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mengfc金虫 (正式写手)
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[求助]
siesta-3.1并行编译出错。
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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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guohuazhong
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2楼2011-10-16 09:41:06
zhangguangping
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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
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
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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) $< --------------------------------- |
3楼2011-10-16 09:41:42
mengfc
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4楼2011-10-16 10:04:05
mengfc
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5楼2011-10-16 15:13:57
mengfc
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6楼2011-10-16 15:15:51
randome
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7楼2011-10-16 19:05:12
randome
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贺仪(金币+2): 多谢指教！ 2011-10-26 22:02:15
mengfc: 金币+5, ★★★很有帮助, 谢谢您 2012-03-25 16:36:37
贺仪(金币+2): 多谢指教！ 2011-10-26 22:02:15
mengfc: 金币+5, ★★★很有帮助, 谢谢您 2012-03-25 16:36:37
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呃。。。当时看错了，具体这样 1. cd obj 2. ../Src/obj_setup.sh 3. ../Src/configure (../Src/configure --help可以看到很多在编译时需要设置的量，当然很多可以用默认的。如果你想编译并行的，可以这样 ../Src/configure MPIFC=mpif90 --enable-mpi) 4. 在3步生成的 arch.make 文件中根据你系统情况进行相应数学库链接的设置 5. make （在当前目录下） |
8楼2011-10-26 19:30:53