntu20.04
     rm -rf /var/lib/apt/cache/* 
 
     pip3 install --upgrade pip
-    pip3 install --no-cache-dir jupyter
+    apt-get update -y
+    apt-get -y install git nvidia-modprobe
+    pip3 install jupyterlab
+    pip3 install ipywidgets
     pip3 install jupyter netcdf4
 
     apt-get install --no-install-recommends -y build-essential 

hpc/nways/Dockerfile

@@ -11,8 +11,13 @@ RUN apt-get -y update && \
         DEBIAN_FRONTEND=noninteractive apt-get -yq install --no-install-recommends python3-pip python3-setuptools nginx zip make build-essential libtbb-dev && \
         rm -rf /var/lib/apt/lists/* && \
         pip3 install --upgrade pip &&\
-        pip3 install --no-cache-dir jupyter &&\
         pip3 install gdown
+        
+RUN apt-get update -y        
+RUN apt-get install -y git nvidia-modprobe
+RUN pip3 install jupyterlab
+# Install required python packages
+RUN pip3 install ipywidgets
 
 ############################################
 # NVIDIA nsight-systems-2020.5.1 ,nsight-compute-2
@@ -39,4 +44,4 @@ ENV PATH="/opt/nvidia/hpc_sdk/Linux_x86_64/21.3/cuda/11.2/include:/usr/local/bin
 
 ADD nways_labs/ /labs
 WORKDIR /labs
-CMD service nginx start && jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/labs
+CMD jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/labs

hpc/nways/Dockerfile_python

@@ -17,7 +17,11 @@ RUN apt-get -y update && \
 
 RUN pip3 install --no-cache-dir -U install setuptools pip
 RUN pip3 install gdown
-RUN pip3 install --no-cache-dir jupyter
+RUN apt-get update -y
+RUN apt-get install -y git nvidia-modprobe
+# Install required python packages
+RUN pip3 install jupyterlab
+RUN pip3 install ipywidgets
 RUN pip3 install --no-cache-dir "cupy-cuda112==8.6.0" \
     numba numpy scipy 
        
@@ -51,4 +55,4 @@ RUN pip3 install --no-cache-dir MDAnalysis
 
 ADD nways_labs/ /labs
 WORKDIR /labs
-CMD service nginx start && jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/labs
+CMD jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/labs

hpc/nways/Singularity

@@ -23,8 +23,11 @@ FROM: nvcr.io/nvidia/nvhpc:21.3-devel-cuda_multi-ubuntu20.04
     rm -rf /var/lib/apt/cache/* 
 
     pip3 install --upgrade pip
-    pip3 install --no-cache-dir jupyter
     pip3 install gdown
+    apt-get update -y
+    apt-get -y install git nvidia-modprobe
+    pip3 install jupyterlab
+    pip3 install ipywidgets
 
     apt-get install --no-install-recommends -y build-essential 
 

hpc/nways/Singularity_python

@@ -23,7 +23,10 @@ FROM:  nvidia/cuda:11.2.2-devel-ubuntu20.04
 
     pip3 install --no-cache-dir -U install setuptools pip
     pip3 install gdown
-    pip3 install --no-cache-dir jupyter
+    apt-get update -y
+    apt-get -y install git nvidia-modprobe
+    pip3 install jupyterlab
+    pip3 install ipywidgets
     pip3 install --no-cache-dir "cupy-cuda112==8.6.0" \
     numba numpy scipy
     pip3 install --upgrade MDAnalysis

hpc/nways/nways_labs/nways_MD/English/C/jupyter_notebook/cudac/nways_cuda.ipynb

@@ -263,7 +263,7 @@
     "## Compile and Run for NVIDIA GPU\n",
     "Now, lets start modifying the original code and add CUDA C constructs. You can either explicitly transfer the allocated data between CPU and GPU or use unified memory which creates a pool of managed memory that is shared between the CPU and GPU.\n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `rdf.cpp` and `dcdread.h` from the current directory at `C/source_code/cudac` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Click on the <b>[rdf.cu](../../source_code/cudac/rdf.cu)</b> and <b>[dcdread.h](../../source_code/cudac/dcdread.h)</b> links and modify `rdf.cu` and `dcdread.h`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -418,7 +418,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/nways/nways_labs/nways_MD/English/C/jupyter_notebook/openacc/nways_openacc.ipynb

@@ -119,7 +119,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now, lets start modifying the original code and add the OpenACC directives. From the top menu, click on *File*, and *Open* `rdf.cpp` and `dcdread.h` from the current directory at `C/source_code/openacc` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Now, lets start modifying the original code and add the OpenACC directives. Click on the <b>[rdf.cpp](../../source_code/openacc/rdf.cpp)</b> and <b>[dcdread.h](../../source_code/openacc/dcdread.h)</b> links, and modify `rdf.cpp` and `dcdread.h`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -352,7 +352,7 @@
     "    }\n",
     "} \n",
     "```\n",
-    "Now, lets start modifying the original code and add the OpenACC kernel directive. From the top menu, click on *File*, and *Open* `rdf.cpp` and `dcdread.h` from the current directory at `C/source_code/openacc` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Now, lets start modifying the original code and add the OpenACC directives. Click on the <b>[rdf.cpp](../../source_code/openacc/rdf.cpp)</b> and <b>[dcdread.h](../../source_code/openacc/dcdread.h)</b> links, and modify `rdf.cpp` and `dcdread.h`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -414,7 +414,8 @@
     "    }\n",
     "} \n",
     "```\n",
-    "Now, lets start modifying the original code and add the OpenACC kernel directive. From the top menu, click on *File*, and *Open* `rdf.cpp` and `dcdread.h` from the current directory at `C/source_code/openacc` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "\n",
+    "Now, lets start modifying the original code and add the OpenACC directives. Click on the <b>[rdf.cpp](../../source_code/openacc/rdf.cpp)</b> and <b>[dcdread.h](../../source_code/openacc/dcdread.h)</b> links, and modify `rdf.cpp` and `dcdread.h`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -539,7 +540,7 @@
     "Let us try adding a data clause to our code and observe any performance differences between the two. \n",
     "**Note: We have removed the managed clause in order to handle data management explicitly.**\n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `rdf.cpp`, `dcdread.h` and `Makefile` from the current directory at `C/source_code/openacc` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Now, lets start modifying the original code and add the OpenACC directives. Click on the <b>[rdf.cpp](../../source_code/openacc/rdf.cpp)</b>, <b>[dcdread.h](../../source_code/openacc/dcdread.h)</b> and <b>[Makefile](../../source_code/openacc/Makefile)</b> links, and modify `rdf.cpp`, `dcdread.h` and `Makefile`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -690,7 +691,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/nways/nways_labs/nways_MD/English/C/jupyter_notebook/openmp/nways_openmp.ipynb

@@ -245,7 +245,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now, lets start modifying the original code and add the OpenMP directives. From the top menu, click on *File*, and *Open* `rdf.cpp` and `dcdread.h` from the current directory at `C/source_code/openmp` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Now, lets start modifying the original code and add the OpenMP directives. Click on the <b>[rdf.cpp](../../source_code/openmp/rdf.cpp)</b> and <b>[dcdread.h](../../source_code/openmp/dcdread.h)</b> links, and modify `rdf.cpp` and `dcdread.h`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -521,7 +521,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/nways/nways_labs/nways_MD/English/C/jupyter_notebook/stdpar/nways_stdpar.ipynb

@@ -137,7 +137,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now, lets start modifying the original code and add stdpar. From the top menu, click on *File*, and *Open* `rdf.cpp` and `dcdread.h` from the current directory at `C/source_code/stdpar` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Now, lets start modifying the original code and add stdpar. Click on the <b>[rdf.cpp](../../source_code/stdpar/rdf.cpp)</b> and <b>[dcdread.h](../../source_code/stdpar/dcdread.h)</b> links, and modify `rdf.cpp` and `dcdread.h`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -381,7 +381,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/nways/nways_labs/nways_MD/English/Fortran/jupyter_notebook/cudafortran/nways_cuda.ipynb

@@ -363,7 +363,7 @@
     "## Compile and Run for NVIDIA GPU\n",
     "Now, lets start modifying the original code and add CUDA C constructs. You can either explicitly transfer the allocated data between CPU and GPU or use unified memory which creates a pool of managed memory that is shared between the CPU and GPU.\n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `rdf.f90` from the current directory at `Fortran/source_code/cudafortran` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Click on the <b>[rdf.f90](../../source_code/cudafortran/rdf.f90)</b> link and modify `rdf.f90`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -514,7 +514,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/nways/nways_labs/nways_MD/English/Fortran/jupyter_notebook/doconcurrent/nways_doconcurrent.ipynb

@@ -89,7 +89,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now, lets start modifying the original code and add DO-CONCURRENT. From the top menu, click on *File*, and *Open* `rdf.f90`  from the current directory at `Fortran/source_code/doconcurrent` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Now, lets start modifying the original code and add DO-CONCURRENT.  Click on the <b>[rdf.f90](../../source_code/doconcurrent/rdf.f90)</b> link and modify `rdf.f90`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -343,7 +343,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/nways/nways_labs/nways_MD/English/Fortran/jupyter_notebook/openacc/nways_openacc.ipynb

@@ -112,7 +112,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now, lets start modifying the original code and add the OpenACC directives. From the top menu, click on *File*, and *Open* `rdf.f90` from the current directory at `Fortran/source_code/openacc` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Now, lets start modifying the original code and add the OpenACC directives. Click on the <b>[rdf.f90](../../source_code/openacc/rdf.f90)</b> link and modify `rdf.f90`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -354,7 +354,7 @@
     "        < loop code >\n",
     "    enddo\n",
     "```\n",
-    "Now, lets start modifying the original code and add the OpenACC kernel directive. From the top menu, click on *File*, and *Open* `rdf.f90` from the current directory at `Fortran/source_code/openacc` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Now, lets start modifying the original code and add the OpenACC directives. Click on the <b>[rdf.f90](../../source_code/openacc/rdf.f90)</b> link and modify `rdf.f90`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -425,7 +425,7 @@
     "       end do\n",
     "    enddo\n",
     "```\n",
-    "Now, lets start modifying the original code and add the OpenACC kernel directive. From the top menu, click on *File*, and *Open* `rdf.f90` from the current directory at `Fortran/source_code/openacc` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Now, lets start modifying the original code and add the OpenACC kernel directive. Click on the <b>[rdf.f90](../../source_code/openacc/rdf.f90)</b> link and modify `rdf.f90`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -566,7 +566,7 @@
     "Let us try adding a data clause to our code and observe any performance differences between the two. \n",
     "**Note: We have removed the managed clause in order to handle data management explicitly.**\n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `rdf.f90` from the current directory at `Fortran/source_code/openacc` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Click on the <b>[rdf.f90](../../source_code/openacc/rdf.f90)</b> link and modify `rdf.f90`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -726,7 +726,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/nways/nways_labs/nways_MD/English/Fortran/jupyter_notebook/openmp/nways_openmp.ipynb

@@ -235,7 +235,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now, lets start modifying the original code and add the OpenMP directives. From the top menu, click on *File*, and *Open* `rdf.f90` from the current directory at `Fortran/source_code/openmp` directory. Remember to **SAVE** your code after changes, before running below cells."
+    "Now, lets start modifying the original code and add the OpenMP directives. Click on the <b>[rdf.f90](../../source_code/openmp/rdf.f90)</b> link and modify `rdf.f90`. Remember to **SAVE** your code after changes, before running below cells."
    ]
   },
   {
@@ -516,7 +516,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/nways/nways_labs/nways_MD/English/Python/jupyter_notebook/Final_Remarks.ipynb

@@ -109,7 +109,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/nways/nways_labs/nways_MD/English/Python/jupyter_notebook/cupy/cupy_RDF.ipynb

@@ -174,7 +174,8 @@
     "    d_x = cp.asarray(d_x)\n",
     "    d_y = cp.asarray(d_y)\n",
     "    d_z = cp.asarray(d_z)\n",
-    "    d_g2 = cp.zeros(sizebin, dtype=cp.int64)\n",
+    "    d_g2 = np.zeros(sizebin, dtype=np.int64)\n",
+    "    d_g2 = cp.asarray(d_g2)\n",
     "\n",
     "    ############################## RAW KERNEL #################################################\n",
     "    nthreads = 128;\n",

hpc/nways/nways_labs/nways_MD/English/Python/jupyter_notebook/cupy/serial_RDF.ipynb

@@ -282,8 +282,9 @@
     "                main()\n",
     "    ```\n",
     "2. **Now, let's start modifying the original code to CuPy code constructs.**\n",
-    "> From the top menu, click on File, and Open **nways_serial.py** from the current directory at **Python/source_code/cupy** directory. Remember to SAVE your code after changes, and then run the cell below. \n",
-    "> Hints: focus on the **pair_gpu** function and you may need to modify few lines in the **main** function as well."
+    "> Click on the <b>[Modify](../../source_code/serial/nways_serial.py)</b>  link, and modify **nways_serial.py** to `CuPy code construct`. Remember to SAVE your code after changes, and then run the cell below. \n",
+    "> Hints: focus on the **pair_gpu** function and you may need to modify few lines in the **main** function as well.\n",
+    "---"
    ]
   },
   {

hpc/nways/nways_labs/nways_MD/English/Python/jupyter_notebook/numba/serial_RDF.ipynb

@@ -283,8 +283,8 @@
     "                main()\n",
     "    ```\n",
     "2. **Now, lets start modifying the original code to Numba code constructs.**\n",
-    "> From the top menu, click on File, and Open **nways_serial.py** from the current directory at **Python/source_code/numba** directory. Remember to SAVE your code after changes, and then run the cell below. \n",
-    "> Hints: focus on the **pair_gpu** function and you may need to modify few lines in the **main** function as well."
+    "> Click on the <b>[Modify](../../source_code/serial/nways_serial.py)</b>  link, and modify **nways_serial.py** to `Numba code construct`. Remember to SAVE your code after changes, and then run the cell below. \n",
+    "> Hints: focus on the **pair_gpu** function and you may need to modify few lines in the **main** function as well.\n"
    ]
   },
   {

hpc/nways/nways_labs/nways_MD/English/nways_MD_start_python.ipynb

@@ -34,14 +34,26 @@
     "\n",
     " Throughout the tutorial we will be following the Analysis - Parallelization - Optimization cycle. Let us begin by understanding the NVIDIA Nsight System tool ecosystem:   \n",
     "\n",
-    "- [Introduction to Profiling](../../profiler/English/jupyter_notebook/profiling.ipynb)\n",
+    "- [Nsight Systems](../../profiler/English/jupyter_notebook/nsight_systems.ipynb)\n",
     "    - Overview of Nsight profiler tools\n",
-    "    - Introduction to NVIDIA Nsight Systems\n",
-    "    - How to use NVIDIA Tools Extension SDK (NVTX) \n",
-    "    - Introduction to NVIDIA Nsight Compute\n",
+    "    - Introduction to Nsight Systems\n",
+    "    - How to view the report\n",
+    "    - How to use NVTX APIs\n",
     "    - Optimization Steps to parallel programming \n",
     "    \n",
-    "We will be working on porting a radial distribution function (RDF) to GPUs. Please choose one approach within the Python programming language to proceed working on RDF. \n",
+    "- [Nsight Compute](../../profiler/English/jupyter_notebook/nsight_compute.ipynb)\n",
+    "    - Introduction to Nsight Compute\n",
+    "    - Overview of sections\n",
+    "    - Roofline Charts\n",
+    "    - Memory Charts\n",
+    "    - Profiling a kernel using CLI\n",
+    "    - How to view the report\n",
+    "\n",
+    "Note: Learn about all terminologies used throught the notebooks in the [GPU Architecture Terminologies](C/jupyter_notebook/GPU_Architecture_Terminologies.ipynb) notebook.\n",
+    "\n",
+    "\n",
+    "We will be working on porting a radial distribution function (RDF) to GPUs. Please choose one approach within the Python programming language to proceed working on RDF.  \n",
+    "    \n",
     "\n",
     "\n",
     "#### Python Programming Language\n",

hpc/nways/nways_labs/nways_start.ipynb

@@ -41,10 +41,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-
     "### Bootcamp Duration\n",
     "The lab material will be presented in an 8-hour session. A Link to the material is available for download at the end of the lab.\n",
-
     "\n",
     "### Content Level\n",
     "Beginner, Intermediate\n",
@@ -78,7 +76,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/openacc/Dockerfile

@@ -9,9 +9,14 @@ FROM nvcr.io/nvidia/nvhpc:20.9-devel-ubuntu20.04
 RUN apt-get -y update && \
     DEBIAN_FRONTEND=noninteractive apt-get -yq install --no-install-recommends python3-pip python3-setuptools nginx zip build-essential && \
     rm -rf /var/lib/apt/lists/* && \
-    pip3 install --no-cache-dir jupyter
+    pip3 install --upgrade pip
 
+RUN apt-get update -y        
+RUN apt-get install -y git nvidia-modprobe
+RUN pip3 install jupyterlab
+# Install required python packages
+RUN pip3 install ipywidgets
 
 ADD English/ /labs
 WORKDIR /labs
-CMD service nginx start && jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/labs
+CMD jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/labs

hpc/openacc/English/C/jupyter_notebook/openacc_c_lab1.ipynb

@@ -351,7 +351,7 @@
    "source": [
     "### Parallelize the Example Code\n",
     "\n",
-    "At this point you have all of the tools you need to begin accelerating your application. The loops you will be parallelizing are in `laplace2d.c`. From the top menu, click on *File*, and *Open* `laplace2d.c` from the current directory at `C/source_code/lab1` directory. Remember to **SAVE** your code after changes, before running below cells.\n",
+    "At this point you have all of the tools you need to begin accelerating your application. The loops you will be parallelizing are in `laplace2d.c`. Click on the <b>[laplace2d.c](../source_code/lab1/laplace2d.c)</b> link and modify `laplace2d.c`. Remember to **SAVE** your code after changes, before running below cells.\n",
     "\n",
     "It is advisable to start with the `calcNext` routine and test your changes by compiling and running the code before moving on to the `swap` routine. OpenACC can be incrementally added to your application so that you can ensure each change is correct before getting too far along, which greatly simplifies debugging.\n",
     "\n",
@@ -540,7 +540,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/openacc/English/C/jupyter_notebook/openacc_c_lab3.ipynb

@@ -158,7 +158,7 @@
    "source": [
     "#### Implementing the Collapse Clause\n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `laplace2d.c` from the current directory at `C/source_code/lab3` directory. Use the **collapse clause** to collapse our multi-dimensional loops into a single dimensional loop.\n",
+    "Click on the <b>[laplace2d.c](../source_code/lab3/laplace2d.c)</b> link and modify `laplace2d.c`. Use the **collapse clause** to collapse our multi-dimensional loops into a single dimensional loop. Remember to **SAVE** your code after changes, before running below cells.\n",
     "\n",
     "Remember to **SAVE** your code after changes, before running below cells.\n",
     "\n",
@@ -281,7 +281,7 @@
    "source": [
     "#### Implementing the Tile Clause\n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `laplace2d.c` from the current directory at `C/source_code/lab3` directory. Replace the `collapse` clause with the `tile` clause to break our multi-dimensional loops into smaller tiles. Try using a variety of different tile sizes, but for now keep one of the dimensions as a **multiple of 32**. We will talk later about why this is important.\n",
+    "Click on the <b>[laplace2d.c](../source_code/lab3/laplace2d.c)</b> link and modify `laplace2d.c`. Replace the `collapse` clause with the `tile` clause to break our multi-dimensional loops into smaller tiles. Try using a variety of different tile sizes, but for now keep one of the dimensions as a **multiple of 32**. We will talk later about why this is important.\n",
     "\n",
     "Remember to **SAVE** your code after changes, before running below cells.\n",
     "\n",
@@ -408,7 +408,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/openacc/English/Fortran/jupyter_notebook/openacc_fortran_lab1.ipynb

@@ -358,7 +358,7 @@
    "source": [
     "### Parallelize the Example Code\n",
     "\n",
-    "At this point you have all of the tools you need to begin accelerating your application. The loops you will be parallelizing are in `laplace2d.f90`. From the top menu, click on *File*, and *Open* `laplace2d.f90` from the current directory at `Fortran/source_code/lab1` directory. Remember to **SAVE** your code after changes, before running below cells.\n",
+    "At this point you have all of the tools you need to begin accelerating your application. The loops you will be parallelizing are in `laplace2d.f90`. Click on the <b>[laplace2d.f90](../source_code/lab1/laplace2d.f90)</b> link and modify `laplace2d.f90`. Remember to **SAVE** your code after changes, before running below cells.\n",
     "\n",
     "It is advisable to start with the `calcNext` routine and test your changes by compiling and running the code before moving on to the `swap` routine. OpenACC can be incrementally added to your application so that you can ensure each change is correct before getting too far along, which greatly simplifies debugging.\n",
     "\n",
@@ -543,7 +543,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/openacc/English/Fortran/jupyter_notebook/openacc_fortran_lab3.ipynb

@@ -155,7 +155,7 @@
    "source": [
     "#### Implementing the Collapse Clause\n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `laplace2d.f90` from the current directory at `Fortran/source_code/lab3` directory. Use the **collapse clause** to collapse our multi-dimensional loops into a single dimensional loop.\n",
+    "Click on the <b>[laplace2d.f90](../source_code/lab3/laplace2d.f90)</b> link and modify `laplace2d.f90`. Use the **collapse clause** to collapse our multi-dimensional loops into a single dimensional loop.\n",
     "\n",
     "Remember to **SAVE** your code after changes, before running below cells.\n",
     "\n",
@@ -265,7 +265,7 @@
    "source": [
     "#### Implementing the Tile Clause\n",
     "\n",
-    "From the top menu, click on *File*, and *Open* `laplace2d.f90` from the current directory at `Fortran/source_code/lab3` directory.  Replace the **collapse clause** with the **tile clause** to break our multi-dimensional loops into smaller tiles. Try using a variety of different tile sizes, but always keep one of the dimensions as a **multiple of 32**. We will talk later about why this is important.\n",
+    "Click on the <b>[laplace2d.f90](../source_code/lab3/laplace2d.f90)</b> link and modify `laplace2d.f90`. Replace the **collapse clause** with the **tile clause** to break our multi-dimensional loops into smaller tiles. Try using a variety of different tile sizes, but always keep one of the dimensions as a **multiple of 32**. We will talk later about why this is important.\n",
     "\n",
     "Remember to **SAVE** your code after changes, before running below cells.\n",
     "\n",
@@ -392,7 +392,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/openacc/English/Lab1.ipynb

@@ -29,7 +29,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/openacc/English/Lab2.ipynb

@@ -29,7 +29,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/openacc/English/Lab3.ipynb

@@ -29,7 +29,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/openacc/English/openacc_start.ipynb

@@ -62,7 +62,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc/openacc/Singularity

@@ -12,7 +12,13 @@ From: nvcr.io/nvidia/nvhpc:20.9-devel-ubuntu20.04
     apt-get -y update
     DEBIAN_FRONTEND=noninteractive apt-get -yq install --no-install-recommends python3-pip python3-setuptools zip build-essential
     rm -rf /var/lib/apt/lists/*
-    pip3 install --no-cache-dir jupyter
+    
+    pip3 install --upgrade pip
+    pip3 install gdown
+    apt-get update -y
+    apt-get -y install git nvidia-modprobe
+    pip3 install jupyterlab
+    pip3 install ipywidgets
 
 %files
 

hpc_ai/ai_science_cfd/Dockerfile

@@ -12,6 +12,12 @@ RUN apt-get update
 RUN apt-get install -y libsm6 libxext6 libxrender-dev git
 # Install required python packages
 RUN pip3 install opencv-python==4.1.2.30 pandas seaborn sklearn matplotlib scikit-fmm tqdm h5py gdown
+RUN pip3 install --upgrade pip
+RUN apt-get update -y        
+RUN apt-get install -y git nvidia-modprobe
+RUN pip3 install jupyterlab
+# Install required python packages
+RUN pip3 install ipywidgets
 
 # TO COPY the data
 COPY English/ /workspace/
@@ -30,5 +36,5 @@ RUN python3 /workspace/python/source_code/dataset.py
 
 ## Uncomment this line to run Jupyter notebook by default
 #CMD jupyter notebook --ip 0.0.0.0 --port 8888 --allow-root
-CMD jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/workspace/python/jupyter_notebook/
+CMD jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/workspace/python/jupyter_notebook/
 

hpc_ai/ai_science_cfd/English/python/jupyter_notebook/Intro_to_DL/Resnets.ipynb

@@ -623,7 +623,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

hpc_ai/ai_science_cfd/README.MD

@@ -35,10 +35,10 @@ For instance:
 and to run the container, run:
 `sudo docker run --rm -it --gpus=all --network=host -p 8888:8888 myimage:1.0`
 
-The container launches jupyter notebook and runs on port 8888
-`jupyter notebook --ip 0.0.0.0 --port 8888 --no-browser --allow-root`
+The container launches jupyter lab and runs on port 8888
+`jupyter-lab --ip 0.0.0.0 --port 8888 --no-browser --allow-root`
 
-Then, open the jupyter notebook in browser: http://localhost:8888
+Then, open the jupyter lab in browser: http://localhost:8888
 Start working on the lab by clicking on the `Start_Here.ipynb` notebook.
 
 ### Singularity Container
@@ -50,9 +50,9 @@ and copy the files to your local machine to make sure changes are stored locally
 `singularity run <image_name>.simg cp -rT /workspace ~/workspace`
 
 Then, run the container:
-`singularity run --nv <image_name>.simg jupyter notebook --notebook-dir=~/workspace/python/jupyter_notebook`
+`singularity run --nv <image_name>.simg jupyter-lab --notebook-dir=~/workspace/python/jupyter_notebook`
 
-Then, open the jupyter notebook in browser: http://localhost:8888
+Then, open the jupyter lab in browser: http://localhost:8888
 Start working on the lab by clicking on the `Start_Here.ipynb` notebook.
 
 ## Troubleshooting

hpc_ai/ai_science_cfd/Singularity

@@ -10,6 +10,12 @@ FROM: nvcr.io/nvidia/tensorflow:21.05-tf2-py3
     pip3 install opencv-python==4.1.2.30 pandas seaborn sklearn matplotlib scikit-fmm tqdm h5py gdown
     mkdir /workspace/python/jupyter_notebook/CFD/data
     python3 /workspace/python/source_code/dataset.py
+    
+    pip3 install --upgrade pip
+    apt-get update -y
+    apt-get -y install git nvidia-modprobe
+    pip3 install jupyterlab
+    pip3 install ipywidgets
 
 %files
      English/* /workspace/

hpc_ai/ai_science_climate/Dockerfile

@@ -12,6 +12,12 @@ RUN apt-get update -y
 RUN apt-get install -y libsm6 libxext6 libxrender-dev git nvidia-modprobe
 # Install required python packages
 RUN pip3 install  opencv-python==4.1.2.30 pandas seaborn sklearn matplotlib scikit-fmm tqdm h5py gdown
+RUN pip3 install --upgrade pip
+RUN apt-get update -y        
+RUN apt-get install -y git nvidia-modprobe
+RUN pip3 install jupyterlab
+# Install required python packages
+RUN pip3 install ipywidgets
 
 ##### TODO - From the Final Repo Changing this 
 
@@ -22,4 +28,4 @@ COPY English/ /workspace/
 RUN python3 /workspace/python/source_code/dataset.py
 
 ## Uncomment this line to run Jupyter notebook by default
-CMD jupyter notebook --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/workspace/python/jupyter_notebook/
+CMD jupyter-lab --no-browser --allow-root --ip=0.0.0.0 --port=8888 --NotebookApp.token="" --notebook-dir=/workspace/python/jupyter_notebook/

hpc_ai/ai_science_climate/README.MD

@@ -32,10 +32,10 @@ For instance:
 and to run the container, run:
 `sudo docker run --rm -it --gpus=all --network=host -p 8888:8888 myimage:1.0`
 
-The container launches jupyter notebook and runs on port 8888
-`jupyter notebook --ip 0.0.0.0 --port 8888 --no-browser --allow-root`
+The container launches jupyter lab and runs on port 8888
+`jupyter-lab --ip 0.0.0.0 --port 8888 --no-browser --allow-root`
 
-Then, open the jupyter notebook in browser: http://localhost:8888
+Then, open the jupyter lab in browser: http://localhost:8888
 Start working on the lab by clicking on the `Start_Here.ipynb` notebook.
 
 ### Singularity Container
@@ -48,9 +48,9 @@ and copy the files to your local machine to make sure changes are stored locally
 
 
 Then, run the container:
-`singularity run --nv <image_name>.simg jupyter notebook --notebook-dir=~/workspace/python/jupyter_notebook`
+`singularity run --nv <image_name>.simg jupyter-lab --notebook-dir=~/workspace/python/jupyter_notebook`
 
-Then, open the jupyter notebook in browser: http://localhost:8888
+Then, open the jupyter lab in browser: http://localhost:8888
 Start working on the lab by clicking on the `Start_Here.ipynb` notebook.
 
 

hpc_ai/ai_science_climate/Singularity

@@ -10,6 +10,12 @@ FROM: nvcr.io/nvidia/tensorflow:21.05-tf2-py3
     pip3 install  opencv-python==4.1.2.30 pandas seaborn sklearn matplotlib scikit-fmm tqdm h5py gdown
     python3 /workspace/python/source_code/dataset.py
     
+    pip3 install --upgrade pip
+    apt-get update -y
+    apt-get -y install git nvidia-modprobe
+    pip3 install jupyterlab
+    pip3 install ipywidgets
+    
 %files
     English/* /workspace/