User:Manoj
VASP BENCHMARKING
Performance on Intel Machine ( E5-2643 @ 3.30GHz)
VASP Naive FFT Library
Following library and flags were used:
MKLDIR = $(HPC_MKL_DIR)
MKLLIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
MKLLIBDIR = $(HPC_MKL_DIR)/lib/intel64
FFTLIB = -lfftw3xf
INCS = -I$(MKLDIR)/include/fftw
FFT_OBJS = fftmpi.o fftmpi_map.o fftw3d.o fft3dlib.o
FFLAGS = -free -names lowercase -assume byterecl
OFLAG = -O2 -xsse2 -unroll-aggressive -warn general
As a first check, SIMD were changed and following is the result for MgMOS (For input file, please ask Charles Taylor or Manoj Srivastava):
| SIMD Instruction | Time(s) |
|---|---|
| sse2 | 158 |
| sse4.1 | 156 |
| sse4.2 | 155 |
| avx | 155 |
| ssse3 | 156 |
MKL FFTs (via FFTW wrappers)
Upon profiling the code, we found that the code spends most of its time in the FFT libraries, so the next step is to change FFTW libraries. Following changes were made:
FFT_OBJS = fftmpi_map.o fftmpiw.o fftw3d.o fft3dlib.o
(The change here is replacement of "fftmpi.o" of the original VASP makefile with "fftmpiw.o")
MKLDIR = $(HPC_MKL_DIR)
MKLLIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
MKLLIBDIR = $(HPC_MKL_DIR)/lib/intel64
FFTLIB = -lfftw3xf
INCS = -I$(MKLDIR)/include/fftw
FFLAGS = -free -names lowercase -assume byterecl
OFLAG = -O2 -xsse2 -unroll-aggressive -warn general
Upon making above changes, about 60% improvement on the run time of the code was found on the Intel machine (E5-2643 @ 3.30GHz). Following table depicts the run time variation with SIMD instruction sets:
| SIMD Instruction | Time(s) |
|---|---|
| sse2 | 97 |
| sse4.1 | 95 |
| sse4.2 | 94 |
| avx | 94 |
| ssse3 | 94 |
FFTW FFTs
We further compiled VASP by using FFT library from FFTW with following flags:
MKLDIR = $(HPC_MKL_DIR)
MKLLIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
MKLLIBDIR = $(HPC_MKL_DIR)/lib/intel64
FFTWDIR = /apps/fftw/3.3.2
FFTLIB = -L$(FFTWDIR)/lib -lfftw3
INCS = -I$(FFTWDIR)/include
FFT_OBJS = fftmpi_map.o fftmpiw.o fftw3d.o fft3dlib.o
FFLAGS = -free -names lowercase -assume byterecl
OFLAG = -O2 -xsse2 -unroll-aggressive -warn general
From our previous experience, we conclude that the performance of VASP does not depend substantially on the SIMD instruction sets, so for FFTW library, we only tried one set. Following is the result:
| SIMD Instruction | Time(s) |
|---|---|
| sse2 | 118 |
Performance on AMD Machine (Opteron 6220 @ 3.0 GHz) and Comparison with Intel ( E5-2643 @ 3.30GHz)
This machine has 16 cores, in numactl terminology numanodes with 4 cores on each nodes. As the result of VASP depends heavily on the choice of FFT libraries, we checked various performance of this machine with different FFTs, namely, FFT provided by VASP package, MKL, and FFTW. We build FFTW libraries with various flags to see if we could find a better choice for FFTs. The libraries and flags used to compile VASP are as follows (FFT libraries were changed depending on which FFT we want to use):
MKLDIR = $(HPC_MKL_DIR)
MKLLIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
MKLLIBDIR = $(HPC_MKL_DIR)/lib/intel64
FFTWDIR = /apps/fftw/3.3.2
FFTLIB = -L$(FFTWDIR)/lib -lfftw3
INCS = -I$(FFTWDIR)/include
FFT_OBJS = fftmpi_map.o fftmpiw.o fftw3d.o fft3dlib.o
FFLAGS = -free -names lowercase -assume byterecl
OFLAG = -O2 -xsse2 -unroll-aggressive -warn general
The results are summarized in the following table:
| FFT Library | Shared L2-Cached time(s) | Exclusive L2-Cache time (s) | Notes |
|---|---|---|---|
| Naive (VASP) | 399 | ||
| MKL | 261 | 159 | |
| FFTW | 333 | 217 | 1 |
| FFTW | - | 203 | 2 |
| FFTW | - | 210 | 3 |
| FFTW | - | 217 | 4 |
| FFTW | - | 213 | 5 |
1 No Flags were used to build FFT.
2 CFLAG=-O3, FFLAG=-O3, -enable sse2
3 enable-mpi CFLAG=-O3, FFLAG=-O3, -enable sse2
4 CC='opencc -march=bdver1' F77='openf90 -march=bdver1' CFLAGS='-msse3 -msse4.1 -msse4.2 -msse4a -mfma4 -O2' FFLAGS='-msse3 -msse4.1 -msse4.2 -msse4a -mfma4 -O2' --enable-fma --enable-mpi
5 FFLAGS/ CFLAGS="-OPT:Ofast -mavx -mfma4 -march=bdver1 -O3 -fomit-frame-pointer -LNO:simd=2 -WOPT:sib=on -LNO:prefetch=2:pf2=0 -CG:use_prefetchnta=on -LNO:prefetch_ahead=4-malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math"