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小木虫论坛-学术科研互动平台 » 计算模拟区 » 第一性原理 » Siesta&Smeagol&Atk » 【求助】siesta进行ordern计算出错求助
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漂浮的萸

金虫 (小有名气)

[交流] 【求助】siesta进行ordern计算出错求助

Cells per Processor =        0        4
  Cells per Processor =        1        0
  Cells per Processor =        2        4
  Cells per Processor =        3        0
  Cells per Processor =        4        4
  Cells per Processor =        5        0
  Cells per Processor =        6        4
  Cells per Processor =        7        0
  Cells per Processor =        8        4
  Cells per Processor =        9        0
  Cells per Processor =       10        4
  Cells per Processor =       11        0
  Cells per Processor =       12        4
  Cells per Processor =       13        0
  Cells per Processor =       14        4
  Cells per Processor =       15        0
  Cells per Processor =       16        0
  Cells per Processor =       17        0
  Cells per Processor =       18        0
  Cells per Processor =       19        0
  Cells per Processor =       20        0
  Cells per Processor =       21        0
  Cells per Processor =       22        0
  Cells per Processor =       23        0

Warning: Bad load balancing: no cells allocated to node           1
Try specifying a number of nodes that is
an exact factor of the number of cells:          32
ERROR STOP from Node:    0
ERROR STOP from Node:    0
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 17012 on
node node1 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
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1楼 2011-04-14 14:31:47
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guohuazhong

至尊木虫 (职业作家)
漂浮的萸(金币+1): 就是用ifort11.1编译的 2011-04-14 18:07:45
zzy870720z: 谢谢提示 2011-04-14 20:35:31
感觉是编译的问题，建议用ifort10.1和MKL10.1来编译，用ifort11.1编译的话可能会碰到这种问题。
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3楼2011-04-14 16:54:16
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guohuazhong

至尊木虫 (职业作家)
★
zzy870720z(金币+1): 谢谢补充 2011-04-14 20:35:48
实在要用ifort11.1来编译的话，可以按照siesta官方网站提供的解决办法来编译，我的就是按他的方法成功编译的，并行运算没有问题，你可以参考一下。

The Intel V11 compiler seems to have trouble compiling some of the constructs in the FoX library. We are working on finding workarounds, but for now it might be necessary to deactivate the FoX library in the Siesta building process. To do so, insert the line

DUMMY_FOX= --enable-dummy

in your arch.make file, and recompile Siesta (i.e, "make clean; make".

Deactivating the FoX library has two consequences:

--  No SystemLabel.xml file is produced

--  No pdos.xml file is produced, but the old-style xml file
    SystemLabel.PDOS is still produced (by the stand-alone wxml library
    which is still part of the Siesta distribution). The information
    in this file should be the same as in pdos.xml.

NOTE: Depending on the patch-level of your compiler, you might be able to compile the FoX library turning off optimization. To do so, make sure that an appropriate line

FFLAGS_DEBUG= -g -O0    # whatever options you might need

appears in the arch.make file, and replace the following
section in the main Makefile:

$(FoX_configured):
    (cd FoX; touch arch.make ; \
         CONFIGURE="$(VPATH)/FoX/configure"; \
         $$CONFIGURE VPATH="$(VPATH)/FoX" \
         FC="$(FC_SERIAL)" FCFLAGS="$(FFLAGS)" \
         --enable-wcml $(DUMMY_FOX) || false )

by

$(FoX_configured):
    (cd FoX; touch arch.make ; \
         CONFIGURE="$(VPATH)/FoX/configure"; \
         $$CONFIGURE VPATH="$(VPATH)/FoX" \
         FC="$(FC_SERIAL)" FCFLAGS="$(FFLAGS_DEBUG)" \
         --enable-wcml $(DUMMY_FOX) || false )

NOTE: Make sure that the space before "(cd FoX  " is actually a TAB.
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4楼2011-04-14 18:36:58
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guohuazhong

至尊木虫 (职业作家)
★
zzy870720z(金币+1): 谢谢补充 2011-04-14 20:36:00
漂浮的萸(金币+1): 我们就是这么编译的，我想找找看有没有用这个算的朋友，加下qq讨论，本人qq515919818 2011-04-15 09:52:45
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http://www.icmab.es/siesta/）
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！
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5楼2011-04-14 18:49:22
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suyh2006302楼
2011-04-14 14:48   回复  
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