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[交流] 【求助】siesta進(jìn)行ordern計(jì)算出錯(cuò)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樓 2011-04-14 14:31:47

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guohuazhong

至尊木蟲 (職業(yè)作家)

漂浮的萸(金幣+1): 就是用ifort11.1編譯的 2011-04-14 18:07:45
zzy870720z: 謝謝提示 2011-04-14 20:35:31

感覺是編譯的問題，建議用ifort10.1和MKL10.1來編譯，用ifort11.1編譯的話可能會(huì)碰到這種問題。

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3樓2011-04-14 16:54:16

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guohuazhong

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★
zzy870720z(金幣+1): 謝謝補(bǔ)充 2011-04-14 20:35:48

實(shí)在要用ifort11.1來編譯的話，可以按照siesta官方網(wǎng)站提供的解決辦法來編譯，我的就是按他的方法成功編譯的，并行運(yùn)算沒有問題，你可以參考一下。

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樓2011-04-14 18:36:58

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★
zzy870720z(金幣+1): 謝謝補(bǔ)充 2011-04-14 20:36:00
漂浮的萸(金幣+1): 我們就是這么編譯的，我想找找看有沒有用這個(gè)算的朋友，加下qq討論，本人qq515919818 2011-04-15 09:52:45

一）如果你堅(jiān)持要用intel ifort 11來進(jìn)行編譯。可以采取如下方式（siesta網(wǎng)站主頁上的方法，見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文件夾中的makefile文件修改第148-153行，將這幾行寫成如下形式
$(FoX_configured):
(cd FoX; touch arch.make ; \
      CONFIGURE="$(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 ; \這一行前是一個(gè)Tab空格，而不是一個(gè)space空格
將這兩個(gè)地方修改好后，
make clen
make
之后生成的siesta可執(zhí)行文件并行計(jì)算不會(huì)出現(xiàn)問題。但要注意的是，arch.make文件中的優(yōu)化級(jí)別是FFLAGS=-g -O2或FFLAGS=-g -O1或FFLAGS=-g -O0，不能是FFLAGS=-g -O3，我試了一下FFLAGS=-g -O3，發(fā)現(xiàn)計(jì)算過程中出現(xiàn)下面的錯(cuò)誤
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
當(dāng)改用FFLAGS=-g -O2和FFLAGS=-g -O0或FFLAGS=-g -O1之后則沒用出現(xiàn)類似的錯(cuò)誤提示，具體原因我就沒去深究了。當(dāng)然不同的優(yōu)化級(jí)別在計(jì)算時(shí)間上會(huì)有一些差異。
比如用FFLAGS=-g -O2時(shí)，運(yùn)行時(shí)間如下（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
當(dāng)改用FFLAGS=-g -O0時(shí)，運(yùn)行時(shí)間如下（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編譯器，而是使用ifort10或以下的版本，建議配合使用openmpi來進(jìn)行并行計(jì)算。
1）安裝openmpi，詳細(xì)步驟不說了，只是在configure的時(shí)候我使用的是如下的命令：
./configure --prefix=要安裝的目錄 F77=ifort FC=ifort FCFLAGS=-em64t FFLAGS=-em64t
FCFLAGS和FFLAGS是告訴編譯器用的是64位的編譯器，如果機(jī)器不是64位的就不用了。
make
make install
安裝完成后還得添加環(huán)境變量，至于怎么添加，網(wǎng)上很多，搜索一下就知道了。
2）編譯siesta
步驟就寫了，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)  $<

編譯成功，祝好運(yùn)！

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5樓2011-04-14 18:49:22

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