Arkansas High Performace Computing Center [hpcwiki]

Compilation

With Intel compiler and either OpenMPI or MVAPICH2:

OpenMPI:
DFLAGS         = -D__INTEL -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK $(MANUAL_DFLAGS)
IFLAGS         = -I../include
MPIF90         = mpif90
CFLAGS         = -O3 -xSSE2 -axavx $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -O2 -xSSE2 -axavx -assume byterecl -g -traceback -par-report0 -vec-report0
FFLAGS_NOOPT   = -O0 -assume byterecl -g -traceback
FFLAGS_NOMAIN  = -nofor_main
LD             = mpif90
LDFLAGS        = -static-intel 
SCALAPACK_LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64
FFT_LIBS       = -L ${MKL_ROOT}/interfaces/fftw3xf -lfftw3xf_intel

MVAPICH2: same except
SCALAPACK_LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64

trestles: same except
no -axavx (though an "optional" code path, it makes the program fail on AMD)

Benchmarks

We run AUSURF112 from Espresso Benchmarks and compare with Glenn Lockwood who ran the AUSURF112 benchmark on SDSC Comet and on the Trestles system when it was at SDSC. Unfortunately, the AUSURF112 benchmark generally ends the simulation with convergence NOT achieved after 2 iterations: stopping, but it does so fairly repeatably so may be timed.

OpenMPI:
module load intel/14.0.3 mkl/14.0.3 openmpi/1.8.8 
mpirun -np 64  -machinefile $PBS_NODEFILE -x LD_LIBRARY_PATH \
/share/apps/espresso/espresso-5.1-intel-openmpi/bin/pw.x -npools 1 <ausurf.in
MVAPICH2:
module load intel/14.0.3 mkl/14.0.3 mvapich2/2.1
mpirun -np 64  -machinefile $PBS_NODEFILE \
/share/apps/espresso/espresso-5.1-intel-mvapich2/bin/pw.x -npools 1 <ausurf.in

The tables shows Lockwood's and our times. We add 32×4 core runs for Trestles as we think node-to-node is the more representative comparison. Our newer versions of OpenMPI show better results on the almost-identical hardware than Lockwood.

(1) Fails with error charge is wrong.

Notes

Each run fails with error messages (depending on MPI type) and RC 1 after terminating normally according to the log. This appears harmless:

   This run was terminated on:  13: 2:44  11Nov2015            
=------------------------------------------------------------------------------=
   JOB DONE.
=------------------------------------------------------------------------------=
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
------------------------------------------------------------
A process or daemon was unable to complete a TCP connection
to another process:
etc.

Continuing Work

ELPA in newer versions of Espresso is reportedly faster than Scalapack.

OpenMPI threading.

MKL threading.

FFTW fft vs. Intel fft on AMD.

On Trestles with Intel tools. It's difficult to find a combination of versions that is new enough to compile qe-6.6 yet will still produce a binary that runs on AMD Bulldozer.

module load intel/17.0.4 impi/19.0.5 impi/19.0.5
OMP_NUM_THREADS=# mpirun -np ## -machinefile machinefile /share/apps/espresso/q-e-qe-6.6/bin/pw.x <ausurf.in

q-e appears to be a code that does not like mpi threads x OMP threads > cores. Performance on two trestles nodes is a lot better than the previous 5.1 benchmarks.

cores Node type         #nodes  #OMP    WALL
32  Trestles AMD           1      1    13m16s
32  Trestles AMD           1      2    50m41s
32  Trestles AMD           2      1     8m32s

Install script

OMP="--enable-openmp"
./install/configure MPIF90=mpiifort F90=ifort F77=ifort FC=ifort CC=icc SCALAPACK_LIBS="-L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" LAPACK_LIBS="-L$MKLROOT/lib/intel64 -lmkl_lapack95_lp64 -lmkl_blas95_lp64" BLAS_LIBS="-lmkl_intel_lp64  -lmkl_intel_thread -lmkl_core -liomp5 -thread" FFT_LIBS="-L$MKLROOT/interfaces/fftw3xf -lfftw3xf_intel" FFLAGS="-O3 -xHOST -D__INTEL -D__GNUC__ -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK -assume byterecl -I$MKLROOT/include/fftw" CFLAGS="-O3 -xHOST -D__INTEL -D__GNUC__ -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK" --with-hdf5=/share/apps/hdf5/1.10.5/intel/impi -with-scalapack=intel --enable-parallel $OMP --prefix=/share/apps/espresso/espresso-6.6-intel-impi-mkl-trestles