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大地飞鹰h

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[交流] 【求助】siesta3.0 安装，错误一箩筐已有6人参与

首先现安装串行，ifort 10， mkl 10，
装siesta，make通过，
make clean ， make transiesta，出现
m_forces.o m_stress.o m_eo.o m_spin.o m_gamma.o m_hsx.o m_fire.o get_target_stress.o fire_optim.o zm_fire_optim.o cell_fire_optim.o m_fire_para.o m_fire_mixing.o write_raw_efs.o m_iodm.o m_sparse.o kpoint_pdos.o  nag.o pxf.o m_ts_options.o m_ts_aux_rout.o m_ts_kpoints.o m_ts_io.o m_ts_scattering.o m_ts_contour.o m_ts_electrode.o m_ts_in_siesta.o libfdf.a \
               \
            dc_lapack.a liblapack.a libblas.a  `FoX/FoX-config --libs --wcml` dc_lapack.a liblapack.a libblas.a
m_ts_aux_rout.o: In function `__m_ts_aux_rout__csolveg':
/home/hu/software/siesta-3.0-rc1/Src/m_ts_aux_rout.F:344: undefined reference to `zgesv_'
collect2: ld 返回 1
make: *** [transiesta] 错误 1
[hu@node02 trans]$

个人以为与数据库有关，转装blas，lapack。
安装lapack-3.2时，出现
Time for 1,000,000 SAXPY ops  = 0.00    seconds
*** Error:  Time for operations was zero
Including SECOND, time       = 0.00    seconds
Average time for SECOND    = 0.00    milliseconds
Time for 1,000,000 DAXPY ops  = 0.00    seconds
*** Error:  Time for operations was zero
Including DSECND, time       = 0.00    seconds
Average time for DSECND    = 0.00    milliseconds
结果编译通不过。
  后来装并行时，又有报错。
[hu@node01 ~]$ mpdcheck -f mpd.hosts -ssh
hu@node03's password: ** ssh timed out to node03
** ssh failed to node03
** here is the output:
[hu@node01 ~]$

共有四台机器，只有第一台通过了lapack编译，之后make transiesta通过，但是运行例子也是报错，如下
siesta:  194************** 96726338.0234 96726338.0234143.3913********
siesta: WARNING: Qtot, Tr[D*S] =    156.000000    63.523758
siesta:  195************** 96503554.1989 96503554.1989143.4410********
整天对着电脑来来回回的装呀装，期待高手指点一二，使我脱离苦海！

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1楼 2010-06-10 20:59:19

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valenhou001

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★ ★
大地飞鹰h(金币+5): 2010-06-11 10:03:10
zzy870720z(金币+2):谢谢专家指导，辛苦了 2010-06-11 11:30:17

下面贴出我用ifort，以及scalapck suite 0.96 编译SIESTA3.0的arch.make(重要的部分),以供参考。参考时，针对自己的scalapack所放的位置自行进行调整。

里面最重要的是，去编译scalapack suite 0.96。我的例子，我是将编译出来的.a文件都放到了/home1/zh/soft/scalapack-intel/lib目录中。

SIESTA_ARCH=x86_64-unknown-linux-gnu--Intel

FPP=
FPP_OUTPUT=
FC=mpif90
RANLIB=ranlib

SYS=nag

SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)

#FFLAGS=-g  -fno-underscoring
FFLAGS=-g
FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
LDFLAGS=

ARFLAGS_EXTRA=

FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=

MATH_LIB=/home1/zh/soft/scalapack-intel/lib
BLAS_LIBS=$(MATH_LIB)/librefblas.a
LAPACK_LIBS=dc_lapack.a $(MATH_LIB)/libreflapack.a
BLACS_LIBS= $(MATH_LIB)/blacsC.a $(MATH_LIB)/blacsF77.a $(MATH_LIB)/blacs.a
SCALAPACK_LIBS=$(MATH_LIB)/libscalapack.a

下面是编译scalapack suite 0.96时，LAPCK, BLACS, SCALAPACK时的编译选项，等：
1、LAPACK的make.inc

SHELL = /bin/sh
PLAT =
FORTRAN  = ifort
OPTS    = -O3
DRVOPTS  = $(OPTS)
NOOPT =  -mp
LOADER = ifort
LOADOPTS =
TIMER = EXT_ETIME
ARCH    = ar
ARCHFLAGS= cr
RANLIB = /usr/bin/ranlib
BLASLIB    = /home1/zh/soft/scalapack-intel/lib/librefblas.a
LAPACKLIB = libreflapack.a
TMGLIB    = tmglib.a
EIGSRCLIB = eigsrc.a
LINSRCLIB = linsrc.a
----------
make blaslib
make lapacklib
将编译得到librefblas.a, libreflapack.a放到了/home1/zh/soft/scalapack-intel/lib

2、BLACS的Bmake.inc
SHELL = /bin/sh
BTOPdir = /home1/zh/soft/scalapack-intel/BLACS
COMMLIB = MPI
PLAT =
BLACSdir = $(BTOPdir)/LIB
BLACSDBGLVL = 0
BLACSFINIT  = $(BLACSdir)/blacsF77.a
BLACSCINIT  = $(BLACSdir)/blacsC.a
BLACSLIB = $(BLACSdir)/blacs.a

MPIINCdir = /home1/zh/soft/openmpi-1.3-intel/include
MPILIB =

BTLIBS = $(BLACSFINIT) $(BLACSLIB) $(BLACSFINIT) $(MPILIB)
INSTdir = $(BTOPdir)/INSTALL/EXE
TESTdir = $(BTOPdir)/TESTING/EXE
FTESTexe = $(TESTdir)/xFbtest_$(COMMLIB)-$(PLAT)-$(BLACSDBGLVL)
CTESTexe = $(TESTdir)/xCbtest_$(COMMLIB)-$(PLAT)-$(BLACSDBGLVL)
SYSINC = -I$(MPIINCdir)
INTFACE = -DAdd_
SENDIS =
BUF =
TRANSCOMM =
WHATMPI =
SYSERRORS =
DEBUGLVL = -DBlacsDebugLvl=$(BLACSDBGLVL)
DEFS1 = -DSYSINC $(SYSINC) $(INTFACE) $(DEFBSTOP) $(DEFCOMBTOP) $(DEBUGLVL)
BLACSDEFS = $(DEFS1) $(SENDIS) $(BUFF) $(TRANSCOMM) $(WHATMPI) $(SYSERRORS)

F77          = /home1/zh/soft/openmpi-1.3-intel/bin/mpif77
F77NO_OPTFLAGS =  -mp
F77FLAGS    = $(F77NO_OPTFLAGS) -O3
F77LOADER    = $(F77)
F77LOADFLAGS =
CC          = /home1/zh/soft/openmpi-1.3-intel/bin/mpicc
CCFLAGS       = -O3
CCLOADER    = $(F77)
CCLOADFLAGS =  -nofor_main
ARCH    = ar
ARCHFLAGS = r
RANLIB = /usr/bin/ranlib
-----
make mpi
将编译得到LIB目录里面的blacs.a  blacsC.a  blacsF77.a放到了/home1/zh/soft/scalapack-intel/lib

3、SCALAPACK的SLmake.inc
SHELL       = /bin/sh

home       = /home1/zh/soft/scalapack-intel/scalapack-1.8.0

PLAT       = LINUX

USEMPI       = -DUsingMpiBlacs

SMPLIB       =
BLACSFINIT = /home1/zh/soft/scalapack-intel/lib/blacsF77.a
BLACSCINIT = /home1/zh/soft/scalapack-intel/lib/blacsC.a
BLACSLIB    = /home1/zh/soft/scalapack-intel/lib/blacs.a
TESTINGdir = $(home)/TESTING

CBLACSLIB    = $(BLACSCINIT) $(BLACSLIB) $(BLACSCINIT)
FBLACSLIB    = $(BLACSFINIT) $(BLACSLIB) $(BLACSFINIT)

PBLASdir    = $(home)/PBLAS
SRCdir       = $(home)/SRC
TESTdir    = $(home)/TESTING
PBLASTSTdir = $(TESTINGdir)
TOOLSdir    = $(home)/TOOLS
REDISTdir    = $(home)/REDIST
REDISTTSTdir  = $(TESTINGdir)

F77          = /home1/zh/soft/openmpi-1.3-intel/bin/mpif77
CC          = /home1/zh/soft/openmpi-1.3-intel/bin/mpicc
NOOPT       =
F77FLAGS    =  $(NOOPT) -O3
CCFLAGS    = -O3
SRCFLAG    =
F77LOADER    = $(F77)
CCLOADER    = $(F77)
F77LOADFLAGS  =
CCLOADFLAGS =  -nofor_main

CDEFS       = -DNO_IEEE $(USEMPI) -DAdd_

ARCH       = ar
ARCHFLAGS    = cr
RANLIB       = /usr/bin/ranlib

SCALAPACKLIB  = $(home)/libscalapack.a
BLASLIB    = /home1/zh/soft/scalapack-intel/lib/librefblas.a
LAPACKLIB    = /home1/zh/soft/scalapack-intel/lib/libreflapack.a

PBLIBS       = $(SCALAPACKLIB) $(FBLACSLIB) $(LAPACKLIB) $(BLASLIB) $(SMPLIB)
PRLIBS       = $(SCALAPACKLIB) $(CBLACSLIB) $(SMPLIB)
RLIBS       = $(SCALAPACKLIB) $(FBLACSLIB) $(CBLACSLIB) $(LAPACKLIB) $(BLASLIB) $(SMPLIB)
LIBS       = $(PBLIBS)

--------
make
将编译得到的libscalapack.a放到/home1/zh/soft/scalapack-intel/lib

再一次说明：根据自己的mpif90, mpicc, mpif77所放的位置，以及scalapack suite所放的位置，自行进行调整。