Skip to content

Latest commit

 

History

History
200 lines (193 loc) · 7.84 KB

install_namd.md

File metadata and controls

200 lines (193 loc) · 7.84 KB
Raw
  • Download the source code and Unpack NAMD
  • Unpack charm inside of NAMD source folder
  • Configure intel compiler, mkl, mpi environment
  • CHARM
    • Reference: link
    • cd charm-6.8.2
    • Edit src/arch/mpi-linux-x86_64/cc-mpicxx.sh and src/arch/mpi-linux-x86_64/conv-mach.sh
      • Convert all mpicxx -> mpiicpc, mpicc -> mpiicc, gcc-> icc, g++-> icpc, mpif77 -> mpiifort, mpif90 -> mpiifort, f95 -> ifort, g77 -> ifort
      • Edit src/arch/common/cc-icc.sh and cc-iccstatic.sh as icc -> mpiicc, icpc -> mpiicpc, ifort -> mpiifort
    • ./build charm++ mpi-linux-x86_64 smp icc
  • NAMD
    • Reference: link, link2
    • Edit arch/Linux-x86_64-icc.arch 
      AMD_ARCH = Linux-x86_64
CHARMARCH = mpi-linux-x86_64-smp-icc
FLOATOPTS = -ip -xCORE-AVX512  -O3 -g -fp-model fast=2 -no-prec-div -qoverride-limits -DNAMD_DISABLE_SSE
CXX = icpc -std=c++11
CXXOPTS = -static-intel -O2 $(FLOATOPTS)
CXXNOALIASOPTS = -O2 -fno-alias $(FLOATOPTS)
CXXCOLVAROPTS = -O2 -ip
CC = icc
COPTS = -static-intel -O2 $(FLOATOPTS)
    • Edit arch/Linux-x86_64.tcl 
      TCLDIR=/share/libs/tcl/8.6.9
TCLINCL=-I$(TCLDIR)/include
TCLLIB=-L$(TCLDIR)/lib -ltcl8.6 -ldl -lpthread
TCLFLAGS=-DNAMD_TCL
TCL=$(TCLINCL) $(TCLFLAGS)
    • ./config Linux-x86_64-icc --with-mkl --charm-base ./charm-6.8.2 --charm-arch mpi-linux-x86_64-smp-icc
      • --with-mkl will use arch/Linux-x86_64.mkl
    • cd Linux-x86_64-icc/
    • make -j 32
    • namd2 is produced

Running namd

verbs - infiniband version

  • CHARM
    • cd charm-6.8.2
    • Edit src/arch/mpi-linux-x86_64/cc-mpicxx.sh and src/arch/mpi-linux-x86_64/conv-mach.sh
      • Convert all mpicxx -> mpiicpc, mpicc -> mpiicc, gcc-> icc, g++-> icpc, mpif77 -> mpiifort, mpif90 -> mpiifort, f95 -> ifort, g77 -> ifort
    • ./build charm++ verbs-linux-x86_64 icc # for infinibands - slightly faster than MPI
  • NAMD
    • Edit arch/Linux-x86_64-icc.arch
AMD_ARCH = Linux-x86_64
CHARMARCH = verbs-linux-x86_64-icc #mpi-linux-x86_64
FLOATOPTS = -ip -xCORE-AVX512  -O3 -g -fp-model fast=2 -no-prec-div -qoverride-limits -DNAMD_DISABLE_SSE
CXX = icpc -std=c++11
CXXOPTS = -static-intel -O2 $(FLOATOPTS)
CXXNOALIASOPTS = -O2 -fno-alias $(FLOATOPTS)
CXXCOLVAROPTS = -O2 -ip
CC = icc
COPTS = -static-intel -O2 $(FLOATOPTS)
- ./config Linux-x86_64-icc --with-mkl --charm-base ./charm-6.8.2 --charm-arch verbs-linux-x86_64-icc
- cd Linux-x86_64-icc/
- make -j 40
- *namd2* is produced
  • Run command
    • charm-6.8.2/bin/charmrun +p 40 Linux-x86_64-icc/namd2 apoa1.namd

NAMD with CUDA or GPU computing

  • Ref: https://www.nvidia.com/en-us/data-center/gpu-accelerated-applications/namd/
  • GCC build
    • CHARM
      • cd charm-6.8.2
      • ./build charm++ verbs-linux-x86_64 smp --with-production # mpi-linux-x86_64 conflicts with cuda
        • SMP is necessary. NAMD instruction: CUDA builds require non-MPI SMP or multicore Charm++ arch for reasonable performance. Consider ibverbs-smp or verbs-smp (InfiniBand), gni-smp (Cray), or multicore (single node).
        • MPI build is not supported: ERROR: CUDA builds require non-MPI SMP or multicore Charm++ arch for reasonable performance.
    • NAMD
      • Edit arc/Linux-x86_64-g++.arch
NAMD_ARCH = Linux-x86_64
CHARMARCH = verbs-linux-x86_64
CXX = g++ -m64 -std=c++0x
CXXOPTS = -O3 -fexpensive-optimizations -ffast-math 
CC = gcc -m64
COPTS = -O3 -fexpensive-optimizations -ffast-math

- Edit Linux-x86_64.mkl

FFTDIR=/share/compiler/intel/19.1/mkl
FFTINCL=-I$(FFTDIR)/include/fftw
FFTLIB=-L$(FFTDIR)/lib/intel64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core
FFTFLAGS=-DNAMD_FFTW -DNAMD_FFTW_3
FFT=$(FFTINCL) $(FFTFLAGS)

- Edit arch/Linux-x86_64.tcl
    ```bash
    TCLDIR=/share/libs/tcl/8.6.9
    TCLINCL=-I$(TCLDIR)/include
    TCLLIB=-L$(TCLDIR)/lib -ltcl8.6 -ldl -lpthread
    TCLFLAGS=-DNAMD_TCL
    TCL=$(TCLINCL) $(TCLFLAGS)
    ```
	- ./config Linux-x86_64-g++.arch --with-mkl --charm-base ./charm-6.8.2 --charm-arch verbs-linux-x86_64-smp --with-cuda --cuda-prefix /usr/nic/libs/cuda/10.0
- cd Linux-x86_64-g++.arch
- make -j 20
- *namd2* is produced
  • Intel Compiler build
    • Configure Intel environment
    • CHARM
      • cd charm-6.8.2
      • ./build charm++ verbs-linux-x86_64 smp icc --with-production
    • NAMD
      • Edit arc/Linux-x86_64-icc.arch
NAMD_ARCH = Linux-x86_64
CHARMARCH = verbs-linux-x86_64-smp-icc
FLOATOPTS = -ip -xCORE-AVX512  -O3 -g -fp-model fast=2 -no-prec-div -qoverride-limits -DNAMD_DISABLE_SSE
CXX = icpc -std=c++11
CXXOPTS = -static-intel -O2 $(FLOATOPTS)
CXXNOALIASOPTS = -O2 -fno-alias $(FLOATOPTS)
CXXCOLVAROPTS = -O2 -ip
CC = icc
COPTS = -static-intel -O2 $(FLOATOPTS)

- Edit Linux-x86_64.mkl

FFTDIR=/share/compiler/intel/18.0/mkl
FFTINCL=-I$(FFTDIR)/include/fftw
FFTLIB=-L$(FFTDIR)/lib/intel64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core
FFTFLAGS=-DNAMD_FFTW -DNAMD_FFTW_3
FFT=$(FFTINCL) $(FFTFLAGS)

	- ./config Linux-x86_64-icc.arch --with-mkl --charm-base ./charm-6.8.2 --charm-arch verbs-linux-x86_64-smp-icc --with-cuda --cuda-prefix /share/libs/cuda/10.0
- cd Linux-x86_64-icc.arch
- make -j 20
- *namd2* is produced
  • Running:
    • Single node run: ../NAMD_CUDA/Linux-x86_64-g++.arch/namd2 +p 40 +devices 0,1 apoa1.namd
    • Multinodes not running. Charmrun> Waiting for 0-th client to connect. No solution at this moment
  • Sample host_nodefile. Usage: ++nodelist ./host_nodefile
host aserver.my.org
host bserver.my.org
  • Sample runscript. Usage: ++runscript ./run_script
#!/bin/bash
export LD_LIBRARY_PATH="${1:h}:$LD_LIBRARY_PATH"
$*
  • If namd2 hangs, use ++verbose to monitor the status

checking charmrun

  • After charm is built,
  • cd <charm_build>/tests/charm++/simplearrayhello/
  • make -j
  • mpirun -n 2 ./hello # check if it runs parallel or not

Update

-using gcc for cuda

  • Building charmrun
    • In src/scripts/charmc, CORE_LIBS="-L/usr/lib64 -libverbs -lconv-core -ltmgr -lconv-util -lconv-partition $TRACE_OBJ"
    • ./build charm++ verbs-linux-x86_64 smp gcc
    • cd tests/charm++/simplearrayhello/
    • make -j 2; ./charmrun +p 4 ./hello
  • Building NAMD
    • Edit arch/Linux-x86_64.tcl
TCLDIR=/usr
TCLINCL=-I$(TCLDIR)/include
TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread
TCLFLAGS=-DNAMD_TCL
TCL=$(TCLINCL) $(TCLFLAGS)

- Edit arch/Linux-x86_64.mkl

FFTDIR=/share/compiler/intel/18.0/mkl
FFTINCL=-I$(FFTDIR)/include/fftw
FFTLIB=-L$(FFTDIR)/lib/intel64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core
FFTFLAGS=-DNAMD_FFTW -DNAMD_FFTW_3
FFT=$(FFTINCL) $(FFTFLAGS)

- Edit arch/Linux-x86_64-g++.arch

NAMD_ARCH = Linux-x86_64
CHARMARCH = verbs-linux-x86_64-smp-gcc
CXX = g++ -m64 -std=c++0x
CXXOPTS = -O3 -fexpensive-optimizations -ffast-math
CC = gcc -m64
COPTS = -O3 -fexpensive-optimizations -ffast-math

- `./config Linux-x86_64-g++.arch --with-mkl --charm-base ./charm-6.8.2 --charm-arch verbs-linux-x86_64-smp-gcc  --with-cuda --cuda-prefix /share/libs/cuda/10.0`
- `cd Linux-x86_64-g++; make -j 40`
  • Running:
    • export LD_LIBRARY_PATH+=:/share/compiler/intel/18.0/mkl/lib/intel64
    • Single node run: ../NAMD_CUDA/Linux-x86_64-g++.arch/namd2 +p 40 +devices 0,1 apoa1.namd
    • Multi node: charmrun +p40 ++ppn20 ++runscript ./runsciprt ++nodelist ./hostfile ../NAMD/Linux-x86_64-g++.arch/namd2 +devices 0,1 stmv.namd ++verbose