[SciPy-User] Error when building scipy.0.9.0 - "f951: undefined symbol: mpfr_get_z_exp"

Xiong Deng dbigbear@gmail....
Mon Aug 29 02:13:08 CDT 2011


Hi ALL,

I am trying to install numpy, scipy on my Linux. I have build and installed
numpy on it kindof correctly with only one failure shown that:

[work@tc-fcr-bid03.tc.baidu.com:~/xiongdeng/soft/scipy-0.9.0]$ python
Python 2.7.1 (r271:86832, Jan 13 2011, 22:17:56)
[GCC 3.4.5 20051201 (Red Hat 3.4.5-2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.test()
Running unit tests for numpy
NumPy version 1.6.1
NumPy is installed in
/home/work/local/python-2.7.1/lib/python2.7/site-packages/numpy
Python version 2.7.1 (r271:86832, Jan 13 2011, 22:17:56) [GCC 3.4.5 20051201
(Red Hat 3.4.5-2)]
nose version 1.1.2
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F...........................................................................................................................................................................................................................................................................................................................................................................................................................K.................................................................................................K......................K.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
FAIL: Test basic arithmetic function errors
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/work/local/python-2.7.1/lib/python2.7/site-packages/numpy/testing/decorators.py",
line 215, in knownfailer
    return f(*args, **kwargs)
  File
"/home/work/local/python-2.7.1/lib/python2.7/site-packages/numpy/core/tests/test_numeric.py",
line 367, in test_floating_exceptions_power
    np.power, ftype(2), ftype(2**fi.nexp))
  File
"/home/work/local/python-2.7.1/lib/python2.7/site-packages/numpy/core/tests/test_numeric.py",
line 271, in assert_raises_fpe
    "Type %s did not raise fpe error '%s'." % (ftype, fpeerr))
  File
"/home/work/local/python-2.7.1/lib/python2.7/site-packages/numpy/testing/utils.py",
line 34, in assert_
    raise AssertionError(msg)
AssertionError: Type <type 'numpy.float64'> did not raise fpe error
'overflow'.

----------------------------------------------------------------------
Ran 3533 tests in 12.494s

FAILED (KNOWNFAIL=3, failures=1)
<nose.result.TextTestResult run=3533 errors=0 failures=1>


HOWEVER, when I am building my scipy, there is a big error, causing
termination of the building process. The messages are as below:

/home/work/local/gcc-4.7/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.0/f951:
symbol lookup error:
/home/work/local/gcc-4.7/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.0/f951:
undefined symbol: mpfr_get_z_exp
error: Command "/home/work/local/gcc-4.7/bin/gfortran -Wall -ffixed-form
-fno-second-underscore -fPIC -O3 -funroll-loops
-I/home/work/local/python-2.7.1/lib/python2.7/site-packages/numpy/core/include
-c -c scipy/special/specfun/specfun.f -o
build/temp.linux-x86_64-2.7/scipy/special/specfun/specfun.o" failed with
exit status 1

IN ADDITION: One thing I have to say: when I compiled and installed gcc-4.7
locally, I did not install GMP, *MPFR*, and MPC. They are installed after
gcc-4.7....The problem may be due to this???? But How can I fix it without
re-installing gcc-4.7 ???


-----------------------------------------------------------------------------------------------------------------

My configuration:

My configuration of the installation:

* ATLAS 3.8.4
* lapack 3.3.1
* numpy 1.6.1
* SciPy version 0.9.0 (when building scipy version 0.8.0, the error is the
same )
* dateutil 1.5
* Python version 2.7.1 (r271:86832, Jan 13 2011, 22:17:56) [GCC 3.4.5
20051201 (Red Hat 3.4.5-2)]
* nose version 1.1.2
* gcc (GCC) 4.7.0 20110820 (experimental)
* LINUX: Linux XXX 2.6.9_5-9-0-0 #1 SMP Wed Jun 23 14:03:19 CST 2010
x86_64 x86_64 x86_64 GNU/Linux
Red Hat Enterprise Linux AS release 4 (Nahant Update 3)

export:

declare -x ATLAS="/home/work/local/lib/libatlas.so"
declare -x G_BROKEN_FILENAMES="1"
declare -x HISTSIZE="1000"
declare -x HOME="/home/work"
declare -x INPUTRC="/etc/inputrc"
declare -x LANG="en_US"
declare -x LAPACK="/home/work/local/lib/liblapack.so"
declare -x LC_CTYPE="zh_CN.gb18030"
declare -x
LD_LIBRARY_PATH=":/home/work/local/lib/:/home/work/local/gcc-4.7/lib/"
declare -x LESSOPEN="|/usr/bin/lesspipe.sh %s"
declare -x LOGNAME="work"
declare -x
LS_COLORS="no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=01;32:*.cmd=01;32:*.exe=01;32:*.com=01;32:*.btm=01;32:*.bat=01;32:*.sh=01;32:*.csh=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tz=01;31:*.rpm=01;31:*.cpio=01;31:*.jpg=01;35:*.gif=01;35:*.bmp=01;35:*.xbm=01;35:*.xpm=01;35:*.png=01;35:*.tif=01;35:"
declare -x MAC="64"
declare -x MAIL="/var/spool/mail/work"
declare -x OLDPWD="/home/work/xiongdeng/soft"
declare -x
PATH="/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/share/baidu/bin:/home/work/local/python-2.7.1/bin/:/home/work/local/vim/bin/:/home/work/local/svn/bin/:/home/work/local/hadoop-client/hadoop/bin/:/home/work/local/script/:/home/work/local/bin/:/home/work/local/gcc-4.7/bin/:/home/work/bin"
declare -x PROMPT_COMMAND="echo -ne \"\\e]0;tc-fcr-bid03\\a\""
declare -x PWD="/home/work/xiongdeng/soft/scipy-0.9.0"
declare -x SDIR_FILE="/home/work/.sdir_label"
declare -x SHELL="/bin/bash"
declare -x SHLVL="1"
declare -x SVN_EDITOR="/home/work/local/vim/bin/vim"
declare -x TERM="linux"
declare -x USER="work"

ll /home/work/local/lib

-rw-r--r--  1 work work 13424422 Aug 29 01:55 libatlas.a
-rwxr-xr-x  1 work work  8463221 Aug 29 01:55 libatlas.so
-rw-r--r--  1 work work   466344 Aug 29 01:55 libcblas.a
-rwxr-xr-x  1 work work   142677 Aug 29 01:55 libcblas.so
-rw-r--r--  1 work work   566602 Aug 29 01:55 libf77blas.a
-rwxr-xr-x  1 work work   158579 Aug 29 01:55 libf77blas.so
-rw-r--r--  1 work work   515618 Aug 23 21:05 libgcc_s.so
-rw-r--r--  1 work work   515618 Aug 23 21:05 libgcc_s.so.1
-rw-r--r--  1 work work 16135904 Aug 27 02:04 libgfortran.a
-rwxr-xr-x  1 work work     1034 Aug 27 02:04 libgfortran.la
-rw-r--r--  1 work work  5962327 Aug 27 02:04 libgfortran.so
-rwxr-xr-x  1 work work  5962327 Aug 27 02:04 libgfortran.so.3
-rwxr-xr-x  1 work work  5962327 Aug 27 02:04 libgfortran.so.3.0.0
-rw-r--r--  1 work work      269 Aug 27 02:04 libgfortran.spec
-rw-r--r--  1 work work  1134848 Aug 24 16:01 libgmp.a
-rwxr-xr-x  1 work work      923 Aug 24 16:01 libgmp.la
lrwxrwxrwx  1 work work       16 Aug 24 16:01 libgmp.so -> libgmp.so.10.0.2
lrwxrwxrwx  1 work work       16 Aug 24 16:01 libgmp.so.10 ->
libgmp.so.10.0.2
-rw-r--r--  1 work work   471045 Aug 24 16:01 libgmp.so.10.0.2
-rw-r--r--  1 work work   642892 Aug 23 21:05 libgomp.a
-rwxr-xr-x  1 work work      958 Aug 23 21:05 libgomp.la
-rw-r--r--  1 work work   329946 Aug 23 21:05 libgomp.so
-rwxr-xr-x  1 work work   329946 Aug 23 21:05 libgomp.so.1
-rwxr-xr-x  1 work work   329946 Aug 23 21:05 libgomp.so.1.0.0
-rw-r--r--  1 work work      170 Aug 23 21:05 libgomp.spec
-rw-r--r--  1 work work  1275386 Aug 23 21:05 libiberty.a
-rw-r--r--  1 work work 10561756 Aug 29 01:55 liblapack.a
-rwxr-xr-x  1 work work  5683831 Aug 29 01:55 liblapack.so
-rw-r--r--  1 work work  1133984 Aug 23 20:48 liblzma.a
-rwxr-xr-x  1 work work      924 Aug 23 20:48 liblzma.la
lrwxrwxrwx  1 work work       16 Aug 23 20:48 liblzma.so -> liblzma.so.5.0.3
lrwxrwxrwx  1 work work       16 Aug 23 20:48 liblzma.so.5 ->
liblzma.so.5.0.3
-rw-r--r--  1 work work   582278 Aug 23 20:48 liblzma.so.5.0.3
-rw-r--r--  1 work work   199486 Aug 24 16:06 libmpc.a
-rwxr-xr-x  1 work work     1027 Aug 24 16:06 libmpc.la
lrwxrwxrwx  1 work work       15 Aug 24 16:06 libmpc.so -> libmpc.so.2.0.0
lrwxrwxrwx  1 work work       15 Aug 24 16:06 libmpc.so.2 -> libmpc.so.2.0.0
-rw-r--r--  1 work work    91064 Aug 24 16:06 libmpc.so.2.0.0
-rw-r--r--  1 work work  2905606 Aug 24 15:53 libmpfr.a
-rwxr-xr-x  1 work work      948 Aug 24 15:53 libmpfr.la
lrwxrwxrwx  1 work work       16 Aug 24 15:53 libmpfr.so -> libmpfr.so.4.0.1
lrwxrwxrwx  1 work work       16 Aug 24 20:58 libmpfr.so.1 ->
libmpfr.so.4.0.1
lrwxrwxrwx  1 work work       16 Aug 24 15:53 libmpfr.so.4 ->
libmpfr.so.4.0.1
-rw-r--r--  1 work work  1317215 Aug 24 15:53 libmpfr.so.4.0.1
-rw-r--r--  1 work work   466902 Aug 29 01:55 libptcblas.a
-rw-r--r--  1 work work   567162 Aug 29 01:55 libptf77blas.a
-rw-r--r--  1 work work  1583884 Aug 23 21:05 libquadmath.a
-rwxr-xr-x  1 work work      985 Aug 23 21:05 libquadmath.la
-rw-r--r--  1 work work   903165 Aug 23 21:05 libquadmath.so
-rwxr-xr-x  1 work work   903165 Aug 23 21:05 libquadmath.so.0
-rwxr-xr-x  1 work work   903165 Aug 23 21:05 libquadmath.so.0.0.0
-rw-r--r--  1 work work   103546 Aug 23 21:05 libssp.a
-rwxr-xr-x  1 work work      946 Aug 23 21:05 libssp.la
-rw-r--r--  1 work work     3534 Aug 23 21:05 libssp_nonshared.a
-rwxr-xr-x  1 work work      928 Aug 23 21:05 libssp_nonshared.la
-rw-r--r--  1 work work    48981 Aug 23 21:05 libssp.so
-rwxr-xr-x  1 work work    48981 Aug 23 21:05 libssp.so.0
-rwxr-xr-x  1 work work    48981 Aug 23 21:05 libssp.so.0.0.0
-rw-r--r--  1 work work 15669078 Aug 23 21:05 libstdc++.a
-rwxr-xr-x  1 work work      973 Aug 23 21:05 libstdc++.la
-rw-r--r--  1 work work  6408505 Aug 23 21:05 libstdc++.so
-rwxr-xr-x  1 work work  6408505 Aug 23 21:05 libstdc++.so.6
-rwxr-xr-x  1 work work  6408505 Aug 23 21:05 libstdc++.so.6.0.17
-rw-r--r--  1 work work     2330 Aug 23 21:05 libstdc++.so.6.0.17-gdb.py
-rw-r--r--  1 work work  1092892 Aug 23 21:05 libsupc++.a
-rwxr-xr-x  1 work work      907 Aug 23 21:05 libsupc++.la
-rw-rw-r--  1 work work   490328 Aug 29 01:55 libtstatlas.a
-rw-rw-r--  1 work work   515296 Aug 27 12:15 lilapack.a

ll /home/work/local/include

drwxr-xr-x  2 work work  4096 Aug 24 14:43 atlas
-rw-rw-r--  1 work work  1773 Aug 27 11:48 atlas_buildinfo.h
-rw-rw-r--  1 work work    90 Aug 27 11:48 atlas_cacheedge.h
-rw-rw-r--  1 work work   147 Aug 27 11:48 atlas_cmv.h
-rw-rw-r--  1 work work   451 Aug 27 11:48 atlas_cmvN.h
-rw-rw-r--  1 work work   387 Aug 27 11:48 atlas_cmvS.h
-rw-rw-r--  1 work work   481 Aug 27 11:48 atlas_cmvT.h
-rw-rw-r--  1 work work   455 Aug 27 11:48 atlas_cNCmm.h
-rw-rw-r--  1 work work   353 Aug 27 11:48 atlas_cr1.h
-rw-rw-r--  1 work work    77 Aug 27 11:48 atlas_csNKB.h
-rw-rw-r--  1 work work   195 Aug 27 11:48 atlas_csysinfo.h
-rw-rw-r--  1 work work     0 Aug 27 11:48 atlas_ctrsmXover.h
-rw-rw-r--  1 work work   147 Aug 27 11:48 atlas_dmv.h
-rw-rw-r--  1 work work   451 Aug 27 11:48 atlas_dmvN.h
-rw-rw-r--  1 work work   387 Aug 27 11:48 atlas_dmvS.h
-rw-rw-r--  1 work work   482 Aug 27 11:48 atlas_dmvT.h
-rw-rw-r--  1 work work   455 Aug 27 11:48 atlas_dNCmm.h
-rw-rw-r--  1 work work   352 Aug 27 11:48 atlas_dr1.h
-rw-rw-r--  1 work work   195 Aug 27 11:48 atlas_dsysinfo.h
-rw-rw-r--  1 work work   112 Aug 27 11:48 atlas_dtrsmXover.h
-rw-rw-r--  1 work work   112 Aug 27 11:48 atlas_pthreads.h
-rw-rw-r--  1 work work   147 Aug 27 11:48 atlas_smv.h
-rw-rw-r--  1 work work   451 Aug 27 11:48 atlas_smvN.h
-rw-rw-r--  1 work work   438 Aug 27 11:48 atlas_smvS.h
-rw-rw-r--  1 work work   637 Aug 27 11:48 atlas_smvT.h
-rw-rw-r--  1 work work   455 Aug 27 11:48 atlas_sNCmm.h
-rw-rw-r--  1 work work   353 Aug 27 11:48 atlas_sr1.h
-rw-rw-r--  1 work work   195 Aug 27 11:48 atlas_ssysinfo.h
-rw-rw-r--  1 work work   112 Aug 27 11:48 atlas_strsmXover.h
-rw-rw-r--  1 work work   191 Aug 27 11:48 atlas_trsmNB.h
-rw-rw-r--  1 work work   562 Aug 27 11:48 atlas_type.h
-rw-rw-r--  1 work work    77 Aug 27 11:48 atlas_zdNKB.h
-rw-rw-r--  1 work work   147 Aug 27 11:48 atlas_zmv.h
-rw-rw-r--  1 work work   451 Aug 27 11:48 atlas_zmvN.h
-rw-rw-r--  1 work work   386 Aug 27 11:48 atlas_zmvS.h
-rw-rw-r--  1 work work   481 Aug 27 11:48 atlas_zmvT.h
-rw-rw-r--  1 work work   455 Aug 27 11:48 atlas_zNCmm.h
-rw-rw-r--  1 work work   353 Aug 27 11:48 atlas_zr1.h
-rw-rw-r--  1 work work   195 Aug 27 11:48 atlas_zsysinfo.h
-rw-rw-r--  1 work work     0 Aug 27 11:48 atlas_ztrsmXover.h
-rw-r--r--  1 work work 33895 Aug 28 16:17 cblas.h
-rw-r--r--  1 work work  8225 Aug 28 16:17 clapack.h
-rw-rw-r--  1 work work  2719 Aug 27 11:48 cmm.h
-rw-rw-r--  1 work work   540 Aug 27 11:48 cXover.h
-rw-rw-r--  1 work work   657 Aug 27 11:48 dmm.h
-rw-rw-r--  1 work work   526 Aug 27 11:48 dXover.h
-rw-r--r--  1 work work 86216 Aug 24 16:01 gmp.h
drwxrwxr-x  2 work work  4096 Aug 23 20:48 lzma
-rw-r--r--  1 work work  9274 Aug 23 20:48 lzma.h
-rw-r--r--  1 work work 13049 Aug 24 16:06 mpc.h
-rw-r--r--  1 work work  6288 Aug 24 15:53 mpf2mpfr.h
-rw-r--r--  1 work work 47981 Aug 24 15:53 mpfr.h
-rw-rw-r--  1 work work   658 Aug 27 11:48 smm.h
-rw-rw-r--  1 work work   523 Aug 27 11:48 sXover.h
-rw-rw-r--  1 work work  2718 Aug 27 11:48 zmm.h
-rw-rw-r--  1 work work   555 Aug 27 11:48 zXover.h


Many thanks
John
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