initializing

hpc/nways/Singularity_python

@@ -6,20 +6,19 @@ FROM:  nvidia/cuda:11.2.2-devel-ubuntu20.04
 
 %environment
     export XDG_RUNTIME_DIR=
-    export PATH="$PATH:/usr/local/bin:/opt/anaconda3/bin:/usr/bin"
+    export PATH="$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$PATH
-    export LD_LIBRARY_PATH="/usr/local/lib:/usr/local/lib/python3.8/dist-packages:/usr/local/cuda/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
+    export LD_LIBRARY_PATH="/usr/include/python3.8:/usr/local/lib:/usr/local/lib/python3.8/dist-packages:/usr/local/cuda/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
+    
 
 %post
     build_tmp=$(mktemp -d) && cd ${build_tmp}
 
     apt-get -y update
     apt-get -y dist-upgrade 
-    DEBIAN_FRONTEND=noninteractive apt-get -yq install --no-install-recommends \
-	    m4 vim-nox emacs-nox nano zip\
- 	    python3-pip python3-setuptools git-core inotify-tools \
-	    curl git-lfs \
-	    build-essential libtbb-dev
+    DEBIAN_FRONTEND=noninteractive apt-get -yq install --no-install-recommends python3-dev \
+	    m4 vim-nox emacs-nox nano zip \
+ 	    python3-pip python3-setuptools nginx zip make build-essential libtbb-dev
     rm -rf /var/lib/apt/cache/* 
 
     pip3 install --no-cache-dir -U install setuptools pip
@@ -27,7 +26,7 @@ FROM:  nvidia/cuda:11.2.2-devel-ubuntu20.04
     pip3 install --no-cache-dir jupyter
     pip3 install --no-cache-dir "cupy-cuda112==8.6.0" \
     numba numpy scipy
-    pip3 install --no-cache-dir MDAnalysis
+    pip3 install --upgrade MDAnalysis
 
     apt-get install --no-install-recommends -y build-essential 
 
@@ -42,10 +41,8 @@ FROM:  nvidia/cuda:11.2.2-devel-ubuntu20.04
     apt-get update -y 
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends nsight-systems-2020.5.1 nsight-compute-2020.2.1 
     apt-get install --no-install-recommends -y build-essential
-
-    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 
-    bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/anaconda3 
-    rm Miniconda3-latest-Linux-x86_64.sh 
+    
+    
     
     cd /
     rm -rf ${build_tmp}

hpc/nways/nways_labs/nways_MD/English/Python/source_code/dataset.py

@@ -5,5 +5,5 @@ import os
 
 ## alk.traj.dcd input file 
 url = 'https://drive.google.com/uc?id=1WZ0rtXZ-uMLfy7htT0gaU4EQ_Rq61QTF&export=download'
-output_fortran = '/labs/nways_MD/English/Python/source_code/input/alk.traj.dcd'
-gdown.download(url, output_fortran, quiet=False,proxy=None)
+output_python = '/labs/nways_MD/English/Python/source_code/input/alk.traj.dcd'
+gdown.download(url, output_python, quiet=False, proxy=None)