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mengfc

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[求助] siesta-3.1并行编译出错。

根据版主贺仪在 http://muchong.com/bbs/viewthread.php?tid=3010970 中第一种方法进行编译。
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.解压文件：$ tar -zxvf
siesta-3.0-rc2.tgz
3.进入要生成执行文件的目录，可以自己随便建立。这样可以利用不同参数编译
不同版本的siesta 放在不同的目录里。这是与siesta-2.0.2 相比，采用的一种新的
执行文件生成机制，例如到Obj 目录生成执行文件：$ cd siesta-3.0-rc2/Obj/
4. 如果Obj 目录和Src 目录是平级的，运行：$ sh ../Src/obj_setup.sh
总之要在你要生成可执行文件的目录下用sh 运行Src/obj_setup.sh。
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

在最后一步make的时候出现如下错误。
ifort: error #10236: File not found:  'libmpi_f90.a'
make: *** [siesta] Error 1

这个libmpi_f90.a在第8步make的时候生成了。我就把它放在了/Obj目录下（我不知道这样做对不对，应该放在哪里？），然后重新编译，又出现如下错误。

/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:246: undefined reference to `blacs_get_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:247: undefined reference to `blacs_gridinit_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:255: undefined reference to `blacs_get_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:256: undefined reference to `blacs_gridinit_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:258: undefined reference to `blacs_gridinfo_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:264: undefined reference to `descinit_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:273: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:274: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:277: undefined reference to `descinit_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:333: undefined reference to `blacs_gridinfo_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:334: undefined reference to `indxg2p_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:335: undefined reference to `indxg2p_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:337: undefined reference to `blacs_gridinfo_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:338: undefined reference to `indxg2p_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:339: undefined reference to `indxg2p_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:343: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:344: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:345: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:346: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:359: undefined reference to `pjlaenv_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:361: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:370: undefined reference to `iceil_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:412: undefined reference to `pzgemr2d_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:413: undefined reference to `pzgemr2d_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:434: undefined reference to `pzhegvx_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:438: undefined reference to `pzgemr2d_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:440: undefined reference to `pzhegvx_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:491: undefined reference to `pzpotrf_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:493: undefined reference to `pzpotrf_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:511: undefined reference to `pzhengst_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:514: undefined reference to `pzhengst_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:535: undefined reference to `pzhemm_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:537: undefined reference to `pzgemm_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:540: undefined reference to `pzhemm_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:542: undefined reference to `pzgemm_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:566: undefined reference to `pzheevd_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:570: undefined reference to `pzheevd_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:576: undefined reference to `pzheevx_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:581: undefined reference to `pzheevx_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:636: undefined reference to `pzgemm_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:640: undefined reference to `pzgemm_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:674: undefined reference to `pztrsm_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:676: undefined reference to `pzgemr2d_'
/home/mengfc/Siesta/siesta-3.1/Src/cdiag.F:678: undefined reference to `pztrsm_'
rdiag.o: In function `rdiag':
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:228: undefined reference to `blacs_get_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:229: undefined reference to `blacs_gridinit_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:237: undefined reference to `blacs_get_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:238: undefined reference to `blacs_gridinit_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:240: undefined reference to `blacs_gridinfo_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:246: undefined reference to `descinit_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:255: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:256: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:259: undefined reference to `descinit_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:306: undefined reference to `blacs_gridinfo_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:308: undefined reference to `blacs_gridinfo_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:311: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:312: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:316: undefined reference to `indxg2p_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:317: undefined reference to `indxg2p_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:318: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:319: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:327: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:328: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:331: undefined reference to `iceil_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:332: undefined reference to `pjlaenv_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:334: undefined reference to `numroc_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:365: undefined reference to `pdgemr2d_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:366: undefined reference to `pdgemr2d_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:388: undefined reference to `pdsygvx_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:392: undefined reference to `pdgemr2d_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:394: undefined reference to `pdsygvx_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:446: undefined reference to `pdpotrf_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:448: undefined reference to `pdpotrf_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:466: undefined reference to `pdsyngst_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:469: undefined reference to `pdsyngst_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:490: undefined reference to `pdsymm_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:492: undefined reference to `pdgemm_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:495: undefined reference to `pdsymm_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:497: undefined reference to `pdgemm_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:521: undefined reference to `pdsyevd_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:524: undefined reference to `pdsyevd_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:530: undefined reference to `pdsyevx_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:535: undefined reference to `pdsyevx_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:590: undefined reference to `pdgemm_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:594: undefined reference to `pdgemm_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:627: undefined reference to `pdtrsm_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:629: undefined reference to `pdgemr2d_'
/home/mengfc/Siesta/siesta-3.1/Src/rdiag.F:631: undefined reference to `pdtrsm_'
make: *** [siesta] Error 1

请问这是什么问题呢？是libmpi_f90.a放置的位置影响的吗？

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1楼 2011-10-15 21:00:48

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mengfc

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引用回帖:

3楼: Originally posted by zhangguangping at 2011-10-16 09:41:42:
用下面我给出的这个make.arch去编译试试。另外不清楚你的mkl什么版本。
首先按照下面的内容修改你的make.arch,修改好之后将其放到Obj下面(假设你在Obj目录下编译)。
1. cd Obj
2. sh ../Src/obj_setup.sh
3. ...

这个方法我试过，但是没法并行计算。
mpirun -np可以用，但是仍旧只是用一个核。这是什么问题呢？

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4楼2011-10-16 10:04:05

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【答案】应助回帖

★ ★
mengfc(金币+5): 谢谢您，试一下 2011-10-16 10:01:36
zzy870720z: 金币+2, 补上奖励，辛苦了 2012-03-25 16:52:42

MPI_INTERFACE=/home/zhou/soft/siesta/siesta-3.0-rc2/Src/MPI/libmpi_f90.a
中直接写成MPI_INTERFACE=libmpi_f90.a
试试

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2楼2011-10-16 09:41:06

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★ ★ ★
mengfc(金币+5): 谢谢您！ 2011-10-16 10:02:47
zzy870720z: 金币+3, 谢谢指教，呵呵 2012-03-25 16:52:55

引用回帖:

1楼: Originally posted by mengfc at 2011-10-15 21:00:48:
根据版主贺仪在 http://muchong.com/bbs/viewthread.php?tid=3010970 中第一种方法进行编译。
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.解压文件：$ tar -zxv ...

用下面我给出的这个make.arch去编译试试。另外不清楚你的mkl什么版本。
首先按照下面的内容修改你的make.arch,修改好之后将其放到Obj下面(假设你在Obj目录下编译)。
1. cd Obj
2. sh ../Src/obj_setup.sh
3. make
就等着编译吧。

不要像你那么麻烦
---------------------------------
.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= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI  -DCDF  -DGRID_DP -DPHI_GRID_SP

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=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)  $<

---------------------------------

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3楼2011-10-16 09:41:42

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2楼: Originally posted by guohuazhong at 2011-10-16 09:41:06:
MPI_INTERFACE=/home/zhou/soft/siesta/siesta-3.0-rc2/Src/MPI/libmpi_f90.a
中直接写成MPI_INTERFACE=libmpi_f90.a
试试

这样就提示找不到libmpi_f90.a这个文件

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5楼2011-10-16 15:13:57

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