超级计算机管理员,关于超级计算机的安装权限问题：不能用sudo命令，该如何是好？ - 第一原理 - 小木虫 - 学术 科研 互动社区...

ahu1221

你和管理员联系啊，让他帮你设置下，还有安装vasp的时候一般管理员将intel的fortran编译器和hpmpi会安装在opt里面，你直接修改下你的环境变量，就可以在你的目录下惊醒vasp的编译了。

c03185

引用回帖:

ahu1221 at 2012-04-12 17:22:48:

你和管理员联系啊，让他帮你设置下，还有安装vasp的时候一般管理员将intel的fortran编译器和hpmpi会安装在opt里面，你直接修改下你的环境变量，就可以在你的目录下惊醒vasp的编译了。

请问能说的详细点吗？我刚开始学习，什么都不懂阿。。

怎么让管理员设置阿？我说sudo不能用，他回复是“your only allowed to install software in your home or data directory for which you don't need the sudo command. ”

intel的fortran编译器和hpmpi会安装在opt里面，该如何调用？

ahu1221

安装fortran编译器是需要管理员权限的，我相信你们超算那边会有这种编译器的，如果没有你可以下载好后找到他，然后让他帮你安装，我们这边装的intel fortran是放在opt里面的，好像默认也是在这个文件夹里面的。如果你们超算还装了intel的mpi就更好了，你可以直接设置你的环境变量，然后进行vasp的编译，如果没有intel的mpi，你可以自己下载opmpi进行配置安装到/opt里面。然后修改环境变量，进行vasp编译。可以这样修改环境变量，以我刚刚说的安装软件的位子为例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，就可以编译了

c03185

引用回帖:

ahu1221 at 2012-04-12 21:24:12:

安装fortran编译器是需要管理员权限的，我相信你们超算那边会有这种编译器的，如果没有你可以下载好后找到他，然后让他帮你安装，我们这边装的intel fortran是放在opt里面的，好像默认也是在这个文件夹里面的。如 ...

请问是在那个目录下编辑 vi .bashrc?

是在VASP目录下，还是集群的本地帐号目录下？

好像集群的本地帐号目录下的.bashrc是只读的

c03185

引用回帖:

ahu1221 at 2012-04-12 21:24:12:

安装fortran编译器是需要管理员权限的，我相信你们超算那边会有这种编译器的，如果没有你可以下载好后找到他，然后让他帮你安装，我们这边装的intel fortran是放在opt里面的，好像默认也是在这个文件夹里面的。如 ...

请问vasp的makefile怎么修改？还需要修改路径吗？

c03185

引用回帖:

ahu1221 at 2012-04-12 21:24:12:

安装fortran编译器是需要管理员权限的，我相信你们超算那边会有这种编译器的，如果没有你可以下载好后找到他，然后让他帮你安装，我们这边装的intel fortran是放在opt里面的，好像默认也是在这个文件夹里面的。如 ...

安装的一些编译器的名称和路径：

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

集群上没有安装atlas。只有intel_mkl。

请问Makefile该如何修改。非常感谢谢阿！！！！！

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 $*$(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)

，

wzbhit

超算上安装是最简单的了，因为编译vasp所需的相关软件的环境变量都是已经设置好的，你需要做的就是修改makefile文件，找到/opt下已安装的相关库的路径，修改到makefile文件，编译即可！

另外，vasp安装完全没必要root权限，获得超算root权限几乎不可能的