CP2K编译与安装
1. 编译环境
编译环境：intel 2018
编译器：intel 2018
MPI：intel 2018
FFTW：intel 2018
MKL：intel 2018
LAPACK：intel 2018
ScaLAPACK：intel 2018
ELPA：intel 2018
Libint：intel 2018
Libxc：intel 2018
Libvdwxc：intel 2018
Libxsmm：intel 2018
2. 运行环境
在安装库之前：
编译安装CP2K-2023.1 使用 intel 2018 mkl
更改文件install_cp2k_toolchain.sh
cd cp2k-2023.1/tools/toolchain
vim install_cp2k_toolchain.sh
将该文件的以下位置代码：
# ------------------------------------------------------------------------
# Work out default settings
# ------------------------------------------------------------------------
# tools to turn on by default:
with_gcc="__SYSTEM__"
改为
with_gcc="__INSTALL__"
将：
# Compiler conflicts
if [ "${with_intel}" != "__DONTUSE__" ] && [ "${with_gcc}" = "__INSTALL__" ]; then
echo "You have chosen to use the Intel compiler, therefore the installation of the GCC compiler will be skipped."
with_gcc="__SYSTEM__"
改为
# Compiler conflicts
if [ "${with_intel}" != "__DONTUSE__" ] && [ "${with_gcc}" = "__INSTALL__" ]; then
echo "You have chosen to use the Intel compiler, therefore the installation of the GCC compiler will be skipped."
with_gcc="__INSTALL__"
注：以上的步骤是使安装编译环境库的过程中即使检测到gcc编译器，也不跳过，仍然安装cp2k-2023.1自带的gcc编译器，这样做的目的是避免在之后的库以及cp2k的编译过程中出现编译错误。
3. 安装所有库
然后开始正式编译：（CPK需要的库最好提前准备放在build文件夹下）
(base) [root@node01 toolchain]# ./install_cp2k_toolchain.sh --with-gcc=install --math-mode=mkl --with-openmpi=install --with-ptscotch=install --with-superlu=install --with-pexsi=install --with-quip=install --with-plumed=install
MPI is detected and it appears to be Intel MPI
You have chosen to use the Intel compiler, therefore the installation of the GCC compiler will be skipped.
You have chosen to install the GCC compiler, therefore MPI libraries have to be installed too
and the use of the Intel compiler and Intel MPI will be disabled.
Compiling with 128 processes for target native.
==================== Installing GCC ====================
gcc-12.2.0.tar.gz is found
Installing GCC from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/gcc-12.2.0
gcc is installed as /opt/apps/cp2k-2023.1/tools/toolchain/install/gcc-12.2.0/bin/gcc
g++ is installed as /opt/apps/cp2k-2023.1/tools/toolchain/install/gcc-12.2.0/bin/g++
gfortran is installed as /opt/apps/cp2k-2023.1/tools/toolchain/install/gcc-12.2.0/bin/gfortran
Step gcc took 385.00 seconds.
Step intel took 0.00 seconds.
==================== Getting proc arch info using OpenBLAS tools ====================
OpenBLAS detected LIBCORE = zen
OpenBLAS detected ARCH = x86_64
==================== Installing CMake ====================
cmake-3.25.1 is already installed, skipping it.
Step cmake took 0.00 seconds.
==================== Installing OpenMPI ====================
openmpi-4.1.4.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/openmpi-4.1.4
Slurm installation found. OpenMPI will be configured with --with-pmi.
Found directory /opt/apps/cp2k-2023.1/tools/toolchain/install/openmpi-4.1.4/bin
Found directory /opt/apps/cp2k-2023.1/tools/toolchain/install/openmpi-4.1.4/lib
Found directory /opt/apps/cp2k-2023.1/tools/toolchain/install/openmpi-4.1.4/include
mpirun is installed as /opt/apps/cp2k-2023.1/tools/toolchain/install/openmpi-4.1.4/bin/mpirun
mpicc is installed as /opt/apps/cp2k-2023.1/tools/toolchain/install/openmpi-4.1.4/bin/mpicc
mpicxx is installed as /opt/apps/cp2k-2023.1/tools/toolchain/install/openmpi-4.1.4/bin/mpicxx
mpif90 is installed as /opt/apps/cp2k-2023.1/tools/toolchain/install/openmpi-4.1.4/bin/mpif90
Step openmpi took 523.00 seconds.
WARNING: (/opt/apps/cp2k-2023.1/tools/toolchain/scripts/stage2/install_mkl.sh, line 23) MKL FFTW3 interface is present, but FFTW library is needed for FFTW-MPI wrappers.
==================== Finding MKL from system paths ====================
MKLROOT is found to be /opt/intel/intel-2018up4/compilers_and_libraries_2018.5.274/linux/mkl
libm is found in ld search path
libdl is found in ld search path
Step mkl took 0.00 seconds.
==================== Installing FFTW ====================
fftw-3.3.10.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/fftw-3.3.10
Step fftw took 67.00 seconds.
==================== Installing LIBINT ====================
libint-v2.6.0-cp2k-lmax-5.tgz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5
Step libint took 143.00 seconds.
==================== Installing LIBXC ====================
libxc-6.0.0.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/libxc-6.0.0
patching file src/mgga_xc_b97mv.c
Step libxc took 41.00 seconds.
==================== Installing Libxsmm ====================
libxsmm-1.17.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/libxsmm-1.17
Step libxsmm took 15.00 seconds.
Step scalapack took 0.00 seconds.
==================== Installing COSMA ====================
COSMA-v2.6.2.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/COSMA-2.6.2
Step cosma took 14.00 seconds.
==================== Installing ELPA ====================
elpa-2022.11.001.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/elpa-2022.11.001/cpu
Step elpa took 73.00 seconds.
==================== Installing PT-Scotch ====================
scotch_6.0.0.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/scotch-6.0.0
Step ptscotch took 3.00 seconds.
==================== Installing SuperLU_DIST ====================
superlu_dist_6.1.0.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/superlu_dist-6.1.0
Step superlu took 9.00 seconds.
==================== Installing PEXSI ====================
pexsi_v1.2.0.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/pexsi-1.2.0
Step pexsi took 58.00 seconds.
==================== Installing QUIP ====================
QUIP-0.9.10.tar.gz is found
fox-b5b69ef9a46837bd944ba5c9bc1cf9d00a6198a7.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/quip-0.9.10
Step quip took 250.00 seconds.
==================== Installing gsl ====================
gsl-2.7.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/gsl-2.7
Step gsl took 67.00 seconds.
==================== Installing PLUMED ====================
plumed-src-2.8.1.tgz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/plumed-2.8.1
Step plumed took 49.00 seconds.
==================== Installing hdf5 ====================
hdf5-1.12.0.tar.bz2 is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/hdf5-1.12.0
Step hdf5 took 108.00 seconds.
==================== Installing libvdwxc ====================
libvdwxc-0.4.0.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/libvdwxc-0.4.0
Step libvdwxc took 24.00 seconds.
==================== Installing spglib ====================
spglib-1.16.2.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/spglib-1.16.2
Step spglib took 6.00 seconds.
==================== Installing libvori ====================
libvori-220621.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/libvori-220621
Step libvori took 17.00 seconds.
Step libtorch took 0.00 seconds.
==================== Installing spfft ====================
SpFFT-1.0.6.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/SpFFT-1.0.6
Step spfft took 6.00 seconds.
==================== Installing spla ====================
SpLA-1.5.4.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/SpLA-1.5.4
Step spla took 7.00 seconds.
==================== Installing SIRIUS ====================
sirius_7.3.2.tar.gz is found
Installing from scratch into /opt/apps/cp2k-2023.1/tools/toolchain/install/sirius-7.3.2
Step sirius took 46.00 seconds.
==================== generating arch files ====================
arch files can be found in the /opt/apps/cp2k-2023.1/tools/toolchain/install/arch subdirectory
Wrote /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/local.ssmp
Wrote /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/local_static.ssmp
Wrote /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/local.sdbg
Wrote /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/local_asan.ssmp
Wrote /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/local_coverage.sdbg
Wrote /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/local.psmp
Wrote /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/local.pdbg
Wrote /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/local_asan.psmp
Wrote /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/local_static.psmp
Wrote /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/local_warn.psmp
Wrote /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/local_coverage.pdbg
========================== usage =========================
Done!
Now copy:
cp /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/* to the cp2k/arch/ directory
To use the installed tools and libraries and cp2k version
compiled with it you will first need to execute at the prompt:
source /opt/apps/cp2k-2023.1/tools/toolchain/install/setup
To build CP2K you should change directory:
cd cp2k/
make -j 128 ARCH=local VERSION="ssmp sdbg psmp pdbg"
arch files for GPU enabled CUDA versions are named "local_cuda.*"
arch files for GPU enabled HIP versions are named "local_hip.*"
arch files for OpenCL (GPU) versions are named "local_opencl.*"
arch files for coverage versions are named "local_coverage.*"
Note that these pre-built arch files are for the GNU compiler, users have to adapt them for other compilers.
It is possible to use the provided CP2K arch files as guidance.
3. compile cp2k-2023.1
cp /opt/apps/cp2k-2023.1/tools/toolchain/install/arch/* /opt/apps/cp2k-2023.1/arch/
source /opt/apps/cp2k-2023.1/tools/toolchain/install/setup
cd /opt/apps/cp2k-2023.1
make -j 128 ARCH=local VERSION="ssmp sdbg psmp pdbg"
4. 写环境变量
#cp2k-2023.1 use gcc-12.2.0 and intel-2018 mkl to compile, the intel ifort not use
#intel-2018#
source /opt/intel/intel-2018up4/compilers_and_libraries_2018.5.274/linux/mkl/bin/mklvars.sh intel64
#cp2k-2023.1
source /opt/apps/cp2k-2023.1/tools/toolchain/install/setup
export PATH=/opt/apps/cp2k-2023.1/exe/local:${PATH}
# how to use: source thisfile
🎉️ source ~/.bashrc之后，可使用诸如cp2k.popt -v命令查看是否成功。
5. 测试
mkdir test
cd test
touch test.inp
写入以下内容
#Generated by Multiwfn
&GLOBAL
PROJECT test
PRINT_LEVEL LOW
RUN_TYPE ENERGY
&END GLOBAL
&FORCE_EVAL
METHOD Quickstep
&SUBSYS
&CELL
A 7.13358000 0.00000000 0.00000000
B 0.00000000 7.13358000 0.00000000
C 0.00000000 0.00000000 7.13358000
&END CELL
&COORD
C 0.00000000 0.00000000 0.00000000
C 0.89169753 0.89169753 0.89169753
C 0.00000000 1.78339506 1.78339506
C 2.67509260 0.89169753 2.67509260
C 1.78339506 0.00000000 1.78339506
C 0.89169753 2.67509260 2.67509260
C 1.78339506 1.78339506 0.00000000
C 2.67509260 2.67509260 0.89169753
C 3.56679013 0.00000000 0.00000000
C 4.45848766 0.89169753 0.89169753
C 3.56679013 1.78339506 1.78339506
C 6.24188272 0.89169753 2.67509260
C 5.35018519 0.00000000 1.78339506
C 4.45848766 2.67509260 2.67509260
C 5.35018519 1.78339506 0.00000000
C 6.24188272 2.67509260 0.89169753
C 0.00000000 3.56679013 0.00000000
C 0.89169753 4.45848766 0.89169753
C 0.00000000 5.35018519 1.78339506
C 2.67509260 4.45848766 2.67509260
C 1.78339506 3.56679013 1.78339506
C 0.89169753 6.24188272 2.67509260
C 1.78339506 5.35018519 0.00000000
C 2.67509260 6.24188272 0.89169753
C 3.56679013 3.56679013 0.00000000
C 4.45848766 4.45848766 0.89169753
C 3.56679013 5.35018519 1.78339506
C 6.24188272 4.45848766 2.67509260
C 5.35018519 3.56679013 1.78339506
C 4.45848766 6.24188272 2.67509260
C 5.35018519 5.35018519 0.00000000
C 6.24188272 6.24188272 0.89169753
C 0.00000000 0.00000000 3.56679013
C 0.89169753 0.89169753 4.45848766
C 0.00000000 1.78339506 5.35018519
C 2.67509260 0.89169753 6.24188272
C 1.78339506 0.00000000 5.35018519
C 0.89169753 2.67509260 6.24188272
C 1.78339506 1.78339506 3.56679013
C 2.67509260 2.67509260 4.45848766
C 3.56679013 0.00000000 3.56679013
C 4.45848766 0.89169753 4.45848766
C 3.56679013 1.78339506 5.35018519
C 6.24188272 0.89169753 6.24188272
C 5.35018519 0.00000000 5.35018519
C 4.45848766 2.67509260 6.24188272
C 5.35018519 1.78339506 3.56679013
C 6.24188272 2.67509260 4.45848766
C 0.00000000 3.56679013 3.56679013
C 0.89169753 4.45848766 4.45848766
C 0.00000000 5.35018519 5.35018519
C 2.67509260 4.45848766 6.24188272
C 1.78339506 3.56679013 5.35018519
C 0.89169753 6.24188272 6.24188272
C 1.78339506 5.35018519 3.56679013
C 2.67509260 6.24188272 4.45848766
C 3.56679013 3.56679013 3.56679013
C 4.45848766 4.45848766 4.45848766
C 3.56679013 5.35018519 5.35018519
C 6.24188272 4.45848766 6.24188272
C 5.35018519 3.56679013 5.35018519
C 4.45848766 6.24188272 6.24188272
C 5.35018519 5.35018519 3.56679013
C 6.24188272 6.24188272 4.45848766
&END COORD
&KIND C
ELEMENT C
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE
&END KIND
&END SUBSYS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
# WFN_RESTART_FILE_NAME to_be_specified
CHARGE 0 #Net charge
MULTIPLICITY 1 #Spin multiplicity
&QS
EPS_DEFAULT 1E-10 #This is default. Set all EPS_xxx to values such that the energy will be correct up to this value
&END QS
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
&MGRID
CUTOFF 350 #Use 500 for high accuracy calculation
REL_CUTOFF 50 #Use 60 for high accuracy calculation
&END MGRID
&SCF
MAX_SCF 128
EPS_SCF 1E-5 #Target accuracy for SCF convergence
# SCF_GUESS RESTART #Uncomment this can restart from WFN_RESTART_FILE_NAME file
&DIAGONALIZATION
ALGORITHM STANDARD #Algorithm for diagonalization. DAVIDSON is faster for large systems
&END DIAGONALIZATION
&MIXING
METHOD BROYDEN_MIXING
ALPHA 0.4 #Default. Mixing 40% of new density matrix with the old one
NBROYDEN 5 #Default is 4. Number of previous steps stored for the actual mixing scheme
&END MIXING
&END SCF
&END DFT
&END FORCE_EVAL
执行计算：
$ mpirun -np 4 cp2k.popt -i cp2k.inp -o cp2k.out