only ./configure --prefix=/usr is running

make command

make without --prefix key

It is difficult to tell what the problem you encountered here is without more information.  Python is supported on many different platforms and regularly built with --prefix being set.  To investigate further, you would need to indicate exactly which version of Python, which version of which operating system platform, and the exact configure and make commands you are using.  Nevertheless, because you seem to be doing a shared (--enable-shared) build with a prefix of /usr, I speculate you *might* be running into the issue documented, and recently fixed, in Issue21166.  You could try removing --enable-shared, or you could try applying the change from that issue, or you could try working around simulating the patch's effect by creating a dummy pybuilddir.txt before running make.

Found problem.
After generating Makefile if comment string, contain LD_CONFIG_PATH all build success.
Operating system Gentooo, python version 2.7.8 from ebuild and downloaded from origin site.

# gcc -v
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.8.3/gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.8.3/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-4.8.3/work/gcc-4.8.3/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.8.3 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.8.3 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.8.3/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.8.3/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/include/g++-v4 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.8.3/python --enable-languages=c,c++ --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.8.3 p1.1, pie-0.5.9' --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-altivec --disable-fixed-point --enable-targets=all --disable-libgcj --disable-libgomp --disable-libmudflap --disable-libssp --disable-libquadmath --enable-lto --without-cloog
Thread model: posix
gcc version 4.8.3 (Gentoo 4.8.3 p1.1, pie-0.5.9)

# emerge --info
Portage 2.2.8-r1 (default/linux/amd64/13.0, gcc-4.8.3, glibc-2.19-r1, 3.16.0 x86_64)
=================================================================
System uname: Linux-3.16.0-x86_64-Intel-R-_Core-TM-_i5-4200M_CPU_@_2.50GHz-with-gentoo-2.2
KiB Mem:     7851264 total,   5629620 free
KiB Swap:   10000424 total,   9632404 free
Timestamp of tree: Tue, 16 Sep 2014 07:15:01 +0000
ld GNU ld (Gentoo 2.23.2 p1.0) 2.23.2
ccache version 3.1.9 [disabled]
app-shells/bash:          4.2_p45
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.8, 3.3.5-r1
dev-util/ccache:          3.1.9-r3
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6, 1.13.4
sys-devel/binutils:       2.23.2
sys-devel/gcc:            4.6.4, 4.7.3-r1, 4.8.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.13 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo qt local
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core-avx-i -msse4.2 -msse4.1 -maes -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=core-avx-i -msse4.2 -msse4.1 -maes -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--jobs 4 --load-average 8"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync metadata-transfer news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.kiev.ua/ftp/ http://portage.org.ua/ ftp://ftp.free.fr/mirrors/ftp.gentoo.org/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage/qt /usr/local/portage/local"
SYNC="rsync://rsync1.ua.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth bzip2 cairo cdr chm cli cracklib crypt css cxx djvu dri dvb dvi freetype gd gdbm gif glibc-omitfp gnutls gpm gstreamer gtk iconv icu ipv6 jabber jpeg lame lm_sensors maildir mmx modules mp3 mp4 mplayer mtp multilib ncurses nfsv3 nls nptl ogg opengl pam pcre readline session slang sse sse2 ssl ssse3 tcpd theora tiff udev unicode v4l v4l2 vaapi wifi wimax win32codecs x264 xcomposite xinerama xv xvid zlib" ABI_X86="64" ALSA_CARDS="hda-intel" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64 pc" INPUT_DEVICES="evdev synaptics keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en ru" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="radeon intel i965 i915 fglrx" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

What also information do you need?

Sorry, I don't see where you have shown exactly what Python ./configure and make commands you are using and it is not at all obvious to me what you mean by "After generating Makefile if comment string, contain LD_CONFIG_PATH all build success".  But, if it is the case that you are using Gentoo tools to build ("python version 2.7.8 from ebuild") then perhaps you should be asking on a Gentoo forum as we have no control or specific knowledge of how Gentoo packages things.  If you can show exactly how a Python build fails using an unpacked Python source package, the Python's ./configure and make, then we can investigate.  In other words, we would need to see the exact sequence of the exact commands you use.  There are just too many variables to try to guess what you might be seeing (other than my original speculation about Issue21166).  Did you try the recommendations above in msg227011?

Since there has been no followup to this issue, I'm going to close it.  Feel free to reopen if you can document a reproducible problem with a Python source release.