[SciPy-User] RHEL6 build issues

Skylar Thompson skylar2@u.washington....
Fri Feb 24 14:11:47 CST 2012


Hi,

I'm trying to build scipy for x86_64 RHEL 6.2. I'm running into problems 
with linking at the end. I keep getting errors like this:


/net/gs/vol3/software/modules-sw-test/gcc/4.6.2/Linux/RHEL6/x86_64/bin/gfortran 
-Wall 
-L/net/gs/vol3/software/modules-sw-test/python/1.5.1/Linux/RHEL6/x86_64//lib/ 
-L/net/gs/vol3/software/modules-sw-test/ATLAS/3.9.63/Linux/RHEL6/x86_64//lib/ 
-L/net/gs/vol3/software/modules-sw-test/gcc/4.6.2/Linux/RHEL6/x86_64/lib64/ 
-L/net/gs/vol3/software/modules-sw-test/gcc/4.6.2/Linux/RHEL6/x86_64/lib/ -L/net/gs/vol3/software/modules-sw-test/gmp/5.0.2/Linux/RHEL6/x86_64//lib/ 
-L/net/gs/vol3/software/modules-sw-test/mpfr/3.1.0/Linux/RHEL6/x86_64//lib/ 
-L/net/gs/vol3/software/modules-sw-test/mpc/0.8.2/Linux/RHEL6/x86_64//lib/ 
-L/net/gs/vol3/software/modules-sw-test/python/2.7.2/Linux/RHEL6/x86_64//lib/ 
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/fftpack/_fftpackmodule.o 
build/temp.linux-x86_64-2.7/scipy/fftpack/src/zfft.o 
build/temp.linux-x86_64-2.7/scipy/fftpack/src/drfft.o 
build/temp.linux-x86_64-2.7/scipy/fftpack/src/zrfft.o 
build/temp.linux-x86_64-2.7/scipy/fftpack/src/zfftnd.o 
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/fftpack/src/dct.o 
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.o 
-L. -Lbuild/temp.linux-x86_64-2.7 -ldfftpack -lfftpack -lpython2.7 
-lgfortran -o build/lib.linux-x86_64-2.7/scipy/fftpack/_fftpack.so
/usr/lib/../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status
/usr/lib/../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status
error: Command 
"/net/gs/vol3/software/modules-sw-test/gcc/4.6.2/Linux/RHEL6/x86_64/bin/gfortran 
-Wall 
-L/net/gs/vol3/software/modules-sw-test/python/1.5.1/Linux/RHEL6/x86_64//lib/ 
-L/net/gs/vol3/software/modules-sw-test/ATLAS/3.9.63/Linux/RHEL6/x86_64//lib/ 
-L/net/gs/vol3/software/modules-sw-test/gcc/4.6.2/Linux/RHEL6/x86_64/lib64/ 
-L/net/gs/vol3/software/modules-sw-test/gcc/4.6.2/Linux/RHEL6/x86_64/lib/ -L/net/gs/vol3/software/modules-sw-test/gmp/5.0.2/Linux/RHEL6/x86_64//lib/ 
-L/net/gs/vol3/software/modules-sw-test/mpfr/3.1.0/Linux/RHEL6/x86_64//lib/ 
-L/net/gs/vol3/software/modules-sw-test/mpc/0.8.2/Linux/RHEL6/x86_64//lib/ 
-L/net/gs/vol3/software/modules-sw-test/python/2.7.2/Linux/RHEL6/x86_64//lib/ 
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/fftpack/_fftpackmodule.o 
build/temp.linux-x86_64-2.7/scipy/fftpack/src/zfft.o 
build/temp.linux-x86_64-2.7/scipy/fftpack/src/drfft.o 
build/temp.linux-x86_64-2.7/scipy/fftpack/src/zrfft.o 
build/temp.linux-x86_64-2.7/scipy/fftpack/src/zfftnd.o 
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/fftpack/src/dct.o 
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.o 
-L. -Lbuild/temp.linux-x86_64-2.7 -ldfftpack -lfftpack -lpython2.7 
-lgfortran -o build/lib.linux-x86_64-2.7/scipy/fftpack/_fftpack.so" 
failed with exit status 1

I've built ATLAS, LAPACK, BLAS, and numpy with a custom-built gfortran 
4.6.2, and I've made sure every build uses that particular gfortran. 
Unfortunately, I can't use the RHEL-provided gcc/gfortran because it 
segfaults when trying to build LAPACK. I've also tried using the Oracle 
Studio compiler suite, with similar errors. I've tried various 
combinations of versions for each component involved, without success.[1]

Has anyone else seen this problem and solved it? Thanks in advance for 
any help!

[1] ATLAS (3.8.4, 3.9.35, and 3.9.63), numpy (1.5.1 and 1.6.1), LAPACK 
(3.3.0 and 3.4.0), and scipy (0.7.2, 0.8.0, 0.9.0, 0.10.0, 0.10.1rc1 and 
rc2).

-- 
-- Skylar Thompson (skylar2@u.washington.edu)
-- Genome Sciences Department, System Administrator
-- Foege Building S046, (206)-685-7354
-- University of Washington School of Medicine


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