应《网络安全法》要求，自2017年10月1日起，未进行实名认证将不得使用互联网跟帖服务。为保障您的帐号能够正常使用，请尽快对帐号进行手机号验证，感谢您的理解与支持！

24小时热门版块排行榜    

CyRhmU.jpeg
小木虫论坛-学术科研互动平台 » 计算模拟区 » 第一性原理 » Vasp&MedeA » 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？
191/2返回列表12下一页
查看: 2385  |  回复: 18
只看楼主@他人 存档 新回复提醒 (忽略) 收藏    在APP中查看

c03185

新虫 (小有名气)

[求助] 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？

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？
如果用sudo命令，提示没有权限。怎样才能在自己的账户路径下安装VASP？
回复此楼

» 猜你喜欢

» 本主题相关价值贴推荐，对您同样有帮助:
1楼2012-04-12 17:06:11
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

ahu1221

金虫 (小有名气)

【答案】应助回帖

★
感谢参与，应助指数 +1
liliangfang: 金币+1, 谢谢交流 2012-04-13 08:36:42
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。
赞一下 回复此楼
交流学习,求进步
2楼2012-04-12 17:22:48
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

c03185

新虫 (小有名气)
引用回帖:
2楼: Originally posted by 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？
赞一下 回复此楼
3楼2012-04-12 17:31:51
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

ahu1221

金虫 (小有名气)

【答案】应助回帖

★ ★
liliangfang: 金币+2, 多谢指教 2012-04-13 08:36:52
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
赞一下 回复此楼
交流学习,求进步
4楼2012-04-12 21:24:12
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

c03185

新虫 (小有名气)
引用回帖:
4楼: Originally posted by 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
赞一下 回复此楼
5楼2012-04-13 04:22:40
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

c03185

新虫 (小有名气)
引用回帖:
4楼: Originally posted by 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？
赞一下 回复此楼
6楼2012-04-13 05:39:55
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

c03185

新虫 (小有名气)
引用回帖:
4楼: Originally posted by 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 <$*.F | /usr/bin/cpp -P -C -traditional >$*$(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)
赞一下 回复此楼
7楼2012-04-13 07:44:55
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

wzbhit

至尊木虫 (著名写手)
★
liliangfang: 金币+1, 谢谢交流 2012-04-13 08:37:17
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

[ 发自手机版 http://muchong.com/3g ]
赞一下 回复此楼
从明天开始坚持吃早饭呀！
8楼2012-04-13 07:50:55
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

c03185

新虫 (小有名气)
引用回帖:
8楼: Originally posted by wzbhit at 2012-04-13 07:50:55:
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 ...

库和编译器的路径，以及Makefile文件在楼上已经贴出了。

makefile中，是用的atlas数学库。而超算上是intel_mkl。

能不能帮我看以下该如何修改阿？
赞一下 回复此楼
9楼2012-04-13 07:55:09
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

ahu1221

金虫 (小有名气)

【答案】应助回帖

★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
c03185: 金币+10, ★★★很有帮助 2012-04-14 17:24:42
liliangfang: 金币+2, 多谢分享 2012-04-15 08:22:12
引用回帖:
7楼: Originally posted by c03185 at 2012-04-13 07:44:55:
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            ...

那个你在你的用户下面可以直接vi .bashrc就可以编译环境变量的，环境变量是可以修改，管理员不会去限制你的。要把mpi.mkl.intel这些库的路径加上，然后makefile的修改可以参考http://www.mdbbs.org/thread-3558-1-1.html
赞一下 回复此楼
交流学习,求进步
10楼2012-04-13 09:18:59
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖
相关版块跳转 我要订阅楼主 c03185 的主题更新
191/2返回列表12下一页
普通表情 龙 兔 虎 猫
信息提示
关闭
请填处理意见
关闭