NVIDIA Driver, CUDA toolkit, Amber14 설치

gpu-0-0~1# cat > /etc/profile.d/cuda.sh

CUDADIR=/share/apps/cuda

if ! echo ${PATH} | /bin/grep -q $CUDADIR/bin ; then

   PATH=$CUDADIR/bin:${PATH}

   LD_LIBRARY_PATH=$CUDADIR/lib64:${LD_LIBRARY_PATH}

fi

export PATH LD_LIBRARY_PATH

gpu-0-0~1# vi /etc/grub.conf

kernel /boot/kickstart/default/vmlinuz-5.5-x86_64 ro root=LABEL=/ ramdisk_size=150000 kssendmac ks selinux=0 rdblacklist=nouveau nouveau.modeset=0

gpu-0-0~1# reboot

gpu-0-0~1# wget http://us.download.nvidia.com/XFree86/Linux-x86_64/340.24/NVIDIA-Linux-x86_64-340.24.run

gpu-0-0~1# sh NVIDIA-Linux-x86_64-340.24.run --kernel-source-path=/usr/src/kernels/2.6.18-308.4.1.el5-x86_64 --no-questions --ui=none --no-questions --accept-license

gpu-0-0~1# echo "blacklist nouveau options nouveau modeset=0" > /etc/modprobe.d/blacklist-nouveau.conf

### CUDA Toolkit 6.0

https://developer.nvidia.com/cuda-downloads

Frontend# http://developer.download.nvidia.com/compute/cuda/6_0/rel/installers/cuda_6.0.37_linux_64.run

Frontend# sh cuda_6.0.37_linux_64.run

Do you accept the previously read EULA? (accept/decline/quit): accept

Install NVIDIA Accelerated Graphics Driver for Linux-x86_64 331.62? ((y)es/(n)o/(q)uit): n

Install the CUDA 6.0 Toolkit? ((y)es/(n)o/(q)uit): y

Enter Toolkit Location [ default is /usr/local/cuda-6.0 ]: /share/apps/cuda/

Do you want to install a symbolic link at /usr/local/cuda? ((y)es/(n)o/(q)uit): y

Install the CUDA 6.0 Samples? ((y)es/(n)o/(q)uit): y

Enter CUDA Samples Location [ default is /root/NVIDIA_CUDA-6.0_Samples ]: /share/apps/cuda/

Installing the CUDA Toolkit in /share/apps/cuda ...

Frontend# cd /share/apps/cuda/NVIDIA_CUDA-6.0_Samples/1_Utilities/deviceQuery

Frontend# make

gpu-0-0~1# ./deviceQuery

./deviceQuery Starting...

 CUDA Device Query (Runtime API) version (CUDART static linking)

Detected 1 CUDA Capable device(s)

Device 0: "GeForce GTX 580"

  CUDA Driver Version / Runtime Version          6.5 / 6.5

  CUDA Capability Major/Minor version number:    2.0

  Total amount of global memory:                 1535 MBytes (1609760768 bytes)

  (16) Multiprocessors, ( 32) CUDA Cores/MP:     512 CUDA Cores

  GPU Clock rate:                                1544 MHz (1.54 GHz)

  Memory Clock rate:                             2004 Mhz

  Memory Bus Width:                              384-bit

  L2 Cache Size:                                 786432 bytes

  Maximum Texture Dimension Size (x,y,z)         1D=(65536), 2D=(65536, 65535), 3D=(2048, 2048, 2048)

  Maximum Layered 1D Texture Size, (num) layers  1D=(16384), 2048 layers

  Maximum Layered 2D Texture Size, (num) layers  2D=(16384, 16384), 2048 layers

  Total amount of constant memory:               65536 bytes

  Total amount of shared memory per block:       49152 bytes

  Total number of registers available per block: 32768

  Warp size:                                     32

  Maximum number of threads per multiprocessor:  1536

  Maximum number of threads per block:           1024

  Max dimension size of a thread block (x,y,z): (1024, 1024, 64)

  Max dimension size of a grid size    (x,y,z): (65535, 65535, 65535)

  Maximum memory pitch:                          2147483647 bytes

  Texture alignment:                             512 bytes

  Concurrent copy and kernel execution:          Yes with 1 copy engine(s)

  Run time limit on kernels:                     No

  Integrated GPU sharing Host Memory:            No

  Support host page-locked memory mapping:       Yes

  Alignment requirement for Surfaces:            Yes

  Device has ECC support:                        Disabled

  Device supports Unified Addressing (UVA):      Yes

  Device PCI Bus ID / PCI location ID:           1 / 0

  Compute Mode:

     < Default (multiple host threads can use ::cudaSetDevice() with device simultaneously) >

deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 6.5, CUDA Runtime Version = 6.5, NumDevs = 1, Device0 = GeForce GTX 580

Result = PASS

# vi test_gpu.sh

#!/bin/sh

#$ -N "test gpu"

#$ -q gpu.q

#$ -cwd

#$ -l gpu=1

/share/apps/cuda/NVIDIA_CUDA-6.0_Samples/1_Utilities/deviceQuery/deviceQuery

# qsub test_gpu.sh

### Amber14 install

# cd /share/apps/

# tar jxvfp Amber14.tar.bz2

# tar jxvfp AmberTools14.tar.bz2

# cd /share/apps/amber14

# export AMBERHOME=`pwd`

# export CUDA_HOME=/share/apps/cuda/

# ./update_amber --update

# cd $AMBERHOME

# ./configure -cuda gnu

# make -j 8 install

Building AmberTools 12 and Amber 12 in parallel

# cd $AMBERHOME

# ./configure -mpi gnu

# make install

Building CUDA-enabled Amber 12 (pmemd.cuda Amber 12 only!)

# cd $AMBERHOME

# ./configure -cuda gnu

# make install

Building CUDA-enabled Amber in parallel

# cd $AMBERHOME

# ./configure -cuda -mpi gnu

# make install