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maomao1210

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[交流] 【讨论】编译器，数学库安装。已有1人参与

经常遇到编译器的安装，以及各种数学库的安装，还有一些常用软件的安装，最基本的能力。呵呵
如果能有个高手把这个总结一下的话，岂不是很好？让大家都来学习一下。
编译器：pgi, ifort,等等
数学库： blas, lapack, atlas, mkl 等等
常用软件就很多了，分子轨道理论方面的，密度泛函方面的，呵呵
希望能有高手给总结一下。让我们都来学习操作操作。
可惜我是一个linux盲，所以只能在这里呼吁了。呵呵。
为了此个项目，我决定拿出我全部的金币做为资助。
pgi 的安装过程，100 金币
ifort 的安装过程，100金币
mpich 的安装过程，100金币
blas+lapack的安装过程，160金币
atlas的安装过程，100金币
mkl的安装过程，100金币
共660金币。
呵呵。总结后，大家都可以来学习一下。
金币就这么多了，所以常用软件的安装就没有金币贡献了，呵呵，等赚了钱再继续来求贤，呵呵。

[ Last edited by maomao1210 on 2010-1-28 at 10:45 ]

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1楼 2010-01-28 10:43:18

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zyz1981

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PGI安装问题汇总

PGI安装问题集锦
PGI是Portland公司开发的编译器，可以编译高性能的fortran（77、9X）、C、C++，尤其是对AMD CPU优化非常好。这里汇总了安装过程中最常见的问题以及解决方案。

一、bash环境设置
相关问题：安装成功后，运行pgf90等命令显示“bash: pgf90: command not found”。
解决：在.bashrc或者.bash_profile中设置环境，做法如下（以我安装pgi6.0为例）
cd ~
vim .bashrc
然后在最后追加
PATH=/usr/pgi/linux86/6.0/bin:$PATH
export PATH
MANPATH=$MANPATH:/usr/pgi/linux86/6.0/man
export MANPATH

LM_LICENSE_FILE=/usr/pgi/license.dat
export LM_LICENSE_FILE
export PGI=/usr/pgi
保存退出
然后source .bashrc
可以使用了。

二、glibc、crtbegin.o问题
问题：受系统安装的gcc编译器版本的影响，安装pgi有时候会遇到，例如我在安装pgi6.0-5时出现 ERROR: unknown glibc version (2.4)，或者还有朋友遇到安装完毕后用pgf90编译fortran程序提示找不到crtbegin.o文件，这属于同一问题。

实际上pgi各模块已经写在硬盘上了，但是环境没设置好，所以还是不能工作。

具体原因：

由于安装文件中的makelocalrc不能正确生成localrc，所以pgi不能正常工作，这与使用哪个发行版无关.

解决方案：
以我的系统为例，我用ubuntu edgy,安装pgi 6.0
1.手动编写一个文本文件localrc，放在/usr/pgi/linux86/6.0/bin目录下
set LFC=-lg2c;
set LDSO=/lib/ld-linux.so.2;
set GCCDIR=/usr/lib/gcc/i486-linux-gnu/4.1.2;
set GCCINC=;
set G77DIR=/usr/lib/gcc/i486-linux-gnu/3.4.6/;
set LOCALRC=YES;
set THROW=__THROW=;
set HAMMER=;
set X86_64=;

这一方案简单有效

2.用如下文件替换安装目录中的makelocalrc文件，然后重新安装（该文件需要设置为可执行）
(忘了抄的哪位高手的)

主要在66，267行附近，314行附近的改动是为了解决安装错误： /usr/pgi/linux86/6.1/bin/makelocalrc: line 315: =安装： / u sr/l ib/gcc/i386-re dhat- linux/4.1.0/: 没有那个文件或目录.

修改后的makelocalrc如下（修改部分已用整行长注释条标出）：

#! /bin/sh
##
## Copyright 1990-2000, The Portland Group, Incorporated.
## Copyright 2000-2005, STMicroelectronics, Incorporated.
## All rights reserved.
##
## STMICROELECTRONICS, INCORPORATED PROPRIETARY INFORMATION
## This software is supplied under the terms of a license agreement
## or nondisclosure agreement with STMicroelectronics and may not be
## copied or disclosed except in accordance with the terms of that
## agreement.
##

# Just in case
PATH=/usr/bin:/bin:$PATH
TMPDIR=${TMPDIR:-/tmp}

usage() {
echo "Usage: $0 [-x|-n] installdir"
echo
echo "Example: $0 -x /usr/pgi/linux86/6.1"
quit 1
}

quit() {
# Cleanup scratch files.
rm -rf $scratch
exit $1
}

copy_files() {
# $1 is source dir, $2 is destination dir
if test -n "$1"; then
if test -d "$1"; then
if test ! -d $2 ; then
mkdir $2
fi
( cd $1 ; tar cf - * | ( cd $2; tar xpf - ))
fi
fi
}

pretty_print() {
echo $@ | awk -F^ '{printf("%20-s %s\n",$1,$2);}'
}

print_line() {
echo $1 $2 $3 $4 $5 $6 >> $newrc
}

get_glibc_version() {
# Determine the GNU LIBC version.

if test -r /lib64/libc.so.6 ; then
LIBC=/lib64/libc.so.6 # should only exist on a 64-bit Linux OS.
elif test -r /lib/libc.so.6 ; then
LIBC=/lib/libc.so.6 # should exist on any Linux OS.
else
echo "ERROR: /lib/libc.so.6: not found or no read permission"
quit
fi

x=`strings $LIBC | grep 'GNU C Library' | cut -d, -f1 | awk '{print $7}'`
if test -n "$x" ; then
#########################################################################################
GLIBC_VERSION=2.4.4 ##原来是"$x"
else
GLIBC_VERSION=2.4.4 ##原来是空的
########################################################################################
fi
unset x
return
}

get_linker_version() {
x=`grep collect2 $out | sed q | sed -e 's/.* -dynamic-linker //' -e 's/ .*//'`
if test -n "$x" ; then
LINKER=$x
else
LINKER=
fi
unset x
return
}

get_specs_file() {
# This command pipeline should be I18N-capable.
x=`awk '/gcc.*specs/ {print $NF}' $out`
if test -n "$x" ; then
SPECSFILE=$x
else
SPECSFILE=
fi
unset x
return
}

# Stop if not Linux.

opsys=`uname -s | tr '[A-Z]' '[a-z]'`
if test "$opsys" != "linux" ; then
echo
echo "$0: `uname -n` is not running Linux"
quit 1
fi

pgi50=1
noexec=1
ofile=0
use_pthreads=1
no_m32_support=0
check_crt_files=0
set_hammer_empty=0
gcc=gcc
g77=g77
scratch=$TMPDIR/PGI-INSTALL.$$
if test ! -d $scratch ; then
mkdir $scratch
fi

while test -n "$1"; do
case $1 in
-n ) noexec=1 ;;
-x ) noexec=0 ;;
-o ) ofile=1 ; noexec=0 ;;
-gcc ) shift; gcc=$1 ;;
-g77 ) shift; g77=$1 ;;
* ) start=$1 ;;
esac
shift
done

if test -z "$start" ; then
usage
fi

if test ! -d $start ; then
echo "$0: $start: directory not found"
usage
fi

if test "$start" = "." ; then
start=`pwd`
fi

if test "$pgi50" -eq 1 ; then
# Example: 5.0 and above:
# start = /usr/pgi/linux86/5.0
# installdir = /usr/pgi/linux86
# version = 5.0
# base = /usr/pgi/linux86/5.0
# target = linux86
installdir=`dirname $start`
version=`basename $start`
base=$start
target=`basename $installdir`
else
# Example: 4.1 and below:
# start = /usr/pgi
# installdir = /usr/pgi
# base = /usr/pgi/linux
# version = 5.0
# target = linux86
installdir=$start
version=`cat $start/.release`
base=$start/linux86
target="linux86"
fi

# Define target-specific options needed below.

arch=`uname -m`
case "${target}:${arch}" in
linux86:x86_64 )
gccopt="-o $scratch/a.out -m32 -v"
g77opt=$gccopt
subdir="/32"
check_crt_files=1
use_64bit_rcfiles=11
install_64_bit=0
lib=/lib
usrlib=/usr/lib
;;
linux86:* )
set_hammer_empty=1
gccopt="-o $scratch/a.out -v"
g77opt=$gccopt
use_64bit_rcfiles=10
install_64_bit=0
lib=/lib
usrlib=/usr/lib
;;
linux86-64:x86_64 )
gccopt="-o $scratch/a.out -v"
g77opt=$gccopt
lib=/lib64
usrlib=/usr/lib64
install_64_bit=1
use_64bit_rcfiles=0
;;
linux86-64:* )
echo "ERROR: target doesn't match architecture"
exit 1
;;
esac

localrc=$base/bin/localrc
newrc=$scratch/localrc.$$

# Find the version of GLIBC used on this system so that the appropriate
# files are copied from lib-linux86-g* to lib and/or liblf.

LIBC=$lib/libc.so.6
if test ! -f $LIBC ; then
echo "ERROR: file $LIBC: not found."
quit 1
fi

get_glibc_version # sets GLIBC_VERSION

case "$GLIBC_VERSION" in
2.3.* )
glibc=232
LIB=$base/lib-linux86-g232
LIBLF=$LIB-lf
INC=$base/include-g23
;;
2.2.9* )
glibc=2293
LIB=$base/lib-linux86-g2293
LIBLF=$LIB-lf
INC=$base/include-g222
;;
2.2.5 )
glibc=225
LIB=$base/lib-linux86-g225
LIBLF=$LIB-lf
INC=$base/include-g222
;;
2.2.4 )
glibc=224
LIB=$base/lib-linux86-g224
LIBLF=$LIB-lf
INC=$base/include-g222
;;
2.2.2 )
glibc=222
LIB=$base/lib-linux86-g22
LIBLF=$LIB-lf
INC=$base/include-g222
;;
2.1.9* | 2.2*)
glibc=22
LIB=$base/lib-linux86-g22
LIBLF=$LIB-lf
INC=$base/include-g22
;;
2.1.[23] )
glibc=212
LIB=$base/lib-linux86-g212
;;
2.1.1 )
glibc=211
LIB=$base/lib-linux86-g211
;;
####################################################################################
2.4.4) ##这都是加上的其实只要改GLIBC_VERSION
glibc=232 ##对应上面半括号中较新版本版本号即可
LIB=$base/lib-linux86-g232
LIBLF=$LIB-lf
INC=$base/include-g23
;;
#####################################################################################
* )
echo "ERROR: unknown glibc version ($GLIBC_VERSION)."
quit 1
;;
esac

# PGI software needs some of the gcc libraries. Run gcc to determine
# to determine which linker and libraries are actually being used.

type $gcc > /dev/null 2>&1
if test $? -eq 1 ; then
echo "ERROR: gcc not found;"
echo " successful use of compilers requires existence of gcc libraries"
quit 1
fi

cfile=$scratch/hello-$$.c
ffile=$scratch/hello-$$.f

cat > $cfile < #include
#include
main(){ printf("Hello world!\n"

; exit(0); }
EOF_HELLO_C

cat > $ffile < program hello
write(*,100)
100 format('Hello world!')
end
EOF_HELLO_F

out=$scratch/gccrun.$$
$gcc $gccopt $cfile > $out 2>&1

if test ! -s $out ; then
echo "ERROR: gcc failed to execute for reasons unknown."
quit 1
fi
########################################################################
####$gccbase=`$gcc -print-search-dirs | sed -e 's/^install: //' -e 1q`
####if test -d $gccbase$subdir ; then
#### GCCDIR="$gccbase$subdir" ##原有的
####fi
####gccversion=`$gcc -dumpversion`
#######################################################################
libgcc=`$gcc -print-libgcc-file-name`
gccbase=`dirname $libgcc`
GCCDIR="$gccbase$subdir" ##自己加的
gccversion=`basename $gccbase`

##########################################################################

# Check and see whether directory that gcc claims to exist actually
# does exist.

if test ! -d $gccbase ; then
echo "ERROR: directory $gccbase: not found;"
echo " successful use of compilers requires existence of gcc libraries!"
quit 1
fi

if test -d ${gccbase}include ; then
GCCINC=${gccbase}include
else
unset GCCINC
fi

# Find the linker

get_linker_version # returns LINKER
if test ! -x $LINKER ; then
echo "ERROR: Linker $LINKER: not found"
quit 1
fi

# Which g77? PGI software needs the g77 libraries, so look for the g77 libs.

type $g77 >/dev/null 2>&1
if test $? -eq 1 ; then
echo "WARNING: g77 not found; this may cause problems during use"
G77DIR='""'
else
out=$scratch/g77run.$$
$g77 $g77opt $ffile > $out 2>&1
libgcc=`$g77 -print-libgcc-file-name`
g77base=`$g77 -print-search-dirs | sed -e 's/^install: //' -e 1q`
if test -d $g77base$subdir ; then
G77DIR="$g77base$subdir"
else
G77DIR='""'
fi
f2c=`cat $out | grep lf2c`
g2c=`cat $out | grep lg2c`
if test -n "$f2c" ; then
G77LIB="-lf2c"
fi
if test -n "$g2c" ; then
G77LIB="-lg2c"
fi
fi

if test -n "$G77LIB" ; then
print_line "set LFC=$G77LIB;"
fi

# Which dynamic linker?

if test "$LINKER" != "/lib/ld-linux.so.1" ; then
print_line "set LDSO=$LINKER;"
fi

# CDK uses its own libmpich.a.

if test -f "$base/bin/mpirun" ; then
print_line "set MPILIB=$base/lib;"
MPILIB=$base/lib/libmpich.a
fi

print_line "set GCCDIR=$GCCDIR;"
print_line "set GCCINC=$GCCINC;"
print_line "set G77DIR=$G77DIR;"

#Add setaff_bind.o and -lnuma at link line
x=$base
x=`echo $x | sed -e 's/.*86-64.*/86-64/'`
if test "$x" = "86-64" ; then
if test -e $usrlib/libnuma.so ; then
print_line 'set NUMAOBJS=$COMPLIBOBJ/setaff_bind.o;'
print_line "set NUMALIBS=-lnuma;"
fi
fi

if test $pgi50 -eq 0 ; then
print_line "set STDRPATH=-rpath \$PGI/linux86/lib;"
fi

print_line 'set LOCALRC=YES;'

if test "$noexec" -eq 1 ; then
pretty_print 'PGI directory' ^ $installdir
pretty_print 'PGI version' ^ $version
pretty_print 'PATH entry' ^ "$base/bin"
pretty_print 'System linker' ^ $LINKER
pretty_print 'GCC directory' ^ $GCCDIR
pretty_print 'GCC headers' ^ $GCCINC
pretty_print 'G77 directory' ^ $G77DIR
pretty_print 'G77 headers' ^ $G77LIB

if test -n "$GLIBC_VERSION" ; then
pretty_print 'GNU C version' ^ $GLIBC_VERSION
pretty_print 'PGI glibc libs' ^ $LIB
pretty_print 'PGI glibc headers' ^ $INC
else
pretty_print 'Glibc version' ^ 'no'
fi

if test -n "$LIBLF" ; then
pretty_print 'Large file support' ^ $LIBLF
else
pretty_print 'Large file support' ^ 'no'
fi

if test -n "$MPILIB" ; then
pretty_print 'MPILIB' ^ $MPILIB
fi

if test $use_pthreads -eq 1 ; then
pretty_print 'Threads' ^ "$usrlib/libpthread.{a,so}"
else
pretty_print 'Threads' ^ "$base/lib/libpgthread.{a,so}"
fi

if test $no_m32_support -eq 1 ; then
pretty_print 'gcc supports -m32' ^ 'no'
else
pretty_print 'gcc supports -m32' ^ 'yes'
fi

quit 0
fi

# Make the necessary changes to meet glibc dependencies.

if test -n "$glibc" ; then
copy_files $LIB $base/lib

case "$glibc" in
22* | 23* )
copy_files $INC $base/include
print_line "set THROW=__THROW=;"
;;
21* )
;;
esac

# Large file support.

if test -n "$LIBLF" ; then
copy_files $LIBLF $base/liblf
else
rm -rf $base/liblf
fi

# Newer distributions of Linux do not need PGI-compiled versions of
# threads libraries.

if test $use_pthreads -eq 1 ; then
# Only create a symlink if the target file exists and
# the link does not.
if test -e $usrlib/libpthread.a ; then
if test ! -h $base/lib/libpgthread.a ; then
ln -s $usrlib/libpthread.a $base/lib/libpgthread.a
fi
fi
if test -e $lib/libpthread.so.0 ; then
if test ! -h $base/lib/libpgthread.so ; then
ln -s $lib/libpthread.so.0 $base/lib/libpgthread.so
fi
fi
fi

# Adjust header files based on the gcc version.

need_stddef=1
case "$gccversion" in
3.3* )
copy_files $base/include-gcc33 $base/include
;;
3.4* )
copy_files $base/include-gcc34 $base/include
need_stddef=0
;;
4.* )
copy_files $base/include-gcc40 $base/include
need_stddef=1
;;
* )
;;
esac

if test $need_stddef -eq 0 ; then
rm -f $base/include/stddef.h
fi

# Changes for 32-bit installs.

if test $set_hammer_empty -eq 1 ; then
print_line "set HAMMER=;"
print_line "set X86_64=;"
fi

if test $install_64_bit -eq 0 ; then
if test -f /etc/redhat-release ; then
grep 'release 9' /etc/redhat-release > /dev/null 2>&1
if test $? -eq 0; then
print_line "set LBSTAT=-lpthread -lpthread_nonshared;"
fi
fi
fi

# Stock distributions may need extra help in finding crt files.

if test $check_crt_files -eq 1 ; then
if test ! -f /usr/lib64/32/crt1.o ; then
print_line "set DEFLIBDIR=/usr/lib;"
print_line "set DEFSTDOBJDIR=/usr/lib;"
print_line "set EXTRAASARGS=--32;"
fi
fi

# For production installations, recover some space by unneeded files.

if test "$version" != "dev" ; then
rm -rf $base/include-g*
echo $GLIBC_VERSION > $base/glibc_version
fi

# Fix the 32/64-bit .*rc files.

if test $use_64bit_rcfiles -eq 11 ; then
files=`ls -1 $base/bin/.pg*-64 2>/dev/null`
for i in $files ; do
x=`echo $i | sed -e 's/-64$//'`
mv -f $i $x
done
rm -f $base/bin/.pg*-32 > /dev/null 2>&1
elif test $use_64bit_rcfiles -eq 10; then
files=`ls -1 $base/bin/.pg*-32 2>/dev/null`
for i in $files ; do
x=`echo $i | sed -e 's/-32$//'`
mv -f $i $x
done
rm -f $base/bin/.pg*-64 > /dev/null 2>&1
fi
fi

# Add timestamp and username.

print_line '# makelocalrc executed by ' `whoami` `date`

# If $ofile is set, then display the file to stdout. Otherwise, write
# it to $localrc.

if test $ofile -eq 1 ; then
echo "##### localrc contents #####"
cat $newrc
echo "############################"
rm -f $newrc
else
if test -f $localrc ; then
mv -f $localrc $localrc.bak
chmod -f 0644 $localrc.bak
fi
mv -f $newrc $localrc
chmod -f 0644 $localrc
fi

# Copy omp_lib.mod from lib directory to include directory
echo
if test -f $base/lib/omp_lib.mod ; then
cp -f $base/lib/omp_lib.mod $base/include/omp_lib.mod
fi
if test -f $base/lib/omp_lib_kinds.mod ; then
cp -f $base/lib/omp_lib_kinds.mod $base/include/omp_lib_kinds.mod
fi
quit 0

(过程中注意：找到软件包中的makelocalrc文件（linux86/bin下），用新的文件替换，同时应该增加makelocalrc可执行权限:chmod +x makelocalrc，很明显，无此步骤照样不成功)

转自：http://quantumv.blog.sohu.com/23690256.html