Dear Kamil, This still seems to suggest that the version in your home directory is not compiled with -fPIC. Try deleting all library files (*.a) and all compiled object code (*.o) from within the LAPACK source tree and try compiling from fresh again. Also note that you need to add the -fPIC flag to both the OPTS and NOOPT variables in your LAPACK make.inc file (which presumably is what your system administrator altered). Cheers, Chris On 29/11/14 22:29, Kamil ÖZDEN wrote:
Dear Dr. Cantwell,
Here is the error message I got :
/*[ 19%] Building CXX object library/LibUtilities/CMakeFiles/LibUtilities.dir/GitRevision.cpp.o*//* *//*Linking CXX shared library libLibUtilities.so*//* *//*/usr/bin/ld: /truba/home/kozden/lib/lapack/netlib-3.5.0-gcc/liblapack.a(dlamch.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC*//* *//*/truba/home/kozden/lib/lapack/netlib-3.5.0-gcc/liblapack.a: could not read symbols: Bad value*//* *//*collect2: ld returned 1 exit status*//* *//*make[2]: *** [library/LibUtilities/libLibUtilities.so.4.0.0] Error 1*//* *//*make[1]: *** [library/LibUtilities/CMakeFiles/LibUtilities.dir/all] Error 2*//* *//*make: *** [all] Error 2*/
Regards, Kamil
30.11.2014 00:08 tarihinde, Chris Cantwell yazdı:
Dear Kamil,
Could you send the current error message you get when you specify the version of the library compiled with -fPIC?
Cheers, Chris
On 29/11/14 21:55, Kamil ÖZDEN wrote:
Dear Dr. Cantwell,
Yes, it is the same version of the library compiled with -fPIC version.
Regards, Kamil
29.11.2014 23:48 tarihinde, Chris Cantwell yazdı:
Dear Kamil,
Can you confirm the library mentioned in the original error message (/truba/sw/centos6.4/lib/lapack/netlib-3.5.0-gcc/liblapack.a) is now the version of the library in your home directory in the latest error message?
Cheers, Chris
On 27/11/14 13:57, Kamil Ozden wrote:
Dear Dr. Moxey,
I got in contact with the system administrator. He told that it is impossible to recompile blas and lapack on the system with -fPIC option.
Alternatively, he copied the Blas and Lapack libraries from the directory in the system to another folder in my home directory and recompiled them there with -fPIC option.
However, when I tried to reinstall Nektar by showing the path of new Blas and Lapack libraries in my home directory I got the same error. Is there any other alternative way to overcome this problem?
Regards, Kamil
On 27-11-2014 13:10, David Moxey wrote:
Hi Kamil,
The issue is related to linking. We generate shared libraries in Nektar++, but here we are trying to link the shared library with a static library. You can only do this if the static library was compiled with the -fPIC option, which generates position-independent code that shared libraries need in order to work at runtime.
If you have a shared library, you should use this. Otherwise, you should recompile BLAS/Lapack installation with the -fPIC option. This may be something that your cluster system administrators can help with.
Thanks,
Dave
> On 27 Nov 2014, at 10:37, Kamil ÖZDEN <kamil.ozden.me@gmail.com> > wrote: > > Dear All, > > I'm trying to install Nektar++ 4.0 to a cluster with the options > > NEKTAR_USE_BLAS_LAPACK ON > NEKTAR_USE_SYSTEM_BLAS_LAPACK ON > > with the path of the libraries as follows: > > NATIVE_BLAS > /truba/sw/centos6.4/lib/blas/netlib-gcc/blas_LINUX.a > NATIVE_LAPACK > /truba/sw/centos6.4/lib/lapack/netlib-3.5.0-gcc/liblapack.a > > However, I'm getting the following error: > > Linking CXX shared library libLibUtilities.so > /usr/bin/ld: > /truba/sw/centos6.4/lib/lapack/netlib-3.5.0-gcc/liblapack.a(dgbtrf.o): > > relocation > R_X86_64_32 against `.rodata' can not be used when making a shared > object; recompile with -fPIC > /truba/sw/centos6.4/lib/lapack/netlib-3.5.0-gcc/liblapack.a: could > not read symbols: Bad value > collect2: ld returned 1 exit status > make[2]: *** [library/LibUtilities/libLibUtilities.so.4.0.0] Error 1 > make[1]: *** [library/LibUtilities/CMakeFiles/LibUtilities.dir/all] > Error 2 > make: *** [all] Error 2 > > What may be the reason for this problem and how can I solve it? > > Regards, > Kamil > > _______________________________________________ > Nektar-users mailing list > Nektar-users@imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
-- David Moxey (Research Associate) d.moxey@imperial.ac.uk | www.imperial.ac.uk/people/d.moxey
Room 363, Department of Aeronautics, Imperial College London, London, SW7 2AZ, UK.
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-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell