Dear Dr. Cantwell, I do your suggestions and add -fPIC to the variables and compiled Nektar with BLAS and LAPACK again. As a result, I did not get the previous error. But I've another error now which is: /*[ 55%] Built target SolverUtils*//* *//*Linking CXX executable UnitTests*//* *//*../LibUtilities/libLibUtilities.so.4.0.0: undefined reference to `_gfortran_stop_numeric'*//* *//*../LibUtilities/libLibUtilities.so.4.0.0: undefined reference to `_gfortran_transfer_character'*//* *//*../LibUtilities/libLibUtilities.so.4.0.0: undefined reference to `_gfortran_compare_string'*//* *//*../LibUtilities/libLibUtilities.so.4.0.0: undefined reference to `_gfortran_st_write_done'*//* *//*../LibUtilities/libLibUtilities.so.4.0.0: undefined reference to `_gfortran_concat_string'*//* *//*../LibUtilities/libLibUtilities.so.4.0.0: undefined reference to `_gfortran_string_len_trim'*//* *//*../LibUtilities/libLibUtilities.so.4.0.0: undefined reference to `_gfortran_transfer_integer'*//* *//*../LibUtilities/libLibUtilities.so.4.0.0: undefined reference to `_gfortran_st_write'*//* *//*collect2: ld returned 1 exit status*//* *//*make[2]: *** [library/UnitTests/UnitTests-4.0.0] Error 1*//* *//*make[1]: *** [library/UnitTests/CMakeFiles/UnitTests.dir/all] Error 2*//* *//*make: *** [all] Error 2*/ Is there another thing that I need to change in make.inc file of BLAS and LAPACK to overcome this problem? Regards, Kamil 30.11.2014 13:08 tarihinde, Chris Cantwell yazdı:
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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