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c03185新蟲 (小有名氣)
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[求助]
關(guān)于超級計算機的安裝權(quán)限問題：不能用sudo命令，該如何是好？
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關(guān)于超級計算機的安裝權(quán)限問題：不能用sudo命令，該如何是好？ 如果用sudo命令，提示沒有權(quán)限。怎樣才能在自己的賬戶路徑下安裝VASP？ |
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ahu1221
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2樓2012-04-12 17:22:48
c03185
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3樓2012-04-12 17:31:51
ahu1221
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【答案】應(yīng)助回帖
★ ★
liliangfang: 金幣+2, 多謝指教 2012-04-13 08:36:52
liliangfang: 金幣+2, 多謝指教 2012-04-13 08:36:52
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安裝fortran編譯器是需要管理員權(quán)限的，我相信你們超算那邊會有這種編譯器的，如果沒有你可以下載好后找到他，然后讓他幫你安裝，我們這邊裝的intel fortran是放在opt里面的，好像默認也是在這個文件夾里面的。如果你們超算還裝了intel的mpi就更好了，你可以直接設(shè)置你的環(huán)境變量，然后進行vasp的編譯，如果沒有intel的mpi，你可以自己下載opmpi進行配置安裝到/opt里面。然后修改環(huán)境變量，進行vasp編譯�？梢赃@樣修改環(huán)境變量，以我剛剛說的安裝軟件的位子為例vi .bashrc然后 export PATH=$PATH:/opt/openmpi/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/mkl/lib/em64:/opt/openmpi/lib 然后就可以修改vasp的makefile，就可以編譯了 |
4樓2012-04-12 21:24:12
c03185
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5樓2012-04-13 04:22:40
c03185
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6樓2012-04-13 05:39:55
c03185
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安裝的一些編譯器的名稱和路徑： intel_compiler/11.0.081 /apps/Bern/intel/Compiler/11.0/081 intel_mkl/10.2.5.035 /apps/Bern/intel/mkl/10.2.5.035 intel_mpi/4.0.0.028 /apps/Bern/intel/impi/4.0.0.028 集群上沒有安裝atlas。只有intel_mkl。 請問Makefile該如何修改。非常感謝謝阿�。。。�！ Makefile如下： .SUFFIXES: .inc .f .f90 .F #----------------------------------------------------------------------- # Makefile for Portland Group F90/HPF compiler release 3.0-1, 3.1 # and release 1.7 # (http://www.pgroup.com/ & ftp://ftp.pgroup.com/x86/, you need # to order the HPF/F90 suite) # we have found no noticable performance differences between # any of the releases, even Athlon or PIII optimisation does # not seem to improve performance # # The makefile was tested only under Linux on Intel platforms # (Suse X,X) # # it might be required to change some of library pathes, since # LINUX installation vary a lot # Hence check ***ALL**** options in this makefile very carefully #----------------------------------------------------------------------- # # Mind that some Linux distributions (Suse 6.1) have a bug in # libm causing small errors in the error-function (total energy # is therefore wrong by about 1meV/atom). The recommended # solution is to update libc. # # BLAS must be installed on the machine # there are several options: # 1) very slow but works: # retrieve the lapackage from ftp.netlib.org # and compile the blas routines (BLAS/SRC directory) # please use g77 or f77 for the compilation. When I tried to # use pgf77 or pgf90 for BLAS, VASP hang up when calling # ZHEEV (however this was with lapack 1.1 now I use lapack 2.0) # 2) most desirable: get an optimized BLAS # for a list of optimized BLAS try # http://www.kachinatech.com/~hjjou/scilib/opt_blas.html # # the two most reliable packages around are presently: # 3a) Intels own optimised BLAS (PIII, P4, Itanium) # http://developer.intel.com/software/products/mkl/ # this is really excellent when you use Intel CPU's # # 3b) or obtain the atlas based BLAS routines # http://math-atlas.sourceforge.net/ # you certainly need atlas on the Athlon, since the mkl # routines are not optimal on the Athlon. # #----------------------------------------------------------------------- # all CPP processed fortran files have the extension .f SUFFIX=.f #----------------------------------------------------------------------- # fortran compiler and linker #----------------------------------------------------------------------- FC=pgf90 # fortran linker FCL=$(FC) #----------------------------------------------------------------------- # whereis CPP ?? (I need CPP, can't use gcc with proper options) # that's the location of gcc for SUSE 5.3 # # CPP_ = /usr/lib/gcc-lib/i486-linux/2.7.2/cpp -P -C # # that's probably the right line for some Red Hat distribution: # # CPP_ = /usr/lib/gcc-lib/i386-redhat-linux/2.7.2.3/cpp -P -C # # SUSE 6.X, maybe some Red Hat distributions: CPP_ = ./preprocess <$*.F | /usr/bin/cpp -P -C -traditional >$*$(SUFFIX) #----------------------------------------------------------------------- # possible options for CPP: # possible options for CPP: # NGXhalf charge density reduced in X direction # wNGXhalf gamma point only reduced in X direction # avoidalloc avoid ALLOCATE if possible # IFC work around some IFC bugs # CACHE_SIZE 1000 for PII,PIII, 5000 for Athlon, 8000 P4 # RPROMU_DGEMV use DGEMV instead of DGEMM in RPRO (usually faster) # RACCMU_DGEMV use DGEMV instead of DGEMM in RACC (faster on P4) # **** definitely use -DRACCMU_DGEMV if you use the mkl library #----------------------------------------------------------------------- CPP = $(CPP_) -DHOST=\"LinuxPgi\" \ -Dkind8 -DNGXhalf -DCACHE_SIZE=2000 -DPGF90 -Davoidalloc \ -DRPROMU_DGEMV #----------------------------------------------------------------------- # general fortran flags (there must a trailing blank on this line) # the -Mx,119,0x200000 is required if you use older pgf90 versions # on a more recent LINUX installation # the option will not do any harm on other 3.X pgf90 distributions #----------------------------------------------------------------------- FFLAGS = -Mfree -Mx,119,0x200000 #----------------------------------------------------------------------- # optimization, # we have tested whether higher optimisation improves # the performance, and found no improvements with -O3-5 or -fast # (even on Athlon system, Athlon specific optimistation worsens performance) #----------------------------------------------------------------------- OFLAG = -O2 -tp p6 OFLAG_HIGH = $(OFLAG) OBJ_HIGH = OBJ_NOOPT = DEBUG = -g -O0 INLINE = $(OFLAG) #----------------------------------------------------------------------- # the following lines specify the position of BLAS and LAPACK # what you chose is very system dependent # P4: VASP works fastest with Intels mkl performance library # Athlon: Atlas based BLAS are presently the fastest # P3: no clue #----------------------------------------------------------------------- # Atlas based libraries ATLASHOME= $(HOME)/archives/BLAS_OPT/ATLAS/lib/Linux_ATHLONXP_SSE1/ BLAS= -L$(ATLASHOME) -lf77blas -latlas # use specific libraries (default library path points to other libraries) #BLAS= $(ATLASHOME)/libf77blas.a $(ATLASHOME)/libatlas.a # use the mkl Intel libraries for p4 (www.intel.com) #BLAS=-L/opt/intel/mkl/lib/32 -lmkl_p4 -lpthread # LAPACK, simplest use vasp.4.lib/lapack_double #LAPACK= ../vasp.4.lib/lapack_double.o # use atlas optimized part of lapack LAPACK= ../vasp.4.lib/lapack_atlas.o -llapack -lcblas # use the mkl Intel lapack #LAPACK= -lmkl_lapack #----------------------------------------------------------------------- LIB = -L../vasp.4.lib -ldmy \ ../vasp.4.lib/linpack_double.o $(LAPACK) \ $(BLAS) # options for linking (none required) LINK = #----------------------------------------------------------------------- # fft libraries: # VASP.4.5 can use FFTW (http://www.fftw.org) # since the FFTW is very slow for radices 2^n the fft3dlib is used # in these cases # if you use fftw3d you need to insert -lfftw in the LIB line as well # please do not send us any querries reltated to FFTW (no support) # if it fails, use fft3dlib #----------------------------------------------------------------------- FFT3D = fft3dfurth.o fft3dlib.o #FFT3D = fftw3d+furth.o fft3dlib.o #======================================================================= # MPI section, uncomment the following lines # # one comment for users of mpich or lam: # You must *not* compile mpi with g77/f77, because f77/g77 # appends *two* underscores to symbols that contain already an # underscore (i.e. MPI_SEND becomes mpi_send__). The pgf90 # compiler however appends only one underscore. # Precompiled mpi version will also not work !!! # # We found that mpich.1.2.1 and lam-6.5.X are stable # mpich.1.2.1 was configured with # ./configure -prefix=/usr/local/mpich_nodvdbg -fc="pgf77 -Mx,119,0x200000" \ # -f90="pgf90 -Mx,119,0x200000" \ # --without-romio --without-mpe -opt=-O \ # # lam was configured with the line # ./configure -prefix /usr/local/lam-6.5.X --with-cflags=-O -with-fc=pgf90 \ # --with-f77flags=-O --without-romio # # lam was generally faster and we found an average communication # band with of roughly 160 MBit/s (full duplex) # # please note that you might be able to use a lam or mpich version # compiled with f77/g77, but then you need to add the following # options: -Msecond_underscore (compilation) and -g77libs (linking) # # !!! Please do not send me any queries on how to install MPI, I will # certainly not answer them !!!! #======================================================================= #----------------------------------------------------------------------- # fortran linker for mpi: if you use LAM and compiled it with the options # suggested above, you can use the following lines #----------------------------------------------------------------------- #FC=mpif77 #FCL=$(FC) #----------------------------------------------------------------------- # additional options for CPP in parallel version (see also above): # NGZhalf charge density reduced in Z direction # wNGZhalf gamma point only reduced in Z direction # scaLAPACK use scaLAPACK (usually slower on 100 Mbit Net) #----------------------------------------------------------------------- #CPP = $(CPP_) -DMPI -DHOST=\"LinuxPgi\" \ # -Dkind8 -DNGZhalf -DCACHE_SIZE=2000 -DPGF90 -Davoidalloc -DRPROMU_DGEMV #----------------------------------------------------------------------- # location of SCALAPACK # if you do not use SCALAPACK simply uncomment the line SCA #----------------------------------------------------------------------- BLACS=/usr/local/BLACS_lam SCA_= /usr/local/SCALAPACK_lam SCA= $(SCA_)/scalapack_LINUX.a $(SCA_)/pblas_LINUX.a $(SCA_)/tools_LINUX.a \ $(BLACS)/LIB/blacsF77init_MPI-LINUX-0.a $(BLACS)/LIB/blacs_MPI-LINUX-0.a $(BLACS)/LIB/blacsF77init_MPI-LINUX-0.a SCA= #----------------------------------------------------------------------- # libraries for mpi #----------------------------------------------------------------------- #LIB = -L../vasp.4.lib -ldmy \ # ../vasp.4.lib/linpack_double.o $(LAPACK) \ # $(SCA) $(BLAS) # FFT: only option fftmpi.o with fft3dlib of Juergen Furthmueller #FFT3D = fftmpi.o fftmpi_map.o fft3dlib.o #----------------------------------------------------------------------- # general rules and compile lines #----------------------------------------------------------------------- BASIC= symmetry.o symlib.o lattlib.o random.o SOURCE= base.o mpi.o smart_allocate.o xml.o \ constant.o jacobi.o main_mpi.o scala.o \ asa.o lattice.o poscar.o ini.o setex.o radial.o \ pseudo.o mgrid.o mkpoints.o wave.o wave_mpi.o $(BASIC) \ nonl.o nonlr.o dfast.o choleski2.o \ mix.o charge.o xcgrad.o xcspin.o potex1.o potex2.o \ metagga.o constrmag.o pot.o cl_shift.o force.o dos.o elf.o \ tet.o hamil.o steep.o \ chain.o dyna.o relativistic.o LDApU.o sphpro.o paw.o us.o \ ebs.o wavpre.o wavpre_noio.o broyden.o \ dynbr.o rmm-diis.o reader.o writer.o tutor.o xml_writer.o \ brent.o stufak.o fileio.o opergrid.o stepver.o \ dipol.o xclib.o chgloc.o subrot.o optreal.o davidson.o \ edtest.o electron.o shm.o pardens.o paircorrection.o \ optics.o constr_cell_relax.o stm.o finite_diff.o \ elpol.o setlocalpp.o INC= vasp: $(SOURCE) $(FFT3D) $(INC) main.o rm -f vasp $(FCL) -o vasp $(LINK) main.o $(SOURCE) $(FFT3D) $(LIB) makeparam: $(SOURCE) $(FFT3D) makeparam.o main.F $(INC) $(FCL) -o makeparam $(LINK) makeparam.o $(SOURCE) $(FFT3D) $(LIB) zgemmtest: zgemmtest.o base.o random.o $(INC) $(FCL) -o zgemmtest $(LINK) zgemmtest.o random.o base.o $(LIB) dgemmtest: dgemmtest.o base.o random.o $(INC) $(FCL) -o dgemmtest $(LINK) dgemmtest.o random.o base.o $(LIB) ffttest: base.o smart_allocate.o mpi.o mgrid.o random.o ffttest.o $(FFT3D) $(INC) $(FCL) -o ffttest $(LINK) ffttest.o mpi.o mgrid.o random.o smart_allocate.o base.o $(FFT3D) $(LIB) kpoints: $(SOURCE) $(FFT3D) makekpoints.o main.F $(INC) $(FCL) -o kpoints $(LINK) makekpoints.o $(SOURCE) $(FFT3D) $(LIB) clean: -rm -f *.g *.f *.o *.L *.mod ; touch *.F main.o: main$(SUFFIX) $(FC) $(FFLAGS)$(DEBUG) $(INCS) -c main$(SUFFIX) xcgrad.o: xcgrad$(SUFFIX) $(FC) $(FFLAGS) $(INLINE) $(INCS) -c xcgrad$(SUFFIX) xcspin.o: xcspin$(SUFFIX) $(FC) $(FFLAGS) $(INLINE) $(INCS) -c xcspin$(SUFFIX) makeparam.o: makeparam$(SUFFIX) $(FC) $(FFLAGS)$(DEBUG) $(INCS) -c makeparam$(SUFFIX) makeparam$(SUFFIX): makeparam.F main.F # # MIND: I do not have a full dependency list for the include # and MODULES: here are only the minimal basic dependencies # if one strucuture is changed then touch_dep must be called # with the corresponding name of the structure # base.o: base.inc base.F mgrid.o: mgrid.inc mgrid.F constant.o: constant.inc constant.F lattice.o: lattice.inc lattice.F setex.o: setexm.inc setex.F pseudo.o: pseudo.inc pseudo.F poscar.o: poscar.inc poscar.F mkpoints.o: mkpoints.inc mkpoints.F wave.o: wave.inc wave.F nonl.o: nonl.inc nonl.F nonlr.o: nonlr.inc nonlr.F $(OBJ_HIGH): $(CPP) $(FC) $(FFLAGS) $(OFLAG_HIGH) $(INCS) -c $*$(SUFFIX) $(OBJ_NOOPT): $(CPP) $(FC) $(FFLAGS) $(INCS) -c $*$(SUFFIX) fft3dlib_f77.o: fft3dlib_f77.F $(CPP) $(F77) $(FFLAGS_F77) -c $*$(SUFFIX) .F.o: $(CPP) $(FC) $(FFLAGS) $(OFLAG) $(INCS) -c $*$(SUFFIX) .F$(SUFFIX): $(CPP) $(SUFFIX).o: $(FC) $(FFLAGS) $(OFLAG) $(INCS) -c $*$(SUFFIX) #----------------------------------------------------------------------- # these special rules are cummulative (that is once failed # in one compiler version, stays in the list forever) # -tpp5|6|7 P, PII-PIII, PIV # -xW use SIMD (does not pay of on PII, since fft3d uses double prec) # all other options do no affect the code performance since -O1 is used #----------------------------------------------------------------------- xcgrad.o : xcgrad.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX) |
7樓2012-04-13 07:44:55
wzbhit
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8樓2012-04-13 07:50:55
c03185
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9樓2012-04-13 07:55:09
ahu1221
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【答案】應(yīng)助回帖
★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
c03185: 金幣+10, ★★★很有幫助 2012-04-14 17:24:42
liliangfang: 金幣+2, 多謝分享 2012-04-15 08:22:12
c03185: 金幣+10, ★★★很有幫助 2012-04-14 17:24:42
liliangfang: 金幣+2, 多謝分享 2012-04-15 08:22:12
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那個你在你的用戶下面可以直接vi .bashrc就可以編譯環(huán)境變量的，環(huán)境變量是可以修改，管理員不會去限制你的。要把mpi.mkl.intel這些庫的路徑加上，然后makefile的修改可以參考http://www.mdbbs.org/thread-3558-1-1.html |
10樓2012-04-13 09:18:59
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| 最具人氣熱帖推薦 [查看全部] | 作者 | 回/看 | 最后發(fā)表 | |
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[考研] 281求調(diào)劑（0805） +3 | 煙汐憶海 2026-03-16 | 8/400 |
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[考研] 303求調(diào)劑 +3 | 睿08 2026-03-17 | 5/250 |
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[考研] 341求調(diào)劑 +5 | 搗蛋豬豬 2026-03-11 | 7/350 |
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[考研] 302求調(diào)劑 +9 | 負心者當(dāng)誅 2026-03-11 | 9/450 |
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[考研] 312求調(diào)劑 +4 | 陌宸希 2026-03-16 | 5/250 |
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[考研] 332求調(diào)劑 +6 | Zz版 2026-03-13 | 6/300 |
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[考研] 一志愿蘇州大學(xué)材料工程（085601）專碩有科研經(jīng)歷三項國獎兩個實用型專利一項省級立項 +6 | 大火山小火山 2026-03-16 | 8/400 |
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[考研] 267一志愿南京工業(yè)大學(xué)0817化工求調(diào)劑 +6 | SUICHILD 2026-03-12 | 6/300 |
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[考研] 070300化學(xué)學(xué)碩求調(diào)劑 +6 | 太想進步了0608 2026-03-16 | 6/300 |
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[考研] 0856求調(diào)劑 +3 | 劉夢微 2026-03-15 | 3/150 |
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[考研] 0856專碩279求調(diào)劑 +5 | 加油加油！? 2026-03-15 | 5/250 |
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[考研] 中科大材料與化工319求調(diào)劑 +3 | 孟鑫材料 2026-03-14 | 3/150 |
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[考研] 復(fù)試調(diào)劑 +4 | z1z2z3879 2026-03-14 | 5/250 |
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[考研] 一志愿中科院，化學(xué)方向，295求調(diào)劑 +4 | 一氧二氮 2026-03-11 | 4/200 |
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[考研] 材料工程調(diào)劑 +9 | 咪咪空空 2026-03-12 | 9/450 |
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[考研] 281求調(diào)劑 +9 | Koxui 2026-03-12 | 11/550 |
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[考研] 【考研調(diào)劑求收留】 +3 | Ceciilia 2026-03-11 | 3/150 |
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[考研] 材料專碩350 求調(diào)劑 +4 | 王金科 2026-03-12 | 4/200 |
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[考研] 314求調(diào)劑 +7 | 無懈可擊的巨人 2026-03-12 | 7/350 |
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[考博] 2026年博士申請 +3 | QwQwQW10 2026-03-11 | 3/150 |
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