Hello numpy users, I am trying to build numpy 1.6.1 and am having problems. It prints the following error message: gcc -pthread -shared build/temp.linux-x86_64-2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux-x86_64-2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64-2.4/numpy/core/_dotblas.so /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-x86_64-2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux-x86_64-2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64-2.4/numpy/core/_dotblas.so" failed with exit status 1 I do not know anything about the setup.py script, so do not know how to add the -fPIC switch. Any help will be greatly appreciated. Regards, ---------- Wadud Miah, High Performance Computing Systems Developer Research Computing Services, University of East Anglia Web: http://www.uea.ac.uk/~xca10fju/ Telephone: 01603 593856 Information Services ----------
On Tue, Oct 4, 2011 at 11:54 AM, Miah Wadud Dr (ITCS) <W.Miah@uea.ac.uk> wrote:
Hello numpy users,
I am trying to build numpy 1.6.1 and am having problems. It prints the following error message:
gcc -pthread -shared build/temp.linux-x86_64-2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux-x86_64-2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64-2.4/numpy/core/_dotblas.so /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-x86_64-2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux-x86_64-2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64-2.4/numpy/core/_dotblas.so" failed with exit status 1
Did you build Atlas by yourself ? If so, it is most likely not usable for shared libraries (mandatory for any python extension, including bumpy). You need to configure atlas with the option "-Fa alg -fPIC". David
Hi David, Thanks for your reply. Nope, I didn't build the ATLAS libraries myself and am trying to do that now. However, whenever I try to build the shared libraries using the configure command: [root@cn130 linux]# ../configure -Fa alg -fPIC --prefix=/gpfs/grace/atlas-3.8.4 it keeps building the static version. The ATLAS documentation stated that I need to provide the above flags to build the dynamic ones but this doesn't seem to work. Any help will be greatly appreciated. Thanks in advance. Regards, Wadud.
-----Original Message----- From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion- bounces@scipy.org] On Behalf Of David Cournapeau Sent: Tuesday, October 04, 2011 6:40 PM To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] build errors
On Tue, Oct 4, 2011 at 11:54 AM, Miah Wadud Dr (ITCS) <W.Miah@uea.ac.uk> wrote:
Hello numpy users,
I am trying to build numpy 1.6.1 and am having problems. It prints the following error message:
gcc -pthread -shared build/temp.linux-x86_64- 2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux-x86_64- 2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64- 2.4/numpy/core/_dotblas.so /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-x86_64- 2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux-x86_64- 2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64- 2.4/numpy/core/_dotblas.so" failed with exit status 1
Did you build Atlas by yourself ? If so, it is most likely not usable for shared libraries (mandatory for any python extension, including bumpy). You need to configure atlas with the option "-Fa alg -fPIC".
David _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Hi again, I have built the ATLAS dynamic shared libraries and now need to tell numpy to build against them which are located in a different location to where it expects them. Do you know how I can do that? The command I am using to build numpy is: python setup.py build --fcompiler=gnu95 but this looks in /usr/lib64/atlas and I need it to look in another location (/gpfs/grace/atlas-3.8.4). Thanks in advance, Regards.
-----Original Message----- From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion- bounces@scipy.org] On Behalf Of Miah Wadud Dr (ITCS) Sent: Thursday, October 06, 2011 11:12 AM To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] build errors
Hi David,
Thanks for your reply. Nope, I didn't build the ATLAS libraries myself and am trying to do that now. However, whenever I try to build the shared libraries using the configure command:
[root@cn130 linux]# ../configure -Fa alg -fPIC --prefix=/gpfs/grace/atlas-3.8.4
it keeps building the static version. The ATLAS documentation stated that I need to provide the above flags to build the dynamic ones but this doesn't seem to work.
Any help will be greatly appreciated. Thanks in advance.
Regards, Wadud.
-----Original Message----- From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion- bounces@scipy.org] On Behalf Of David Cournapeau Sent: Tuesday, October 04, 2011 6:40 PM To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] build errors
On Tue, Oct 4, 2011 at 11:54 AM, Miah Wadud Dr (ITCS) <W.Miah@uea.ac.uk> wrote:
Hello numpy users,
I am trying to build numpy 1.6.1 and am having problems. It prints the following error message:
gcc -pthread -shared build/temp.linux-x86_64- 2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux- x86_64- 2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64- 2.4/numpy/core/_dotblas.so /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-x86_64- 2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux- x86_64- 2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64- 2.4/numpy/core/_dotblas.so" failed with exit status 1
Did you build Atlas by yourself ? If so, it is most likely not usable for shared libraries (mandatory for any python extension, including bumpy). You need to configure atlas with the option "-Fa alg -fPIC".
David _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
You can use the BLAS and LAPACK environment variables. export BLAS=/path/to/libatlas.so export LAPACK=/path/to/libatlas.so python setup.py build .... I've recently had problems with ATLAS solving equation systems incorrectly for certain inputs with no adequate explanation. Re-running the same simulation but linking to Goto2 BLAS/LAPACK instead solved the problem. Strange, yet worrisome. YMMV! Cheers Paul On Thu, Oct 6, 2011 at 3:05 PM, Miah Wadud Dr (ITCS) <W.Miah@uea.ac.uk> wrote:
Hi again,
I have built the ATLAS dynamic shared libraries and now need to tell numpy to build against them which are located in a different location to where it expects them. Do you know how I can do that? The command I am using to build numpy is:
python setup.py build --fcompiler=gnu95
but this looks in /usr/lib64/atlas and I need it to look in another location (/gpfs/grace/atlas-3.8.4).
Thanks in advance, Regards.
-----Original Message----- From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion- bounces@scipy.org] On Behalf Of Miah Wadud Dr (ITCS) Sent: Thursday, October 06, 2011 11:12 AM To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] build errors
Hi David,
Thanks for your reply. Nope, I didn't build the ATLAS libraries myself and am trying to do that now. However, whenever I try to build the shared libraries using the configure command:
[root@cn130 linux]# ../configure -Fa alg -fPIC --prefix=/gpfs/grace/atlas-3.8.4
it keeps building the static version. The ATLAS documentation stated that I need to provide the above flags to build the dynamic ones but this doesn't seem to work.
Any help will be greatly appreciated. Thanks in advance.
Regards, Wadud.
-----Original Message----- From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion- bounces@scipy.org] On Behalf Of David Cournapeau Sent: Tuesday, October 04, 2011 6:40 PM To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] build errors
On Tue, Oct 4, 2011 at 11:54 AM, Miah Wadud Dr (ITCS) <W.Miah@uea.ac.uk> wrote:
Hello numpy users,
I am trying to build numpy 1.6.1 and am having problems. It prints the following error message:
gcc -pthread -shared build/temp.linux-x86_64- 2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux- x86_64- 2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64- 2.4/numpy/core/_dotblas.so /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-x86_64- 2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux- x86_64- 2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64- 2.4/numpy/core/_dotblas.so" failed with exit status 1
Did you build Atlas by yourself ? If so, it is most likely not usable for shared libraries (mandatory for any python extension, including bumpy). You need to configure atlas with the option "-Fa alg -fPIC".
David _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
participants (3)
-
David Cournapeau -
Miah Wadud Dr (ITCS) -
Paul Anton Letnes