ABINIT Discussion Forums

Dear all,

I encountered the problem of configuring MKL. Could some experts help me with it? Even after reading Joe and Alain's posts, I have no idea how to configure with -O3 xHOST -ip. Is it set in FCFLAGS?
The following is my configuration:

rundong@rundong-home:~/Downloads/abinit-6.4.1/build$ ../configure --enable-64bit-flags=yes --prefix=/opt/abinit FCFLAGS_EXTRA="-heap-arrays 1024" --enable-mpi=yes --with-mpi-prefix=/opt/openmpi --enable-mpi-io=yes --with-linalg-includes="-I/opt/Compiler/11.1/073/mkl/include" --with-linalg-flavor=mkl --with-linalg-libs="-L/opt/intel/Compiler/11.1/073/mkl/lib/em64t -llibmkl_intel_lp64 -llibmkl_sequential -llibmkl_core" --enable-bse-unpacked=yes --enable-gw-cutoff=yes --enable-gw-dpc=yes --enable-gw-optimal=yes --enable-gw-wrapper=yes --enable-mpi-io-test=yes

no matter what I try, the log file keeps telling me

ld: cannot find -llibmkl_intel_lp64

no matter what I have done, such as changing the /etc/ld.so.conf file. By the way, a configuration without MKL just worked fine.
Help is desperately needed.
Many thanks in advance

Regards,
Rundong

Hello Rundong,

There is at least a problem in your

--with-linalg-libs="-L/opt/intel/Compiler/11.1/073/mkl/lib/em64t -llibmkl_intel_lp64 -llibmkl_sequential -llibmkl_core"

If you want to link against a library named libmkl_intel_lp64.so, you have to strip the "lib" part of the name to append to "-l" i.e. -lmkl_intel_lp64 will link against libmkl_intel_lp64.so but -llibmkl_intel_lp64 will fail to find a liblibmkl_intel_lp64.so file. This is the explanation for the error message from ld.

You can push your own optimization flags with FCFLAGS but it has drawbacks - the per-directory optimizations will be messed. I would rather advise to leave FCFLAGS untouched and try --enable-optim=aggressive configuration mod if you have a recent abinit source; it should switch to higher performance settings but don't forget to run the test suite to check accuracy.

Kind regards,

Alain

Hi, Alain,

Thank you very much for the timely help. It solved my problem. Now I have mkl serial version. I guess if I need mpi version I should install intel mpi.
As you suggested, I also used aggressive approach.

Best regards,
Rundong

It depends on what you mean by Intel MPI. Intel sells its own proprietary MPI Library. I have no experience with that one; don't even know if it compiles Abinit.
What is routinely tested is MPI-2 libraries provided by OpenMPI or MPICH2. Both are working fine. The idea is to build an MPI library, parallelizing compilers and launchers (named mpicc, mpif90, mpirun, ...) with the backend compilers (gcc/gfortran or icc/ifort) you intend to use; not a complicated task but has to be adapted to your hardware environment (a plain SMP box, a cluster with Infiniband, ...). And then reconfigure Abinit with --enable-mpi and --with-mpi-prefix=xxx (xxx as your mpif90 resides in xxx/bin/mpif90). Check the options syntax with configure --help; I may have misspelled them - and they change from time to time.

Kind regards,

Alain

Thanks again, Alain.
I have setup openmpi stuff on my computer, but your suggestions is very inspirational.

Best regards,
Rundong