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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 » help---------openmpi
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板桥霜

木虫 (正式写手)
引用回帖:
19楼: Originally posted by liqizuiyang at 2014-09-02 11:58:55
PLEASE DO EXACTLY as the instructions below.
In my case, this will build opempi successfuly with all the tests passed.

========================================================
1. Copy the source ...

1.
#mkdir /home/han/build/openmpi-1.6.4
#cd openmpi-1.6.4
#tar -xf /cluster/lab-host/forvasp/openmpi-1.6.4
2.
cd /home/han/build/openmpi-1.6.4
export CC=icc
export CXX=icpc
export FC=ifort
export F77=ifort
export CFLAGS=-O2
export CXXFLAGS=-O2
export FCFLAGS=-O2
export FFLAGS=-O2
4.
/.configure --prefix=/home/han/program/oepnmpi-1.6.4/
5.
make check
.....
.....
libtool: link: cannot find the library `../../ompi/libmpi.la' or unhandled argument `../../ompi/libmpi.la'
make[3]: *** [predefined_gap_test] Error 1
make[3]: Leaving directory `/home/han/build/openmpi-1.6.4/ompi/debuggers'
make[2]: *** [check-am] Error 2
make[2]: Leaving directory `/home/han/build/openmpi-1.6.4/ompi/debuggers'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/home/han/build/openmpi-1.6.4/ompi'
make: *** [check-recursive] Error 1
BTW, I'm the administrator of the cluster and I have the root previledges.

what should I do now?
thanks
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21楼2014-09-02 12:48:58
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liqizuiyang

木虫 (著名写手)
引用回帖:
21楼: Originally posted by 板桥霜 at 2014-09-02 12:48:58
1.
#mkdir /home/han/build/openmpi-1.6.4
#cd openmpi-1.6.4
#tar -xf /cluster/lab-host/forvasp/openmpi-1.6.4
2.
cd /home/han/build/openmpi-1.6.4
export CC=icc
export CXX=icpc
export FC=ifort
...

Note this:
==================================
2. Create a new directory named "build" under $HOME.
mkdir build

3. Go to build and set environmental variables.
cd build
===================================

The 'build' directory is a sub-directory of $HOME, not 'openmpi-1.6.4'. Both 'build' and 'openmpi-1.6.4' are sub-directories of $HOME.

Also, note this:
"../openmpi-1.6.4/configure --prefix=$HOME/code/openmpi-1.6.4".

It is not "./openmpi-1.6.4".
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22楼2014-09-02 14:46:29
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板桥霜

木虫 (正式写手)
引用回帖:
22楼: Originally posted by liqizuiyang at 2014-09-02 14:46:29
Note this:
==================================
2. Create a new directory named "build" under $HOME.
mkdir build

3. Go to build and set environmental variables.
cd build
============ ...

still got some errors, here are my operations:
[root@lab-host openmpi-1.6.4]# cd /home
[root@lab-host home]# ls
build  han  lost+found
[root@lab-host home]# cd build
[root@lab-host build]# ls
openmpi-1.6.4
[root@lab-host build]# cd openmpi-1.6.4/
[root@lab-host openmpi-1.6.4]# ls
acinclude.m4  CMakeLists.txt  configure     examples  Makefile                 NEWS  README
aclocal.m4    config          configure.ac  INSTALL   Makefile.am              ompi  README.WINDOWS.txt
AUTHORS       config.log      contrib       libtool   Makefile.in              opal  test
autogen.sh    config.status   Doxyfile      LICENSE   Makefile.man-page-rules  orte  VERSION
[root@lab-host openmpi-1.6.4]# ../openmpi-1.6.4/configure --prefix=/home/han/program/openmpi-1.6.4/
...
...
make check
...
...
CCLD   predefined_gap_test
libtool: link: cannot find the library `../../ompi/libmpi.la' or unhandled argument `../../ompi/libmpi.la'
make[3]: *** [predefined_gap_test] Error 1
make[3]: Leaving directory `/home/build/openmpi-1.6.4/ompi/debuggers'
make[2]: *** [check-am] Error 2
make[2]: Leaving directory `/home/build/openmpi-1.6.4/ompi/debuggers'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/home/build/openmpi-1.6.4/ompi'
make: *** [check-recursive] Error 1


getting crazy~~~~~~
help please~~~~
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23楼2014-09-02 16:21:52
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板桥霜

木虫 (正式写手)
and I have allready exported the enverimental varibles
[root@lab-host openmpi-1.6.4]# env
HOSTNAME=lab-host
SELINUX_ROLE_REQUESTED=
TERM=xterm
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=192.168.41.127 4992 22
SELINUX_USE_CURRENT_RANGE=
QTDIR=/usr/lib/qt-3.3
OLDPWD=/home/build
QTINC=/usr/lib/qt-3.3/include
SSH_TTY=/dev/pts/1
USER=root
LD_LIBRARY_PATH=/cluster/lab-p1/composer_xe_2013_sp1.2.144/compiler/lib/ia32/:
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01r=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42w=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.tbz=01;31:*.tbz2=01;31:*.bz=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:
CXXFLAGS=-O2
MAIL=/var/spool/mail/root
PATH=/cluster/lab-p1/bin:/usr/lib/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin
FCFLAGS=-O2
PWD=/home/build/openmpi-1.6.4
LANG=en_US.UTF-8
KDE_IS_PRELINKED=1
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
LOADEDMODULES=
KDEDIRS=/usr
F77=ifort
SELINUX_LEVEL_REQUESTED=
CXX=icpc
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
HISTCONTROL=ignoredups
SHLVL=1
HOME=/root
CFLAGS=-O2
FC=ifort
LOGNAME=root
QTLIB=/usr/lib/qt-3.3/lib
CVS_RSH=ssh
SSH_CONNECTION=192.168.41.127 4992 192.168.41.149 22
MODULESHOME=/usr/share/Modules
LESSOPEN=|/usr/bin/lesspipe.sh %s
CC=icc
G_BROKEN_FILENAMES=1
FFLAGS=-O2
module=() {  eval `/usr/bin/modulecmd bash $*`
}
_=/bin/env
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24楼2014-09-02 16:33:48
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liqizuiyang

木虫 (著名写手)
内容已删除
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25楼2014-09-02 16:55:27
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liqizuiyang

木虫 (著名写手)
引用回帖:
24楼: Originally posted by 板桥霜 at 2014-09-02 16:33:48
and I have allready exported the enverimental varibles
# env
HOSTNAME=lab-host
SELINUX_ROLE_REQUESTED=
TERM=xterm
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=192.168.41.127 4992 22
SELINUX_USE_C ...

Since your logged in the cluster as 'root', I may guess that you are an advanced Unix/Linux user. However, it seems that you lack some basic knowledge of Unix/Linux. In fact, $HOME in your case is '/home/han', not '/home'.

So first of all, log in the cluster as an ordinary user. If you are now logged as 'root', try 'logout' or 'su han'.

Please follow the following instrctions EXACTLY.
--------------------------------------------------------------------

At the beginning, I assume that you have already put the source code under /home/han.

cd /home/han
tar -xf openmpi-1.6.4.tar.bz2
mkdir /home/han/build
cd /home/han/build
export CC=icc
export CXX=icpc
export FC=ifort
export F77=ifort
export CFLAGS=-O2
export CXXFLAGS=-O2
export FCFLAGS=-O2
export FFLAGS=-O2
/home/han/openmpi-1.6.4/configure --prefix=/home/han/program/openmpi-1.6.4
make
make check
make install
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26楼2014-09-02 17:25:30
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板桥霜

木虫 (正式写手)
问题应该出现在编译器安装目录上，原来安装到/cluster下面，而han用户在node上面没有访问权限。装到/home/compiler里面就可以了，奇怪
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27楼2014-09-04 08:55:58
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