numba and cupy revised

hpc/nways/Dockerfile_python

@@ -22,8 +22,9 @@ 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 
+RUN pip3 install --upgrade numpy==1.19.5
+RUN pip3 install --no-cache-dir "cupy-cuda112==9.0.0" \
+    numba==0.53.1 scipy 
        
         
 ############################################

hpc/nways/Singularity_python

@@ -7,7 +7,7 @@ FROM:  nvidia/cuda:11.2.2-devel-ubuntu20.04
 %environment
     export XDG_RUNTIME_DIR=
     export PATH="$PATH:/usr/local/bin:/usr/bin"
-    export PATH=/opt/nvidia/nsight-systems/2020.5.1/bin:/opt/nvidia/nsight-compute/2020.2.1:/bin:/usr/local/cuda/bin$PATH
+    export PATH=/opt/nvidia/nsight-systems/2021.3.1/bin:/opt/nvidia/nsight-compute/2021.2.2:/bin:/usr/local/cuda/bin$PATH
     export LD_LIBRARY_PATH="/usr/include/python3.8:/usr/local/lib:/usr/local/lib/python3.8/dist-packages:/usr/local/cuda/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
     
 
@@ -22,30 +22,38 @@ FROM:  nvidia/cuda:11.2.2-devel-ubuntu20.04
     rm -rf /var/lib/apt/cache/* 
 
     pip3 install --no-cache-dir -U install setuptools pip
-    pip3 install gdown
-    apt-get update -y
+    apt-get -y update
     apt-get -y install git nvidia-modprobe
+    pip3 install 'chardet>=3.0.2,<3.1.0' 'idna>=2.5,<2.8' 'urllib3>=1.21.1,<1.24' 'certifi>=2017.4.17'
     pip3 install jupyterlab
     pip3 install ipywidgets
-    pip3 install --no-cache-dir "cupy-cuda112==8.6.0" \
-    numba numpy scipy
-    pip3 install --upgrade MDAnalysis
+    pip3 install gdown
+    pip3 install --upgrade numpy==1.19.5
+    pip3 install --no-cache-dir "cupy-cuda112==9.0.0" \
+    numba==0.53.1 scipy
+    
+    
 
-    apt-get install --no-install-recommends -y build-essential 
+    #apt-get install --no-install-recommends -y build-essential 
 
     python3 /labs/nways_MD/English/Python/source_code/dataset.py
 
-
-# NVIDIA nsight-systems-2020.5.1 ,nsight-compute-2
+    touch /labs/nways_MD/English/Python/jupyter_notebook/cupy/RDF.dat
+    touch /labs/nways_MD/English/Python/jupyter_notebook/cupy/Pair_entropy.dat
+    
+# NVIDIA nsight-systems-2021.3.1 ,nsight-compute-2021.2.2
     apt-get update -y   
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends apt-transport-https ca-certificates gnupg wget
     apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys F60F4B3D7FA2AF80
     echo "deb https://developer.download.nvidia.com/devtools/repos/ubuntu2004/amd64/ /" >> /etc/apt/sources.list.d/nsight.list 
     apt-get update -y 
-    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends nsight-systems-2020.5.1 nsight-compute-2020.2.1 
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends nsight-systems-2021.3.1 nsight-compute-2021.2.2 
     apt-get install --no-install-recommends -y build-essential
     
+    pip3 install --no-cache-dir MDAnalysis
     
+    chmod -R 777 /labs/nways_MD/English/Python/jupyter_notebook/cupy/RDF.dat
+    chmod -R 777 /labs/nways_MD/English/Python/jupyter_notebook/cupy/Pair_entropy.dat
     
     cd /
     rm -rf ${build_tmp}

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

@@ -87,7 +87,7 @@
     "\n",
     "-----\n",
     "\n",
-    "# <div style=\"text-align: center ;border:3px; border-style:solid; border-color:#FF0000  ; padding: 1em\">[HOME](../../nways_start.ipynb)</div> \n",
+    "# <center><div style=\"text-align: center;border:3px; border-style:solid; border-color:#FF0000; padding: 1em;\"> [HOME](../../nways_start.ipynb)</div></center> \n",
     "-----\n",
     "\n",
     "\n",
@@ -95,6 +95,13 @@
     "\n",
     "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). "
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -113,7 +120,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.8"
   }
  },
  "nbformat": 4,

hpc/nways/nways_labs/nways_start.ipynb

@@ -76,7 +76,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.8"
   }
  },
  "nbformat": 4,