CPMD安装 | 红颜丽人

CPMD安装

大部分转自 http://simulation.5d6d.net/thread-24147-1-1.html，部分来自同学，偷艺。。。

1.
首先确认要安装机器的配置和操作系统，我的是这样的
lsb_release –a 查看系统详细信息：
LSB Version:
:core-3.0-ia32:core-3.0-noarch:graphics-3.0-ia32:graphics-3.0-noarch
Distributor ID: RedHatEnterpriseAS
Description:
Red Hat Enterprise Linux AS release 4 (Nahant Update 4)
Release:
4
Codename:
NahantUpdate4
cat /proc/cpuinfo | grep name | cut -f2 -d: | uniq –c
查看CPU配置
4
Intel(R) Xeon(TM) CPU 3.40GHz
下载或寻找对应版本的Intel编译器，Intel的MKL数据库，如果要并行还需要下载并行软件包MPICH2或其他MPI软件包
我的是32位的操作系统，intel的cpu，我下载了如下两个编译器：
l_fc_p_10.1.008_ia32.tar.gz； l_cc_p_10.1.008_ia32.tar.gz
mkl数据库为：l_mkl_p_10.0.011.tgz
2.
Intel编译器和mkl的安装
查看各个安装软件的压缩包中的install.txt

从中找到Perform the following steps to install the compiler. 按步骤安装

注意r我的serial numbe是以文件的形式存在，直接指定路径即可：/…/ licenses/*.lic

打开.bashrc 设置环境变量

export PATH=/…/intel/fc/10.1.018/bin:$PATH

export PATH=/…/intel/cc/10.1.008/bin:$PATH

export cc=icc

export fc=ifort

source /…/fc/10.1.018/bin/ifortvars.sh

source /…/intel/idb/10.1.018/bin/idbvars.sh

source /…/intel/cc/10.1.008/bin/iccvars.sh

source /…/intel/idb/10.1.008/bin/idbvars.sh

source /…/intel/mkl/10.0.011/tools/environment/mklvars32.sh

source 一下.bashrc文件

which ifort，which icc

查看路径是否一致。

3.
CPMD串行的安装
具体的安装过程已有人总结过，我在这里注意提一下我的Makefile的设置,我选用的是PC-IFC平台，
./mkcofin.sh PC-IFC >Makefile
make clean
make
根据make提示的信息修改
首先删除Makefile中FFLAGS表示中无法识别的如w95，tpp6等信息(FFlags是设置ifort编译参数的)
其次在LFLAGS中建立mkl数据库的链接，这一块要看mkl的说明书，参看/…/intel/mkl/10.0.011/lib 目录中的 *.a *.os 文件查看和串行相关的参数设置
Mkl的说明书中有Detailed directory structure
lib/32 Contains all libraries for IA-32 architecture
Static Libraries
Interface layer
libmkl_intel.a Interface library for Intel® compiler
libmkl_gf.a Interface library for GNU Fortran compiler
Threading layer
libmkl_intel_thread.a Parallel drivers library supporting Intel compiler
libmkl_gnu_thread.a Parallel drivers library supporting GNU compiler
libmkl_sequential.a Sequential drivers library
Computational layer
libmkl_core.a Kernel library for IA-32 architecture
libmkl_ia32.a Dummy library. Contains references to Intel MKL libraries
libmkl_lapack.a Dummy library. Contains references to Intel MKL libraries
libmkl_solver.a Sparse Solver, Interval Solver, and GMP routines
libmkl_solver_sequential.a Sequential version of Sparse Solver, Interval Solver, and GMP
routines library
libmkl_scalapack.a Dummy library. Contains references to Intel MKL libraries
libmkl_scalapack_core.a ScaLAPACK routines
libmkl_cdft.a Dummy library. Contains references to Intel MKL libraries
libmkl_cdft_core.a Cluster version of FFTs
RTL layer
libguide.a Intel® Legacy OpenMP* run-time library for static linking
libiomp5.a Intel® Compatibility OpenMP* run-time library for static
linking libmkl_blacs.a BLACS routines supporting the following MPICH versions:
• Topspin* MPICH version 1.2.5 configured with ch_vapi
device
• Myricom* MPICH version 1.2.5.10
• ANL* MPICH version 1.2.5.2
libmkl_blacs_intelmpi.a BLACS routines supporting Intel MPI 1.0
libmkl_blacs_intelmpi20.a BLACS routines supporting Intel MPI 2.0 and 3.0, and MPICH2.0
libmkl_blacs_openmpi.a BLACS routines supporting OpenMPI.

具体每个mkl版本这部分说明可能有所不同

根据这部分说明

我的设置如下：
FFLAGS = -c -O3
LFLAGS = -L/…/intel/mkl/10.0.011/lib/32 -lmkl_intel -lmkl_sequential -lmkl_core -lmkl_ia32 -lmkl_lapack -lmkl_solver_sequential -lmkl_scalapack -lmkl_cdft -lguide -lbiomp5 -lpthread –static
CFLAGS = -c -O2 -Wall
CPP = /lib/cpp -P -C -traditional
CPPFLAGS = -D__Linux -D__PGI -DFFT_DEFAULT -DLINUX_IFC
NOOPT_FLAG =
CC = icc
FC = ifort
LD = ifort
AR = ar
修改后再次make 看有没有问题一般undefined均为库参数指代不对或不恰当或多余的原因。再次make clean，make

4.
CPMD并行的安装
我选用的是PC-IFC-MPI平台，
首先安装mpich2并行软件
安装成功后，设置环境变量(.bashrc)：
export PATH=/home/myanping/mpich2-install/bin/:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/myanping/mpich2-install/lib/
source一下.bashrc文件

./mkcofin.sh PC-IFC-MPI >Makefile
make clean
make
根据make提示的信息修改删除Makefile中FFLAGS表示中无法识别的如w95，tpp6等信息(FFlags是设置ifort编译参数的)
在LFLAGS中不仅要建立适合并行的mkl数据库的链接，还有建立mpi库的链接
我的设置如下：
FFLAGS = -c -O3
LFLAGS = -L/home/myanping/intel/mkl/10.0.011/lib/32 -lmkl_intel -lmkl_intel_thread -lmkl_core -lmkl_ia32 -lmkl_lapack -lmkl_solver -lmkl_scalapack -lmkl_cdft -lguide -lbiomp5 -lmkl_blacs -lmkl_blacs_intelmpi -lpthread -static -Vaxlib \ -L/home/myanping/mpich2-install/lib -lfmpich -lmpich
CFLAGS = -c -O2 -Wall
CPP = /lib/cpp -P -C -traditional
CPPFLAGS = -D__Linux -D__PGI -DFFT_DEFAULT \

-DPARALLEL -DMYRINET -DLINUX_IFC
NOOPT_FLAG =
CC = mpicc
FC = mpif77
LD = mpif77
AR = ar
make clean
make
编译成功。

最关键的步骤修改 Makefiel中的”Default Configuration for PC-IFC”。
这是其中各个部分代表的意思
FFLAGS Fortran flags
LFLAGS Link editor flags
CFLAGS C compiler flags
CPP Preprocessor program
CPPFLAGS CPP flags
FC Fortran compiler
LD Link editor
AR Archive library maintainer
RANLIB Converts archives to random libraries
SRC Source files directory (default=.)
DEST Object files directory (default=.)
Use to write irat.inc in the right directory
BIN Use to put the cpmd.x executable (default=.)
（只是个人意见）主要修改的部分LFLAGS，需要详细的看你的MKL文件/opt/intel/mkl/10.2.5.035/lib中有哪些东西，根据不同版本的MKL内容修改，这里我借鉴了myanping在分子模拟论坛中MKL列表（网址1）
Detailed directory structure
lib/32 Contains all libraries for IA-32 architecture
Static Libraries
Interface layer
libmkl_intel.a Interface library for Intel® compiler
libmkl_gf.a Interface library for GNU Fortran compiler
Threading layer
libmkl_intel_thread.a Parallel drivers library supporting Intel compiler
libmkl_gnu_thread.a Parallel drivers library supporting GNU compiler
libmkl_sequential.a Sequential drivers library
Computational layer
libmkl_core.a Kernel library for IA-32 architecture
libmkl_ia32.a Dummy library. Contains references to Intel MKL libraries
libmkl_lapack.a Dummy library. Contains references to Intel MKL libraries
libmkl_solver.a Sparse Solver, Interval Solver, and GMP routines
libmkl_solver_sequential.a Sequential version of Sparse Solver, Interval Solver, and GMP
routines library
libmkl_scalapack.a Dummy library. Contains references to Intel MKL libraries
libmkl_scalapack_core.a ScaLAPACK routines
libmkl_cdft.a Dummy library. Contains references to Intel MKL libraries
libmkl_cdft_core.a Cluster version of FFTs
RTL layer
libguide.a Intel® Legacy OpenMP* run-time library for static linking
libiomp5.a Intel® Compatibility OpenMP* run-time library for static
linking libmkl_blacs.a BLACS routines supporting the following MPICH versions:
• Topspin* MPICH version 1.2.5 configured with ch_vapi
device
• Myricom* MPICH version 1.2.5.10
• ANL* MPICH version 1.2.5.2
libmkl_blacs_intelmpi.a BLACS routines supporting Intel MPI 1.0
libmkl_blacs_intelmpi20.a BLACS routines supporting Intel MPI 2.0 and 3.0, and MPICH2.0
libmkl_blacs_openmpi.a BLACS routines supporting OpenMPI.
具体每个mkl版本这部分说明可能有所不同。
又去掉了FFLAGS中的一些无法识别的如w95，tpp6等信息，在CPPFLAGS中添加了-DINTEL_MKL，在LD添加了-i-static，最终版本
#————— Default Configuration for PC-IFC —————
SRC = .
DEST = .
BIN = .
FFLAGS = -c -O3
LFLAGS = -L/opt/intel/mkl/10.2.5.035/lib/32 -lmkl_intel -lmkl_blas95 -lmkl_blacs -lmkl_lapack -lmkl_sequential -lmkl_core -lmkl_solver_sequential -lguide -liomp5 -lpthread -lmkl_solver -lmkl_vml_ia
CFLAGS = -c -O2 -Wall
CPP = /lib/cpp -P -C -traditional
CPPFLAGS = -D__Linux -D__PGI -DFFT_DEFAULT -DLINUX_IFC -DINTEL_MKL
NOOPT_FLAG =
CC = gcc
FC = ifort
LD = ifort -i-static
AR = ar
#—————————————————————————-
# Personal Configuration
#—————————————————————————-
#—————————————————————————-
# End of Personal Configuration
#—————————————————————————-
CFGDEST = .
CFGMACH = PC-IFC

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