Hi I'm working again with the solver mkl-cpardiso. I did my implementation, the
configuration works well, the problem is during compilation. The linking flags
petsc is using are the followings:
-Wl,-rpath,/home/jbermeol/software/test/arch-linux2-c-opt/lib
-L/home/jbermeol/software/test/arch-linux2-c-opt/lib -lpetsc -Wl,--start-group
-L/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64 -lmkl_intel_lp64
-lmkl_intel_thread -lmkl_core -Wl,--end-group -lpthread -lm -liomp5 -mt_mpi
-Wl,--start-group
-L/home/jbermeol/testPetscSolvers/intel_mkl_cpardiso/lib/intel64
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -lcpardiso_lp64
-lcpardiso_mpi_lp64 -lpthread -lm -liomp5 -lifcore
-Wl,-rpath,/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64
-L/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64 -lmkl_intel_lp64
-lmkl_sequential -lmkl_core -lpthread -lm -lX11 -lpthread
-Wl,-rpath,/apps/rhel6/intel/impi/4.1.0.030/intel64/lib
-L/apps/rhel6/intel/impi/4.1.0.030/intel64/lib
-Wl,-rpath,/apps/rhel6/intel/composer_xe_2013.3.163/compiler/lib/intel64
-L/apps/rhel6/intel/composer_xe_2013.3.163/compiler/lib/intel64
-Wl,-rpath,/apps/rhel6/intel/composer_xe_2013.3.163/ipp/lib/intel64
-L/apps/rhel6/intel/composer_xe_2013.3.163/ipp/lib/intel64
-Wl,-rpath,/apps/rhel6/intel/composer_xe_2013.3.163/tbb/lib/intel64
-L/apps/rhel6/intel/composer_xe_2013.3.163/tbb/lib/intel64
-Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.4.7
-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7
-Wl,-rpath,/home/jbermeol/software/test/-Xlinker
-Wl,-rpath,/opt/intel/mpi-rt/4.1 -lifport -lifcore -lm -lm -lmpigc4 -ldl
-lmpigf -lmpi -lmpigi -lrt -lpthread -limf -lsvml -lirng -lipgo -ldecimal
-lcilkrts -lstdc++ -lgcc_s -lirc -lirc_s -ldl
The problem is with flag "-mt_mpi", this flag is telling to the Intel compiler,
please link with the library libmpi_mt.so(this is a thread safe library for
intel mpi). However petsc adds the flag "-lmpi" that links with libmpi.so.
Because of this I'm gettig the following error:
ld: MPIR_Thread: TLS definition in
/apps/rhel6/intel/impi/4.1.0.030/intel64/lib/libmpi_mt.so section .tbss
mismatches non-TLS definition in
/apps/rhel6/intel/impi/4.1.0.030/intel64/lib/libmpi.so section .bss
So the first question would be where is this "-lmpi" library flag added??
Second how can I compile using the thread save mpi library from intel??
Is there a way to set a dependency such that the solver cpardiso is not
installed if petsc is compiled without this thread safe library??
I don't know yet how to check if petsc is been configure with mkl blas/lapack
Thanks
