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

Xiong Deng dbigbear@gmail....
Mon Aug 29 04:13:53 CDT 2011


Hi,

I just find out that the gcc-4.7 is downloaded as a binary distri. I did not
compile gcc-4.7 myself...

The gcc included on my system is gcc 3.4.5 and there seems no gfortran built
on it (However there is a g77 on it, which cause problems while building
numpy/scipy....)...In addition, there are not mpc, mpfr, gmp on it with gcc
3.4.5, so I need a new gcc with gfortran, mpc ,mpfr ,gmp, which is necessay
for numpy/scipy....

Btw: I am not sure if there is a way to install mpc, mpfr, and gmp, after
gcc has been installed and link gcc with mpc, mpfr, gmp...

Many thanks
XIong


Message: 2
Date: Mon, 29 Aug 2011 10:12:03 +0200
From: David Cournapeau <cournape@gmail.com>
Subject: Re: [SciPy-User] Error when building scipy.0.9.0 - "f951:
       undefined symbol: mpfr_get_z_exp"
To: SciPy Users List <scipy-user@scipy.org>
Message-ID:
       <CAGY4rcUTB=7nmS0Q6P_5Dd50YeO0W5PNxuQTHdaJJDYPXx8wew@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

On Mon, Aug 29, 2011 at 9:13 AM, Xiong Deng <dbigbear@gmail.com> wrote:
> 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 ???
>
> Most likely, you did not build gcc  and gfortran correctly. Why don't
> you use the gcc included on your system ?
>
> cheers,
>
> David
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