Install Nvidia CUDA-9.1 environment on Ubuntu WinBash

1. Install NVIDIA Graphics Driver

Determine the latest version of Nvidia driver available for your graphics card
Detecting NVIDIA card model

lspci -vnn | grep VGA
Visit the graphics drivers PPA homepage here and determine the latest versions of Nvidia drivers available

Remove Previous Installations (Important)
Search what packages from nvidia you have installed.

dpkg -l | grep -i nvidia

except the package nvidia-common all other packages should be purged.
sudo apt-get remove --purge nvidia-*

sudo apt-get autoremove
sudo reboot

Update gcc-6 g++6

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install gcc-6 g++-6

sudo ln -s /usr/bin/gcc-6 /usr/bin/gcc -f
sudo ln -s /usr/bin/g++-6 /usr/bin/g++ -f

checking

gcc -v

Add the graphics drivers PPA

sudo add-apt-repository ppa:graphics-drivers/ppa
sudo apt-get update

Install
sudo apt-get install nvidia-390 nvidia-390-dev
sudo reboot
lsmod | grep nvidia
or

nvidia-smi

If there is no output, then your installation has probably failed. It is also possible that the driver is not available in your system's driver database. You can run the following command to check if your system is running on the open source driver nouveau. If the output is negative for nouveau, then all is well with your installation.
lsmod | grep nouveau

Prevent automatic updates that might break the drivers
sudo apt-mark hold nvidia-390

2. Install CUDA

Preparation for installing of CUDA 9 + SDK
We install a number of build/dev packages which we require later:

sudo apt-get install g++ freeglut3-dev build-essential libx11-dev libxmu-dev libxi-dev libglu1-mesa libglu1-mesa-dev

We notice that the default gcc/g++ version on 17.10 is 7.2.0 (Ubuntu 7.2.0-8ubuntu3) :

gcc -v

CUDA 9 requires gcc 6. Thus, we install it and set the corresponding sym-links:

sudo apt install gcc-6
sudo apt install g++-6
sudo ln -s /usr/bin/gcc-6 /usr/local/cuda/bin/gcc
sudo ln -s /usr/bin/g++-6 /usr/local/cuda/bin/g++

Note that the default gcc version is still 7.2; can be checked by running gcc -v again.
Installation of CUDA 9 + SDK
Download a version of CUDA 9, such as

wget https://developer.nvidia.com/compute/cuda/9.0/Prod/local_installers/cuda_9.0.176_384.81_linux-run

Make the downloaded file executable and run it using sudo:

chmod +x cuda_9.1.85_387.26_linux.run 
sudo ./cuda_cuda_9.1.85_387.26_linux.run --override

We install CUDA with the following configurations:

You are attempting to install on an unsupported configuration. Do you wish to continue?
y
Install NVIDIA Accelerated Graphics Driver for Linux-x86_64 384.81?
n
Install the CUDA 9.0 Toolkit?
y
Enter Toolkit Location
[default location]
Do you want to install a symbolic link at /usr/local/cuda?
y
Install the CUDA 9.0 Samples?
y
Enter CUDA Samples Location
[default location]

Test the CUDA 9 installation using the SDK
Build your favorite CUDA sample and run it:

cd ~/NVIDIA_CUDA-9.0_Samples/5_Simulations/smokeParticles
make
../../bin/x86_64/linux/release/smokeParticles 

After the installation finishes, configure runtime library.

sudo bash -c "echo /usr/local/cuda/lib64/ > /etc/ld.so.conf.d/cuda.conf"
sudo ldconfig

It is also recommended for Ubuntu users to append string /usr/local/cuda/bin to system file /etc/environments so that nvcc will be included in $PATH. This will take effect after reboot.

Install cuDNN

The recommended way for installing cuDNN is to first copy the tgz file to /usr/local and then extract it, and then remove the tgz file if necessary. This method will preserve symbolic links. At last, execute sudo ldconfig to update the shared library cache.

** References:
1) How can I install CUDA 9 on Ubuntu 17.10
2) Install NVIDIA Driver and CUDA on Ubuntu / CentOS / Fedora Linux OS
3) Install Nvidia CUDA-7.5 environment in CentOS 6
4) Things to know when installing NVIDIA drivers
5) Install the latest NVIDIA driver on Linux
6) GTX 1070 on Ubuntu 16.04 with Cuda 8.0 and Theano

Install Intel Compiler with MPI_cuda on Ubuntu bash shell

Install OpenMPI with Intel compilerA. Prerequisites:
- Enable Ubuntu Bash Shell for Windows 10:

           https://docs.microsoft.com/en-us/windows/wsl/install-win10

- When apt-get install is unable to locate a package, try

1. Make sure you have enabled Ubuntu repositories:

sudo add-apt-repository main
sudo add-apt-repository universe
sudo add-apt-repository restricted
sudo add-apt-repository multiverse

2. Don't forget to update (make apt aware of your changes):

sudo apt-get update

3. Finally install the package:

sudo apt-get install <package>

B. install Intel compiler:

Dependencies You will need to install GCC C and C++ compilers on all the machines.

sudo apt-get install gcc
sudo apt-get install gcc-c++

go to folder contain source code Intel (create folder c:/Ubuntu/local )
    cd /mnt/c/Ubuntu/local$

extract the tgz file by running:

tar -xvf opt-intel-11.1.059.tar

(this complier just need to unpack)

Downloand NAMD Source Code

Step 2: Extract the package of NAMD

$ tar -xvf NAMD_2.12_Source.tar.gz
$ cd NAMD_2.12_Source          # let call it is $NAMD_SRC

Step 3: Building TCL-8.5.9 and FFTW libraries

(cd to NAMD_2.12_Source if you're not already there)

wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz 
tar xzf fftw-linux-x86_64.tar.gz 
mv linux-x86_64 fftw

wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz 
wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz 
tar -xvf tcl8.5.9-linux-x86_64.tar.gz 
tar -xvf tcl8.5.9-linux-x86_64-threaded.tar.gz 
mv tcl8.5.9-linux-x86_64 tcl 
mv tcl8.5.9-linux-x86_64-threaded tcl-threaded

Step 4: Building CHARM-6.7.1

$ cd NAMD_2.12_Source          
$ tar -xvf charm-6.7.1.tar
$ cd charm-6.7.1
./build charm++ {arch} {C compiler} {Fortran compiler} {other options} 

$ MPICXX=mpiicpc CXX=icpc ./build charm++  mpi-linux-x86_64 mpicxx ifort --with-production --no-shared -O3 -DCMK_OPTIMIZE=1

$ cd $NAMD_SRC

Step 5: Compile NAMD.
Make sure you're in the main NAMD directory, then configure and run make:

$ ./config Linux-x86_64-icc --charm-arch mpi-linux-x86_64-ifort-mpicxx
$ cd Linux-x86_64-icc
$ make -j16

You should see the namd2 executable

Step 10: mpirun

$ mpirun -np 32 -machinefile $MACHINEFILE namd2  something.conf > job$LSB_JOBID.log

References:

1) “Unable to locate package” while trying to install packages with APT
2) How to Setup the Intel Compilers on a Cluster

3)