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namd_2.13_gpu.sh
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#!/bin/bash
# this script will download and install a CPU-only version of NAMD with MPI
# you will need "module load intel intel-mpi" in your Slurm script
wget https://www.ks.uiuc.edu/Research/namd/2.13/download/412487/NAMD_2.13_Source.tar.gz
tar xzf NAMD_2.13_Source.tar.gz
cd NAMD_2.13_Source
tar xf charm-6.8.2.tar
cd charm-6.8.2
module purge
module load rh/devtoolset/7
module list
./build charm++ multicore-linux-x86_64 --with-production
#ERROR: CUDA builds require non-MPI SMP or multicore Charm++ arch for reasonable performance.
# http://www.ks.uiuc.edu/Research/namd/2.13/notes.html
cd multicore-linux-x86_64/tests/charm++/megatest
make pgm
#srun -N 1 -n 1 -c 4 -t 1 ./pgm ### uncomment this line to run tests
cd ../../../../..
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 xzf tcl8.5.9-linux-x86_64.tar.gz
tar xzf 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
module load cudatoolkit/10.1
cd arch
wget https://raw.githubusercontent.com/PrincetonUniversity/hpc_beginning_workshop/master/RC_example_jobs/namd/Linux-x86_64-gcc.arch
#wget https://raw.githubusercontent.com/PrincetonUniversity/hpc_beginning_workshop/master/RC_example_jobs/namd/Linux-x86_64-gcc.cuda
#wget https://raw.githubusercontent.com/PrincetonUniversity/hpc_beginning_workshop/master/RC_example_jobs/namd/Linux-x86_64-gcc.arch
#wget https://raw.githubusercontent.com/PrincetonUniversity/hpc_beginning_workshop/master/RC_example_jobs/namd/Linux-x86_64-gcc.cuda
#touch Linux-x86_64-gcc.cuda
#touch Linux-x86_64-gcc.fftw
#touch Linux-x86_64-gcc.tcl
#touch Linux-x86_64-gcc.base
cd ..
./config Linux-x86_64-gcc --with-cuda --cuda-prefix /usr/local/cuda-10.1 \
--cuda-gencode arch=compute_60,code=sm_60 --charm-arch multicore-linux-x86_64
cd Linux-x86_64-gcc
make