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漂浮的萸金蟲(chóng) (小有名氣)
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[交流]
【求助】siesta進(jìn)行ordern計(jì)算出錯(cuò)求助
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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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zzy870720z(金幣+1): 謝謝補(bǔ)充 2011-04-14 20:35:48
zzy870720z(金幣+1): 謝謝補(bǔ)充 2011-04-14 20:35:48
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實(shí)在要用ifort11.1來(lái)編譯的話，可以按照siesta官方網(wǎng)站提供的解決辦法來(lái)編譯，我的就是按他的方法成功編譯的，并行運(yùn)算沒(méi)有問(wèn)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. |
4樓2011-04-14 18:36:58
guohuazhong
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3樓2011-04-14 16:54:16
guohuazhong
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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(méi)有用這個(gè)算的朋友，加下qq討論，本人qq515919818 2011-04-15 09:52:45
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(méi)有用這個(gè)算的朋友，加下qq討論，本人qq515919818 2011-04-15 09:52:45
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一）如果你堅(jiān)持要用intel ifort 11來(lái)進(jìn)行編譯。可以采取如下方式（siesta網(wǎng)站主頁(yè)上的方法，見(jiàn)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(xiě)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(wèn)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(guò)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(méi)用出現(xiàn)類似的錯(cuò)誤提示，具體原因我就沒(méi)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(lái)進(jìn)行并行計(jì)算。 1）安裝openmpi，詳細(xì)步驟不說(shuō)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(xiě)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)！ |
5樓2011-04-14 18:49:22
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