分类：
2011-05-02 20:16:18
1.将siesta-3.0-rc2.tgz文件拷贝到一个临时的目录里面（如tem）
2.解压文件：$ tar -zxvf
5. 在执行文件生成目录里运行Src/configure，即： $ ../Src/configure
6.进入/Src/MPI
7.修改Makefile
vi Makefile
把
ARCH_MAKE_DEFAULT=../arch.make
修改为绝对路径
ARCH_MAKE_DEFAULT=/home/zhou/soft/siesta/siesta-3.0-rc2/Obj/arch.make
8.再make
9.再切换到Obj目录
10.修改arch.make
#
# This file is part of the SIESTA package.
#
# Copyright (c) Fundacion General Universidad Autonoma de Madrid:
# E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal
# and J.M.Soler, 1996- .
#
# Use of this software constitutes agreement with the full conditions
# given in the SIESTA license, as signed by all legitimate users.
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90
SIESTA_ARCH=x86_64-unknown-linux-gnu--Intel
FPP=
FPP_OUTPUT=
FC=/public/openmpi-141-icc/bin/mpif90
RANLIB=ranlib
SYS=nag
SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)
FFLAGS= -O2 -i-static
FFLAGS_DEBUG= -g
LDFLAGS=-Vaxlib
FPPFLAGS= -DMPI
# -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI
ARFLAGS_EXTRA=
FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=
BLAS_LIBS=-L/public/intel/mkl/lib/em64t -lmkl_solver_lp64 -lmkl_intel_lp64 -lguide
LAPACK_LIBS=-L/public/intel/mkl/lib/em64t -lmkl_sequential -lmkl_core
BLACS_LIBS=-L/public/intel/mkl/lib/em64t -lmkl_blacs_openmpi_lp64
SCALAPACK_LIBS=-L/public/intel/mkl/lib/em64t -lmkl_scalapack_lp64
COMP_LIBS=
NETCDF_LIBS=
NETCDF_INTERFACE=
LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS)
#SIESTA needs an F90 interface to MPI
#This will give you SIESTA's own implementation
#If your compiler vendor offers an alternative, you may change
#to it here.
MPI_INTERFACE=/home/zhou/soft/siesta/siesta-3.0-rc2/Src/MPI/libmpi_f90.a
MPI_INCLUDE=/public/openmpi-141-icc/include
#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.
.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<
11，make
完成了
这是我根据网上的编译不成功后自己看代码 改的
其实另外一个方法不会这么麻烦 就是我们在Sys目录下编译步骤如下：
1.将siesta-3.0-rc2.tgz文件拷贝到一个临时的目录里面（如tem）
2. tar -zxvf siesta-3.0-rc2.tgz
3 ，cd Syc
4 ， cd ..
5 ，sh ./obj_setup.sh
6 ， ./configure
7 ， vi arch.make 内容和上面的一样
8 ， cd MPI
9 ， make
10 ，cd ..
11 ，make
||
siesta-3.0-rc2的并行编译
网上很多人反映siesta-3.0-rc2的并行编译的时候没什么问题，但是不能并行计算，并行计算的时候往往会报错。比如堆栈和内存报错等等。这几天闲着没事，对siesta进行了编译，发现确实存在这类问题。
特别是用intel ifort11编译的时候。后来我发现用以下两种方法可以解决siesta并行计算的问题。
（一）如果你坚持要用intel ifort 11来进行编译。可以采取如下方式（siesta网站主页上的方法，见）
在生成的arch.make文件中新加入
DUMMY_FOX= --enable-dummy
FFLAGS_DEBUG= -g -O2
而后在Obj文件夹中的makefile文件修改第148-153行，将这几行写成如下形式
$(FoX_configured):
(cd FoX; touch arch.make ; \
CONFIGURE="$(VPATH)/FoX/configure"; \
$$CONFIGURE VPATH="$(VPATH)/FoX" \
FC="$(FC_SERIAL)" FCFLAGS="$(FFLAGS_DEBUG)" \
--enable-wcml $(DUMMY_FOX) || false )
注意(cd FoX; touch arch.make ; \这一行前是一个Tab空格，而不是一个space空格
将这两个地方修改好后，
make clen
make
之后生成的siesta可执行文件并行计算不会出现问题。但要注意的是，arch.make文件中的优化级别是FFLAGS=-g -O2或FFLAGS=-g -O1或FFLAGS=-g -O0，不能是FFLAGS=-g -O3，我试了一下FFLAGS=-g -O3，发现计算过程中出现下面的错误
SPLIT: Orbitals with angular momentum L= 0
SPLIT: Basis orbitals for state 4s
izeta = 1
lambda = 1.000000
rc = 6.000769
energy = -0.359899
kinetic = 0.368794
potential(screened) = -0.728693
potential(ionic) = -6.200046
WARNING: Minimum split_norm parameter: 0.52689. Will not be able to generate orbital with split_norm = 0.15000
See manual for new split options
ERROR STOP from Node: 0
当改用FFLAGS=-g -O2和FFLAGS=-g -O0或FFLAGS=-g -O1之后则没用出现类似的错误提示，具体原因我就没去深究了。当然不同的优化级别在计算时间上会有一些差异。
比如用FFLAGS=-g -O2时，运行时间如下（用的Fe.fdf例子）
* Running on 8 nodes in parallel
>> Start of run: 6-DEC-2010 17:19:33
>> End of run: 6-DEC-2010 17:27:54
当改用FFLAGS=-g -O0时，运行时间如下（用的Fe.fdf例子）
* Running on 8 nodes in parallel
>> Start of run: 6-DEC-2010 16:48:25
>> End of run: 6-DEC-2010 16:58:58
（二）如果你不使用ifort11编译器，而是使用ifort10或以下的版本，建议配合使用openmpi来进行并行计算。
1）安装openmpi，详细步骤不说了，只是在configure的时候我使用的是如下的命令：
./configure --prefix=要安装的目录 F77=ifort FC=ifort FCFLAGS=-em64t FFLAGS=-em64t
FCFLAGS和FFLAGS是告诉编译器用的是64位的编译器，如果机器不是64位的就不用了。
make
make install
安装完成后还得添加环境变量，至于怎么添加，网上很多，搜索一下就知道了。
2）编译siesta
步骤就写了，大家都知道。下面是我的arch.make文件
#
# This file is part of the SIESTA package.
#
# Copyright (c) Fundacion General Universidad Autonoma de Madrid:
# E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal
# and J.M.Soler, 1996- .
#
# Use of this software constitutes agreement with the full conditions
# given in the SIESTA license, as signed by all legitimate users.
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90
SIESTA_ARCH=x86_64-unknown-linux-gnu--unknown
FPP=
FPP_OUTPUT=
FC=mpif90
RANLIB=ranlib
SYS=nag
SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)
FFLAGS=-g -O2 #-i-static
FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI
LDFLAGS=
FFLAGS_DEBUG= -g -O2 # whatever options you might need,guohuazhong
DUMMY_FOX= --enable-dummy # whatever options you might need,guohuazhong
ARFLAGS_EXTRA=
FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=
BLAS_LIBS=-L/public/software/intel/Compiler/11.1/059/mkl/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_lapack -lmkl_core -lguide -pthread
LAPACK_LIBS=-L/public/software/intel/Compiler/11.1/059/mkl/lib/em64t -lmkl_sequential -lmkl_core -pthread
BLACS_LIBS=-L/public/software/intel/Compiler/11.1/059/mkl/lib/em64t -lmkl_blacs_openmpi_lp64 -pthread
SCALAPACK_LIBS=-L/public/software/intel/Compiler/11.1/059/mkl/lib/em64t -lmkl_scalapack_lp64 -pthread
COMP_LIBS=
COMP_LIBS=dc_lapack.a liblapack.a libblas.a ######guohuazhong screened
NETCDF_LIBS=
NETCDF_INTERFACE=
LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS)
#SIESTA needs an F90 interface to MPI
#This will give you SIESTA's own implementation
#If your compiler vendor offers an alternative, you may change
#to it here.
MPI_INTERFACE=libmpi_f90.a
MPI_INCLUDE=/public/software/mpi/openmpi1.4.2-intel/include
#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.
.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<
编译成功，祝好运！
