Difference between revisions of "User:Manoj"

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Revision as of 20:44, 6 June 2013

STREAM

A few words about numactl

NUMA is an acronym for Non Uniform Memory Access, and numactl is a tool to assign memory to the node. Following are a few important keywords one should know before embarking on the numactl mission: 

physcpubind = ID of the cores
cpunodebind = ID of the nodes
membind = ID of the node that the memory is assigned to

For example, on an AMD machine with 16 cores, or in the terminology of NUMA, 4 nodes with 4 cores on each node, the command line 

–membind=0 –physcpubind=0-3

asigns four threads running on cores 0 to 3 (node 0) with the memory also assigned to the node 0. However, the command line 

–membind=1 –physcpubind=0-3

assigns four threads on the cores 0 to 3 (node 0) but the memory is assigned to the node 1. As this memory is not local to the node that the threads are running on, the performance will be affected. Assigning memory locally to the node can also be done by ”-l” option of the numactl.

Alternatively, above command lines can be shortened by using "cpunodebind". For example, 

–membind=0 –cpunodebind=0

means that the memory is assigned to node 0 and the threads are also running on node 0. One should note that with the use of "cpunodebind" the number of threads will be equal to the number of cores on the node, so in this case number of threads has to be equal to four. However, if we wish to run two threads on node 0, its only possible with "physcpubind". You have more control of running your threads with "physcpubind" as you can choose the cores that you wish to run your jobs on. For detail description please follow the manual page of numactl.

Intel (2 x E5-2643 @ 3.30GHz)

Streams is a well-known memory bandwidth benchmark. Before we attempt to find the maximum bandwidth, it's necessary to find out the architecture of the machine. The command "numactl --hardware" on this machine produces: 

available: 2 nodes (0-1)
node 0 cpus: 0 1 2 3
node 0 size: 32739 MB
node 0 free: 30624 MB
node 1 cpus: 4 5 6 7
node 1 size: 32768 MB
node 1 free: 31280 MB
node distances:
node   0   1
  0:  10  21
  1:  21  10

From the above result, we can conclude that there are two numa nodes with four cores on each: in total eight cores.

Before measuring the maximum memory bandwidth of the server, we first determine the number of threads required to achieve the maximum bandwidth of a given NUMA node. Results are summarized in the following table:

Number
of threads		 Bandwidth
(GB/s)
1 9.5
2 18.8
3 21.4
4 34.0

From the above table, we conclude that the maximum number of threads that we need to run on each node is four. Above table was obtained by running the threads on node 0 and assigning the memory on the same node as well. This result can be reproduced on other nodes as well.

Following table describes the effect of variation of memory allocation with respect to the processors where the threads are running on the memory bandwidth(number of threads is four):

MEM
CPU		 0 1
0 34.0 17.4
1 18.9 33.5

In the above table, variation of the memory nodes are in the rows while cpu nodes are in the column. You can clearly see the effect of memory binding with the respect to the cores where the threads are running. Please note that the above table resembles the "node distance table " obtained using "numactl --hardware" earlier.

AMD (2 x 6220 @ 3.0 GHz)

This is an Interlagos machine with 16 cores (numa 4 nodes with 4 cores each). Each core has 4 GB of memory, which results in the memory of machine to be 64GB. I compiled the code with open64 compiler. It is noteworthy that gcc compiler gives about half of the bandwidth as open64, while intel compiler results on this machine vary (64GB to 40 GB). "numactl --hardware" produces: 

available: 4 nodes (0-3)
node 0 cpus: 0 1 2 3
node 0 size: 16382 MB
node 0 free: 2930 MB
node 1 cpus: 4 5 6 7
node 1 size: 16384 MB
node 1 free: 5082 MB
node 2 cpus: 8 9 10 11
node 2 size: 16384 MB
node 2 free: 2281 MB
node 3 cpus: 12 13 14 15
node 3 size: 16368 MB
node 3 free: 550 MB
node distances:
node   0   1   2   3
  0:  10  16  16  16
  1:  16  10  16  16
  2:  16  16  10  16
  3:  16  16  16  10

Following table describes memory bandwidth on a single node by varying number of threads:

Number
of threads		 Bandwidth
(GB/s)
1 14.0
2 15.0
3 17.8
4 18.5

Again, similar to the Intel machine, the maximum number of threads we need to run on each node is four.

Following table describes the effect of variation of memory allocation with respect to the processors where the threads are running on the memory bandwidth(number of threads is four):

MEM
CPU		 0 1 2 3
0 18.1 11.8 6.5 5.6
1 11.8 18.7 5.5 6.5
2 6.5 5.5 18.5 11.6
3 5.6 6.5 11.8 18.5

Contrary to the Intel machine, the above table does not agree with the "node distance" produced by the "numactl --hardware"!

AMD (4 x 6378 @ 2.4 GHz)

In NUMA terminology, this server has 8 nodes with 8 cores on each. 

numactl --hardware  

available: 8 nodes (0-7)
node 0 cpus: 0 1 2 3 4 5 6 7
node 0 size: 32765 MB
node 0 free: 29324 MB
node 1 cpus: 8 9 10 11 12 13 14 15
node 1 size: 32768 MB
node 1 free: 31892 MB
node 2 cpus: 16 17 18 19 20 21 22 23
node 2 size: 32768 MB
node 2 free: 31900 MB
node 3 cpus: 24 25 26 27 28 29 30 31
node 3 size: 32768 MB
node 3 free: 31911 MB
node 4 cpus: 32 33 34 35 36 37 38 39
node 4 size: 32768 MB
node 4 free: 31964 MB
node 5 cpus: 40 41 42 43 44 45 46 47
node 5 size: 32768 MB
node 5 free: 31942 MB
node 6 cpus: 48 49 50 51 52 53 54 55
node 6 size: 32768 MB
node 6 free: 31866 MB
node 7 cpus: 56 57 58 59 60 61 62 63
node 7 size: 32752 MB
node 7 free: 31960 MB
node distances:
node   0   1   2   3   4   5   6   7
  0:  10  16  16  22  16  22  16  22
  1:  16  10  22  16  22  16  22  16
  2:  16  22  10  16  16  22  16  22
  3:  22  16  16  10  22  16  22  16
  4:  16  22  16  22  10  16  16  22
  5:  22  16  22  16  16  10  22  16
  6:  16  22  16  22  16  22  10  16
  7:  22  16  22  16  22  16  16  10

Memory bandwidth on a single node by varying number of threads:

Number
of threads		 Bandwidth
(GB/s)
1 13.0
2 14.1
3 17.1
4 17.4
5 17.1
6 16.7
7 16.6
8 16.1

Following table describes the variation of memory bandwidth when we change memory allocation with respect to the cores where threads are running (Number of threads=4)

MEM
CPU		 0 1 2 3 4 5 6 7
0 17.3 8.0 5.6 4.1 5.7 4.1 5.5 4.0
1 8.2 17.6 6.5 6.5 4.0 5.5 4.0 5.4
2 5.7 6.5 17.9 7.9 5.6 4.1 5.6 4.1
3 4.1 6.5 8.1 17.8 4.1 5.6 4.1 5.7
4 5.6 4.0 5.7 4.2 17.7 7.9 5.7 4.1
5 4.0 5.6 4.1 5.6 8.1 17.7 4.0 5.5
6 5.4 4.0 5.6 4.1 5.7 4.1 17.8 7.9
7 3.9 5.4 4.0 5.6 4.2 5.6 8.1 17.7

Bandwidth in terms of Socket

A socket for AMD 6200 and 6300 machine is two NUMA nodes combined together. The sockets have 16 cores for the 6378 server while 8 cores for 6220 server. The memory bandwidth for each NUMA node is maximum with about 4 threads, and we wonder what is the maximum bandwidth for a socket. A reasonable guess from our previous results is to use 8 threads for the socket with 4 distributed over each NUMA node. If we run the stream with 8 cores as follows: 

numactl --physcpubind=0,1,2,3,8,9,10,11 --membind=0,1 ./stream

we get 34.7 GB/s memory bandwidth.

By running, 

numactl --physcpubind=0,2,4,6,8,10,12,14 --membind=0,1 ./stream

also yields 35 GB/s bandwidth.

By varying the membind to different sockets as follows: 

numactl --physcpubind=0,2,4,6,8,10,12,14 --membind=0,1 ./stream
numactl --physcpubind=0,2,4,6,8,10,12,14 --membind=2,3 ./stream
numactl --physcpubind=0,2,4,6,8,10,12,14 --membind=4,5 ./stream
numactl --physcpubind=0,2,4,6,8,10,12,14 --membind=6,7 ./stream
numactl --physcpubind=16,18,20,22,24,26,28,30 --membind=0,1 ./stream
numactl --physcpubind=16,18,20,22,24,26,28,30 --membind=2,3 ./stream
numactl --physcpubind=16,18,20,22,24,26,28,30 --membind=4,5 ./stream
numactl --physcpubind=16,18,20,22,24,26,28,30 --membind=6,7 ./stream
numactl --physcpubind=32,34,36,38,40,42,44,46 --membind=0,1 ./stream
numactl --physcpubind=32,34,36,38,40,42,44,46 --membind=2,3 ./stream
numactl --physcpubind=32,34,36,38,40,42,44,46 --membind=4,5 ./stream
numactl --physcpubind=32,34,36,38,40,42,44,46 --membind=6,7 ./stream
numactl --physcpubind=48,50,52,54,56,58,60,62 --membind=0,1 ./stream
numactl --physcpubind=48,50,52,54,56,58,60,62 --membind=2,3 ./stream
numactl --physcpubind=48,50,52,54,56,58,60,62 --membind=4,5 ./stream
numactl --physcpubind=48,50,52,54,56,58,60,62 --membind=6,7 ./stream

we get following table (In terms of socket, i.e. node 0-1 is socket 1, node 2-3 is socket 2 and so on)

MEM
CPU		 1 2 3 4
1 35.2 11.2 11.0 10.7
2 11.3 35.3 11.2 11.1
3 10.9 11.2 35.2 11.0
4 10.7 11.1 11.1 35.4

VASP

This page describes benchmarking of Vienna Ab-initio Simulation Package (VASP), a plane wave density functional theory code, used in studying electronic structure of materials.

Intel (2 x E5-2643 @ 3.30GHz)

Native FFT Library

Following libraries 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, Streaming SIMD Extension (SSE) was changed and following is the result of a self consistent field (SCF) calculation for MgMOS (For input files, 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 spent most of its time in the FFT libraries, so the next step was to change the FFT libraries. Following changes were made: 

FFT_OBJS = fftmpi_map.o fftmpiw.o fftw3d.o fft3dlib.o

(The change here is replacement of "fftmpi.o" in 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 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 the FFTW package 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 concluded that the performance of VASP did 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

AMD (2 x 6220 @ 3.0 GHz)

This machine has 16 cores, in numactl terminology 4 NUMA nodes with 4 cores on each nodes. As the result of VASP depends heavily on the choice of FFT libraries, we checked performance of this machine with different FFTs, namely, FFT provided by VASP package, MKL, and FFTW. We built 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 wanted 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

From the computer architecture point of view, the bulldozer core aka module of AMD server lies in between a true dual core processor and a single core processor with simultaneous multithreading capability. The cores on AMD servers share some of the resources such as L2 cache and floating point unit (FPU), so the performance of a code would get affected if the threads are run on the shared cores or exclusive cores. For detail information about bulldozer core, please have a look at http://en.wikipedia.org/wiki/Bulldozer_%28microarchitecture%29


The results are summarized in the following table:

Run Scheme Native MKL FFTW FFTW FFTW FFTW FFTW FFTW
Shared
time(s)		 399 261 333 319 334 336 315 319
Exclusive
time (s)		 274 159 217 219 215 217 213 211
Notes - - 1 2 3 4 5 6

In the above table, "shared" represents cores that share resources such as L2-Cache and FPU, while "exclusive" stands for cores which do not share any resources.


1 Default compiler Flags were used to build FFT.
2 CFLAGS=-O3, FFLAGS=-O3, -enable sse2
3 enable-mpi CFLAGS=-O3, FFLAGS=-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"
6 ufhpc compiler options. FFTWDIR = /apps/fftw/3.3.2

Performance Comparison

Following is a summary of results for the test case of MgMOS ran on the Intel and AMD servers with 8 processors.

Server Native MKL FFTW
Intel 158 97 118
Intel (Scaled) 174 106 130
AMD (Shared) 399 261 319
AMD (Exclusive) 274 159 211
AMD Shared/AMD Exc. 1.46 1.64 1.51
AMD Exc./Intel (scaled) 1.57 1.50 1.62
Notes - - 1

In the above table, "shared" represents cores that share resources such as L2-Cache and FPU, while "exclusive" stands for cores which do not share any resources.

1 Compiled by UFHPC (Charles Taylor or Craig Prescott)

LAMMPS

Scaling with Number of Processors

LAMMPS is compiled with the following flags: 

module load intel openmpi
CC = mpiCC
CCFLAGS = -O2 -xsse2
FFT_INC =  -I$(HPC_MKL_DIR)/include/fftw
FFT_PATH =
FFT_LIB = -L$(HPC_MKL_DIR)/lib/intel64 -lfftw3xc -lmkl_intel_lp64 -lmkl_sequential -lmkl_core

The benchmarking runs are done by the input file provided with the package. (LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 neighbors per atom), NVE integration). Following table describes the variation of run time with number of processors on the Intel server:

# processors Time(s)
8 158
4 309
1 1139

We find linear scaling with number of processors on the intel machine.

We also ran the "lj" benchmark on the AMD server (for comparison, we provide results on the Intel server as well):

# processors lj
Time(s)		 chain
Time(s)		 eam
Time(s)		 rhodo
Time(s)		 Notes
16 180 84 476 2877 -
8 329 149 908 5506 -
4 547 248 1509 9398 -
1 1651 724 4708 - -
Intel (8 proc) 158 67 396 2361 1
Scaled
Intel (8 proc)		 217 92 545 3246 2
Scaled Intel(8 proc)/
AMD (16 proc)		 1.20 1.15 1.14 1.13 3

1 Intel: E5 2643 @ 3.3 GHz, AMD: Opetron 6378 @ 2.4 GHz
2 Scaling was done by the factor of 3.3/2.4=1.375
3 Comparison of 8 processors run on Intel vs 16 processors run on AMD

Comparison of Intel, Open64 and GNU Builds

LAMMPS with Intel compiler: 

module load intel openmpi
CC = mpiCC
CCFLAGS = -O2 -msse2
FFT_INC = -I$(HPC_MKL_DIR)/include/fftw
FFT_PATH =
FFT_LIB = -L$(HPC_MKL_DIR)/lib/intel64 -lfftw3xc -lmkl_intel_lp64 -lmkl_sequential -lmkl_core

LAMMPS with open64 compiler: 

module load open64/.4.5.2 openmpi
CC = mpiCC
CCFLAGS = -O2 -msse2
MPI_DIR = /usr/mpi/open64/openmpi-1.6
MPI_INC = -I$(MPI_DIR)/include
MPI_LIB = -L$(MPI_DIR)/lib64 -lmpi
MPI_PATH =
FFT_DIR = /home/manoj/FFTW/charlie/3.3.2
FFT_INC = -I$(FFT_DIR)/include/fftw3
FFT_PATH = 
FFT_LIB = -L$(FFT_DIR)/lib -lfftw3

LAMMPS with gnu compiler: 

module load gcc/.4.7.2 openmpi
CC = g++
CCFLAGS = -O2 -msse2
MPI_DIR = /usr/mpi/gnu/openmpi-1.6
MPI_INC = -I$(MPI_DIR)/include
MPI_LIB = -L$(MPI_DIR)/lib64 -lmpi -lmpi_cxx
MPI_PATH =
FFT_DIR = /home/manoj/FFTW/gnu/3.3.2
FFT_INC = -I$(FFT_DIR)/include/fftw3
FFT_PATH = 
FFT_LIB = -L$(FFT_DIR)/lib -lfftw3

For testing, we only ran "lj" benchmark and found:

Compiler Intel
Time(s)		 Intel
Time(s)		 AMD
Time(s)		 AMD
Time(s)
Intel 158 151 329 321
Open64 173 - 352 337
GNU 152 145 341 320
NOTES 1 2 1,3 2,3

1 Basic Flags:
Intel: -O2 -msse2
Open64: -O2 -msse2
GNU: -O2 -msse2

2 Fancy Flags:
Intel: -O2 -mavx -unroll-aggresive -ipo -opt-prefetch -use-intel-optimized-headers
Open64: CCFLAGS =-OPT:Ofast -mavx -mfma4 -march=bdver1 -O2 -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
GNU: CCFLAGS= -O2 -mavx -fsched-pressure -flto -funroll-all-loops -fprefetch-loop-arrays -minline-all-stringops -fno-tree-pre -ftree-vectorize

3 Runs on AMD servers are "naive":caches are shared and so are FPUs (Floating point unit)

Intel (2 x E5-2643 @ 3.30GHz)

Intel Compiler and SIMD Sets

We used Intel compiler as follows: 

module load intel openmpi
CC = mpiCC
CCFLAGS = -O2 -xSSE2
FFT_INC =  -I$(HPC_MKL_DIR)/include/fftw
FFT_PATH =
FFT_LIB = -L$(HPC_MKL_DIR)/lib/intel64 -lfftw3xc -lmkl_intel_lp64 -lmkl_sequential -lmkl_core

Following table shows variation of Streaming SIMD Extension (SSE) sets(# threads=8):

Extension
set		 Time(s)
sse2 158
sse3 157
ssse3 157
sse4.1 158
sse4.2 157
avx 152

"avx" instruction set is slightly better than the other sets!

The binaries for the above SIMD sets use "-x" option for the build, which does not work for the instruction sets other than "-sse2" on the AMD server, so for the next step we build our binaries with "-m" option and run it on the intel and AMD servers to see whether we could successfully run the binaries on both servers. Following table demonstrates the result for the "lj" benchmark:

SIMD
Instruction		 Intel
Time(s)		 AMD
Time(s)
sse2 158 329
sse3 157 329
ssse3 157 329
sse4.1 158 330
sse4.2 157 329
avx 152 319
Notes - 1

1 Runs on AMD servers are "naive":caches are shared and so are FPUs (Floating point unit).

Clearly on both, Intel as well as AMD servers, "avx" instructions are better choice for the "lj" benchmark. We ran other benchmarks for the SIMD sets:

SIMD
Instruction		 chain eam rhodo
- Intel AMD Intel AMD Intel AMD
sse2 67 149 396 908 2361 5506
sse3 67 149 398 908 2355 5486
ssse3 66 149 399 907 2359 5485
sse4.1 68 148 395 908 2351 5420
sse4.2 66 148 396 909 2346 5479
avx 65 145 387 897 2290 5360
Notes - 1 - 1 - 1

For all the benchmarks, "avx" seems to be a better choice compared to other instruction sets.

1 Runs on AMD servers are "naive":caches are shared and so are FPUs (Floating point unit).

MKL vs FFTW FFTs

We profiled the code to see where does it spend most of its time. Below is a summary of all the time spent in the FFTs for all the benchmarks that we tried.

lj: 

time   seconds   seconds    calls   s/call   s/call  name
0.00    185.61     0.00        1     0.00     0.00  LAMMPS_NS::FFT3d::timing1d(double*, int, int)
0.00    185.61     0.00        1     0.00     0.00  fft_1d_only

chain: 

time   seconds   seconds    calls   s/call   s/call  name
0.00     70.62     0.00        1     0.00     0.00  LAMMPS_NS::FFT3d::timing1d(double*, int, int)
0.00     70.62     0.00        1     0.00     0.00  fft_1d_only

eam: 

time   seconds   seconds    calls   s/call   s/call  name
0.00    381.72     0.00        1     0.00     0.00  LAMMPS_NS::FFT3d::timing1d(double*, int, int)
0.00    381.72     0.00        1     0.00     0.00  fft_1d_only

rhodo: 

time   seconds   seconds    calls   s/call   s/call  name
0.81    118.18     1.04 10423040     0.00     0.00  kf_work(FFT_DATA*, FFT_DATA const*, unsigned long, int, int*, kiss_fft_state*)
0.72    119.10     0.92 31269120     0.00     0.00  kf_bfly4(FFT_DATA*, unsigned long, kiss_fft_state*, unsigned long)

We can clearly see that the code does not spend any significant time in the FFT routines for any benchmarks. So, if we change the FFT from MKL to FFTW, it should not change the performance at all. As a check, we built LAMMPS with FFTW FFTs using: 

module load intel openmpi fftw
CC = mpiCC
CCFLAGS = -O2 -mavx
FFT_DIR = /apps/fftw/3.3.2
FFT_INC = -I$(FFT_DIR)/include/fftw3
FFT_PATH = 
FFT_LIB = -L$(FFT_DIR)/lib -lfftw3

For the test, we ran "lj" benchmark on the Intel server and found:

FFT Time(s)
MKL 152
FFTW 152

As expected, there is no difference between the FFTs from FFTW or MKL on the performance of LAMMPS.

AMD (4 x 6378 @ 2.4 GHz)

In this section, we descirbe the effect of shared cache of the AMD server on the performance of LAMMPS. The results are summarized in the following table (# threads=8):

Run Scheme lj chain eam rhodo
Shared
time(s)		 319 145 897 5360
Exclusive
time (s)		 277 126 778 4426

In the above table, "shared" represents cores that share resources such as L2-Cache and FPU, while "exclusive" stands for cores which do not share any resources.

Performance Comparison

Following is a table for performance comparison of Intel and AMD servers when the job was run using 8 threads.

Server lj chain eam rhodo
Intel 158 65 387 2290
Intel (Scaled) 217 89 532 3149
AMD (Shared) 319 145 897 5360
AMD (Exclusive) 277 126 778 4426
AMD Shared/AMD Exc. 1.15 1.15 1.15 1.21
AMD Exc./Intel (scaled) 1.28 1.42 1.46 1.41

In the above table, "shared" represents cores that share resources such as L2-Cache and FPU, while "exclusive" stands for cores which do not share any resources.

GROMACS

Comparison of Intel, Open64 and GNU Builds

Intel compiler: 

module load intel openmpi
export F77=mpif77
export F90=mpif90
export CC=mpicc
export CFLAGS="-O2 -msse2"
export FFLAGS="-O2 -msse2"
./configure --prefix=/home/manoj/profile/gromacs/gromacs-4.5.5 --enable-shared=yes --enable-mpi --without-x --disable-float --with-fft=mkl LIBS="-L/opt/intel/composerxe
/lib/intel64 -lfftw3xc -lmkl_intel_lp64 -lmkl_sequential -lmkl_core"
make
make install

Open64 compiler: 

module load open64/.4.5.2 openmpi
export F77=openf90
export F90=openf90
export CC=opencc
export CFLAGS="-O2 -msse2"
export FFLAGS="-O2 -msse2"
export CPPFLAGS="-I/home/manoj/FFTW/fpic-charlie/3.3.2/include"
export LDFLAGS="-L/home/manoj/FFTW/fpic-charlie/3.3.2/lib"
./configure --prefix=/home/manoj/profile/gromacs/gromacs-4.5.5 --enable-shared=yes --enable-mpi --without-x --disable-float
make
make install

GNU compiler: 

module load gcc/.4.7.2 openmpi
export F77=gfortran
export F90=f95
export CC=gcc
export CFLAGS="-O2 -msse2"
export FFLAGS="-O2 -msse2"
export CPPFLAGS="-I/home/manoj/FFTW/gnu/3.3.2/include"
export LDFLAGS="-L/home/manoj/FFTW/gnu/3.3.2/lib"
./configure --prefix=/home/manoj/profile/gromacs/gromacs-4.5.5 --enable-shared=yes --enable-mpi --without-x --disable-float
make
make install

There are some test cases in "gromacs-4.5.5/share/tutor" directory, however not all of them work. So far, I could only get "water", "methane", and "mixed" to work. Instructions to run MD simulations are on http://manual.gromacs.org/online/water.html page. You first need to create a " .tpr" file using 

./grompp_d -v

After this, you can run "mdrun_d" for the molecular dynamics simulation.

In the input file provided by GROMACS, there is a mistake in the "grompp.mdp" file. The line starting with "bd-temp" has to be commented out. Upon some internet search, I found that the file, "grompp.mdp" is the input file for an older version of GROMACS, and apparently some of the parameters have become obsolete.

Following results are for the MD simulation on water using 8 processors on Intel (E5-2643) and AMD (Opetran-6378) servers:

Compiler Intel
Time(s)		 Intel
Time(s)		 AMD
Time(s)		 AMD
Time(s)
Intel 157 157 361 363
Open64 167 - 392 383
GNU 160 - 377 368
NOTES 1 2 1,3 2,3

1 Basic Flags:
Intel: -O2 -msse2
Open64: -O2 -msse2
GNU: -O2 -msse2

2 Fancy Flags:
Intel: -O2 -mavx -unroll-aggresive -opt-prefetch -use-intel-optimized-headers
Open64: CCFLAGS =-OPT:Ofast -mavx -mfma4 -march=bdver1 -O2 -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
GNU: CCFLAGS= -O2 -mavx -fsched-pressure -flto -funroll-all-loops -fprefetch-loop-arrays -minline-all-stringops -fno-tree-pre -ftree-vectorize

3 Runs on AMD servers are "naive":caches are shared and so are FPUs (Floating point unit)

Scaling with Number of Processors

"Water" benchmark was run using gromacs compiled with the intel and openmpi (fancy flags) as shown on above section.

Following table describes the variation of run time with number of processors on the Intel (E5-2643) server:

# processors Time(s) Factor
1 950 1.00
4 252 3.76
8 157 6.05

We find linear scaling with number of processors on the intel server.

We also ran the same benchmark on the AMD (Opetran-6378) server (for comparison, we provide results on the Intel server as well):

# processors water
Time(s)		 Notes
16 241 -
8 363 -
4 532 -
1 1288 -
Intel (8 proc) 157 1
Scaled
Intel (8 proc)		 216 2
AMD (16 proc)/
Scaled Intel(8 proc)		 1.12 3

1 Intel: E5 2643 @ 3.3 GHz, AMD: Opetron 6378 @ 2.4 GHz
2 Scaling was done by the factor of 3.3/2.4=1.375
3 Comparison of 8 processors run on Intel vs 16 processors run on AMD

Instruction Set Dependence

GROMACS is compiled with the following flags: 

module load intel openmpi mkl
export F77=mpif77
export F90=mpif90
export CC=mpicc
export CFLAGS="-O2 -msse2 -unroll-aggresive -opt-prefetch -use-intel-optimized-headers"
export FFLAGS="-O2 -msse2 -unroll-aggresive -opt-prefetch -use-intel-optimized-headers"
./configure --prefix=/home/manoj/profile/gromacs/gromacs-4.5.5 --enable-shared=yes --enable-mpi --without-x --disable-float --with-fft=mkl LIBS="-L/opt/intel
/composerxe/lib/intel64 -lfftw3xc -lmkl_intel_lp64 -lmkl_sequential -lmkl_core"
make
make install

Table captures the dependence of instruction sets on Intel (E5-2643) and AMD (Opetran-6378) machine with 8 processes:

SIMD
Instruction		 Intel AMD
sse2 158 364
sse3 158 362
ssse3 157 362
sse4.1 159 360
sse4.2 157 362
avx 157 363
Notes - 1

GROMACS seems to be instruction set independent.
1 Runs on AMD servers are "naive":caches are shared and so are FPUs (Floating point unit)

MKL vs FFTW

There is a problem in profiling the code. We don't see as many subroutines as we wish to see. Intel compiler is still OK, but GNU compiler is worse: it only shows only one subroutine. We don't see any FFT routine in the test case that we are using.

Intel Compiler 

time    seconds   seconds    calls   s/call   s/call  name
68.42      0.13     0.13        6    21.67    28.33  do_md
15.79      0.16     0.03  2160054     0.00     0.00  copy_rvec
 5.26      0.17     0.01   600018     0.00     0.00  clear_mat
 5.26      0.18     0.01                             _intel_fast_memcpy
 5.26      0.19     0.01                             _intel_fast_memcpy.P
 0.00      0.19     0.00   720018     0.00     0.00  copy_mat
 0.00      0.19     0.00        6     0.00    28.33  mdrunner
 0.00      0.19     0.00        3     0.00     0.00  copy_rvec
 0.00      0.19     0.00        1     0.00     0.00  copy_mat
 0.00      0.19     0.00        1     0.00     0.00  get_nthreads
 0.00      0.19     0.00        1     0.00     0.00  mdrunner_start_threads


GNU Compiler 

time     seconds   seconds    calls   s/call   s/call  name
100.01     0.02     0.02        1    20.00    20.00  do_md


To see the FFT dependence, we built GROMACS with FFTW FFTs using: 

module load intel openmpi fftw
export F77=mpif77
export F90=mpif90
export CC=mpicc
export CFLAGS="-O2 -mavx -unroll-aggresive -opt-prefetch -use-intel-optimized-headers"
export FFLAGS="-O2 -mavx -unroll-aggresive -opt-prefetch -use-intel-optimized-headers"
#export CFLAGS="-O2 -msse2" 
#export FFLAGS="-O2 -msse2" 
export CPPFLAGS="-I/apps/fftw/3.3.2/include"
export LDFLAGS="-L/apps/fftw/3.3.2/lib -lfftw3"
./configure --prefix=/home/manoj/profile/gromacs/gromacs-4.5.5 --enable-shared=yes --enable-mpi --without-x --disable-float
make
make install

We ran "water" benchmark on the Intel(E5-2643) and AMD (Opetran-6378) servers using 8 processors and found:

FFT Intel
Time(s)		 AMD
Time(s)
MKL 157 363
FFTW 157 360

There seems to be no difference between the FFTs from FFTW or MKL on the performance of GROMACS.

Shared vs Exclusive run on AMD servers (4 x 6378 @ 2.4 GHz)

We descirbe the effect of shared FPU and L2-cache of the AMD server. The results are summarized in the following table (# processes=8):

Run Scheme Time(s)
Shared
time(s)		 363
Exclusive
time (s)		 266

In the above table, "shared" represents cores that share resources such as L2-Cache and FPU, while "exclusive" stands for cores which do not share any resources.

Performance Comparison

Following is a table for performance comparison of Intel and AMD servers when the job was run using 8 processors:

Server Time(s) Notes
Intel 157 1
Intel (Scaled) 216 2
AMD (Shared) 363 3
AMD (Exclusive) 266 4
AMD Shared/AMD Exc. 1.36 -
AMD Exc./Intel (scaled) 1.23 -

1 Intel: E5 2643 @ 3.3 GHz, AMD: Opetron 6378 @ 2.4 GHz
2 Scaling was done by the factor of 3.3/2.4=1.375
3 "Shared" represents cores that share resources such as L2-Cache and FPU
4 "Exclusive" represents cores that don't share resources such as L2-Cache and FPU

DL_POLY

Comparison of Intel, Open64 and GNU Builds

Intel compiler: 

module load intel openmpi
$(MAKE) LD="mpif90 -v -o " \
                LDFLAGS="-shared-intel" \
                FC="mpif90 -c" \
                FCFLAGS="-O3 -mavx -opt-prefetch -use-intel-optimized-headers" \
                EX=$(EX) BINROOT=$(BINROOT) $(TYPE)

GNU compiler: 

module load gcc/.4.7.2 openmpi
$(MAKE) LD="mpif90 -v -o " \
                LDFLAGS=" " \
                FC="mpif90 -c" \
                FCFLAGS="-O3 -mavx -fsched-pressure -flto -funroll-all-loops -fprefetch-loop-arrays -minline-all-stringops -fno-tree-                 
                pre -ftree-vectorize" \
                EX=$(EX) BINROOT=$(BINROOT) $(TYPE)


Open64 compiler:

Open64 shows a problem in the subroutine config_module.f90 at line 62. This subroutine resizes the length of an array. The line 

Character( Len = * ), Allocatable, Intent( InOut ) :: a(:)

makes "a" an allocatable array of strings, but the length of string is not defined. Intel and GNU compiler can handle this, however the open64 compiler can not. We made one assignment modification at this line (Interested readers should look up the code) and made the open64 compiler work. 

 
 module load open64/.4.5.2 openmpi
 $(MAKE) LD="mpif90 -v -o " \
                LDFLAGS=" " \
                FC="mpif90 -c" \
                FCFLAGS="-OPT:Ofast -mavx -mfma4 -march=bdver1 -O2 -fomit-frame-pointer -LNO:simd=2 -WOPT:sib=on -LNO:prefetch=2:pf2=0 -CG:use_prefetchnta=on -LNO:prefetch_ahead=4-malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math " \
                EX=$(EX) BINROOT=$(BINROOT) $(TYPE)

We downloaded 42 benchmarks from the DL_POLY website. The number of benchmarks are higher so we looked in to the result of profiling and found that there are in fact only 15 cases that use different codes inside the DL_POLY package and we are going to present our results based on those.

Following results are for the various benchmarks using 8 processors on Intel (E5-2643) servers:

Wall Time
Compiler Intel-Basic
Time(s)		 Intel-Fancy
Time(s)		 GNU-Basic
Time(s)		 GNU-Fancy
Time(s)		 Open64-Basic
Time(s)
Test1 66 62 71 83 75
Test3 69 65 76 75 79
Test4 74 87 77 78 87
Test5 70 65 81 75 87
Test7 95 88 105 99 106
Test9 67 57 85 69 117
Test11 72 61 85 83 91
Test13 63 58 65 62 72
Test14 106 114 113 136 91
Test17 67 65 74 72 77
Test18 102 89 104 99 115
Test27 136 131 154 - 158
Test31 114 96 121 121 134
Test35 80 81 90 90 93
CPU Time
Compiler Intel-Basic
Time(s)		 Intel-Fancy
Time(s)		 GNU-Basic
Time(s)		 GNU-Fancy
Time(s)		 Open64-Basic
Time(s)
Test1 65 60 - - 74
Test3 68 64 - - 79
Test4 70 64 - - 79
Test5 61 59 - - 86
Test7 88 84 - - 104
Test9 59 57 - - 116
Test11 72 60 - - 90
Test13 57 56 - - 67
Test14 39 42 - - 43
Test17 64 63 - - 75
Test18 94 88 - - 112
Test27 136 116 - - 157
Test31 113 94 - - 134
Test35 80 80 - - 92


We tried to compare intel and open64 builds on the AMD server and following table depicts that comparison:

Compiler Intel-Fancy
Time(s)		 Open64-Basic
Time(s)		 Open64-Fancy
Time(s)
Test1 95 91 90
Wall Time
Test3 221 235 219
Test4 213 225 211
Test5 142 173 161
Test7 300 310 295
Test9 144 219 209
Test11 158 202 183
Test13 247 262 245
Test14 186 165 149
Test17 190 201 189
Test18 356 353 385
Test27 323 377 334
Test31 269 313 290
Test35 228 251 240
CPU Time
Compiler Intel-Fancy
Time(s)		 Open64-Basic
Time(s)		 Open64-Fancy
Time(s)
Test1 91 90 90
Test3 219 233 218
Test4 204 218 203
Test5 141 171 160
Test7 298 309 293
Test9 137 219 207
Test11 157 202 183
Test13 245 259 242
Test14 149 147 143
Test17 189 201 189
Test18 348 350 *383
Test27 323 370 332
Test31 268 312 290
Test35 227 251 239


1 Basic Flags:
Intel: -O2 -msse2
Open64: -O2 -msse2
GNU: -O2 -msse2

2 Fancy Flags:
Intel: -O2 -mavx -opt-prefetch -use-intel-optimized-headers
GNU: CCFLAGS= -O2 -mavx -fsched-pressure -flto -funroll-all-loops -fprefetch-loop-arrays -minline-all-stringops -fno-tree-pre -ftree-vectorize
Open64 -OPT:Ofast -mavx -mfma4 -march=bdver1 -O2 -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

More studies on Test 14

intel compiler:

Intel server: CPU time = 39s, Wall Time= 49s 

 %   cumulative   self              self     total
time   seconds   seconds    calls   s/call   s/call  name
13.56      4.85     4.85      182     0.03     0.03  constraints_shake_vv_
 9.09      8.10     3.25       14     0.23     0.27  link_cell_pairs_
 7.94     10.94     2.84       78     0.04     0.04  deport_atomic_data_
 5.65     12.96     2.02                             __intel_ssse3_rep_memcpy
 5.56     14.95     1.99       14     0.14     0.14  ewald_spme_forces_IP_spme_forces_
 5.29     16.84     1.89       14     0.14     0.63  ewald_spme_forces_

AMD server: CPU Time=151s Wall Time =190s 

 %   cumulative   self              self     total
time   seconds   seconds    calls   s/call   s/call  name
19.85     23.87    23.87       91     0.26     0.27  constraints_shake_vv_
12.33     38.70    14.83       78     0.19     0.19  deport_atomic_data_
 6.82     46.90     8.20       13     0.63     0.64  constraints_rattle_
 6.06     54.19     7.29       14     0.52     0.60  link_cell_pairs_
 5.61     60.94     6.75     3836     0.00     0.00  gpfa_module_mp_gpfa3f_
 5.32     67.34     6.40       14     0.46     0.46  bspgen_
 5.15     73.53     6.19       52     0.12     0.77  npt_b0_vv_

Open64 Compiler

Intel server: CPU Time= 45s, Wall Time=290s 

 %   cumulative   self              self     total
time   seconds   seconds    calls   s/call   s/call  name
15.64      5.64     5.64      182     0.03     0.03  constraints_shake_vv__
12.06      9.99     4.35       14     0.31     0.69  ewald_spme_forces__
11.37     14.09     4.10       14     0.29     0.34  link_cell_pairs__
 9.45     17.50     3.41       78     0.04     0.04  deport_atomic_data__
 5.52     19.49     1.99  3378329     0.00     0.00  images_
 5.16     21.35     1.86     3808     0.00     0.00  GPFA2F.in.GPFA_MODULE
 5.16     23.21     1.86       26     0.07     0.07  constraints_rattle__

AMD server: CPU Time= 156s, Wall Time=164s 

 %   cumulative   self              self     total
time   seconds   seconds    calls   s/call   s/call  name
18.38     22.58    22.58       91     0.25     0.25  constraints_shake_vv__
13.07     38.64    16.06       78     0.21     0.21  deport_atomic_data__
 8.29     48.82    10.18       14     0.73     2.73  ewald_spme_forces__
 7.54     58.09     9.27       14     0.66     0.76  link_cell_pairs__
 5.99     65.45     7.36       13     0.57     0.58  constraints_rattle__
 5.86     72.65     7.20     3836     0.00     0.00  GPFA3F.in.GPFA_MODULE
 5.34     79.21     6.56       14     0.47     0.47  bspgen_

Scaling with Number of Processors

From the data of the above section, we conclude that intel build with fancy flags is better choice for the code and so we do our further runs only using the intel build.

Following table describes the variation of run time with number of processors on the Intel (E5-2643) server:

#proc Test1 Test3 Test4 Test5 Test7 Test9 Test11 Test13 Test14 Test17 Test18 Test27 Test31 Test35
1
(Factor)		 91
(1.00)		 389
(1.00)		 541
(1.00)		 511
(1.00)		 502
(1.00)		 755
(1.00)		 397
(1.00)		 292
(1.00)		 255
(1.00)		 302
(1.00)		 445
(1.00)		 651
(1.00)		 612
(1.00)		 -
4
(Factor)		 90
(1.01)		 122
(3.18)		 160
(3.38)		 119
(4.29)		 173
(2.90)		 119
(6.34)		 119
(3.34)		 116
(2.52)		 147
(1.73)		 105
(2.87)		 147
(3.03)		 229
(2.84)		 184
(3.33)		 136
(-)
8
(Factor)		 62
(1.47)		 65
(5.98)		 87
(6.22)		 65
(7.86)		 88
(5.70)		 57
(13.2)		 61
(6.51)		 58
(5.03)		 114
(2.23)		 65
(4.65)		 89
(5.00)		 131
(4.96)		 96
(6.38)		 81
(-)

Following table depicts the result in the scaled manner. It's basically the same table as above.

#proc Test1 Test3 Test4 Test5 Test7 Test9 Test11 Test13 Test14 Test17 Test18 Test27 Test31 Test35
1 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 -
4 1.01 3.18 3.38 4.29 2.90 6.34 3.34 2.52 1.73 2.87 3.03 2.84 3.33 -
8 1.47 5.98 6.22 7.86 5.70 13.2 6.51 5.03 2.23 4.65 5.00 4.96 6.38 -

We also ran the same benchmark on the AMD (Opetran-6378) server (for comparison, we provide results on the Intel server as well):

#proc Test1 Test3 Test4 Test5 Test7 Test9 Test11 Test13 Test14 Test17 Test18 Test27 Test31 Test35 Notes
1 91 395 619 788 1406 1292 825 393 441 882 898 651 651 - -
4 102 362 375 277 521 285 307 376 267 318 497 554 477 381 -
8 95 221 213 142 300 144 158 247 186 190 356 323 269 228 -
16 90 127 112 78 167 74 90 170 116 145 193 192 152 170 -
Intel(8-proc) 62 65 87 65 88 57 61 58 114 65 89 131 96 81 1
Scaled Intel 85 89 120 89 121 78 84 80 157 89 122 180 132 111 2
AMD (16 proc)/
Intel(8 proc)		 1.06 1.43 0.93 0.88 1.38 .95 1.07 2.14 0.74 1.63 1.58 1.07 1.15 1.53 3

Table for the scaling with respect to 1 processor runs:

#proc Test1 Test3 Test4 Test5 Test7 Test9 Test11 Test13 Test14 Test17 Test18 Test27 Test31 Test35
1 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 -
4 0.89 1.09 1.65 2.84 2.70 4.53 2.69 1.05 1.65 2.77 1.81 1.18 1.36 -
8 0.96 1.79 2.91 5.55 4.69 8.97 5.22 1.59 2.37 4.64 2.52 2.02 2.42 -
16 1.01 3.11 5.53 10.1 8.42 17.46 9.17 2.31 3.80 6.08 4.65 3.39 4.28 -


1 Intel: E5 2643 @ 3.3 GHz, AMD: Opetron 6378 @ 2.4 GHz
2 Scaling was done by the factor of 3.3/2.4=1.375
3 Comparison of 8 processors run on Intel vs 16 processors run on AMD

MKL vs FFTW FFTs

We profiled the code to see where does it spend most of its time. Below is a summary of the profile for all the benchmarks that we tried.

Test1:

Intel 

time   seconds   seconds    calls   s/call   s/call  name
28.26      7.16     7.16   675309     0.00     0.00  vdw_forces_
25.57     13.64     6.48      201     0.03     0.03  link_cell_pairs_
17.72     18.13     4.49   675309     0.00     0.00  ewald_real_forces_
 7.22     19.96     1.83      201     0.01     0.01  ewald_spme_forces_IP_spme_forces_
 5.17     21.27     1.31      201     0.01     0.02  ewald_spme_forces_
 3.95     22.27     1.00      201     0.00     0.12  two_body_forces_
 3.83     23.24     0.97   675309     0.00     0.00  images_
 3.08     24.02     0.78      201     0.00     0.00  bspgen_
 1.42     24.38     0.36    11658     0.00     0.00  gpfa_module_mp_gpfa3f_
 1.07     24.65     0.27      202     0.00     0.00  shellsort2_
 0.67     24.82     0.17     1206     0.00     0.00  export_atomic_data_

AMD 

time   seconds   seconds    calls   s/call   s/call  name
23.43     18.45    18.45  3379737     0.00     0.00  vdw_forces_
21.47     35.36    16.91     1000     0.02     0.02  link_cell_pairs_
14.23     46.57    11.21  3379737     0.00     0.00  ewald_real_forces_
11.77     55.84     9.27      500     0.02     0.02  bspgen_
 5.78     60.39     4.55     1000     0.00     0.00  ewald_spme_forces_IP_spme_forces_
 4.57     63.99     3.60     1000     0.00     0.02  ewald_spme_forces_
 4.36     67.42     3.43                             deport_atomic_data_
 3.34     70.05     2.63  3379737     0.00     0.00  images_
 2.76     72.22     2.17      500     0.00     0.14  two_body_forces_
 2.13     73.90     1.68                             spec_dexp2
 1.24     74.88     0.98    29000     0.00     0.00  gpfa_module_mp_gpfa3f_
 1.05     75.71     0.83      998     0.00     0.00  nvt_b0_vv_
 0.86     76.39     0.68      501     0.00     0.00  shellsort2_

Test3:

Intel 

time   seconds   seconds    calls   s/call   s/call  name
17.53     26.21    26.21  1298431     0.00     0.00  vdw_forces_
14.82     48.37    22.16      201     0.11     0.13  link_cell_pairs_
14.22     69.62    21.25    26532     0.00     0.00  gpfa_module_mp_gpfa2f_
11.73     87.16    17.54  1298431     0.00     0.00  ewald_real_forces_
 6.62     97.06     9.90     1200     0.01     0.01  deport_atomic_data_
 4.04    103.10     6.04      201     0.03     0.21  ewald_spme_forces_
 3.80    108.78     5.68      200     0.03     0.03  constraints_shake_vv_
 3.37    113.82     5.04 43159044     0.00     0.00  local_index_
 3.32    118.79     4.97  2355005     0.00     0.00  images_
 3.06    123.36     4.57      200     0.02     0.03  constraints_rattle_
 2.99    127.82     4.47 326609967     0.00     0.00  match_
 2.57    131.66     3.84      201     0.02     0.02  ewald_spme_forces_IP_spme_forces_
 2.01    134.67     3.01      201     0.01     0.60  two_body_forces_
 1.10    136.32     1.65      201     0.01     0.01  parallel_fft_mp_forward_3d_fft_z_
 1.04    137.87     1.55      201     0.01     0.06  parallel_fft_mp_forward_3d_fft_y_
 0.98    139.33     1.46      201     0.01     0.01  bspgen_

AMD 

time   seconds   seconds    calls   s/call   s/call  name
15.14     28.44    28.44  1299553     0.00     0.00  vdw_forces_
12.46     51.85    23.41      201     0.12     0.14  link_cell_pairs_
11.54     73.53    21.68    26532     0.00     0.00  gpfa_module_mp_gpfa2f_
 9.90     92.13    18.60  1299553     0.00     0.00  ewald_real_forces_
 7.30    105.85    13.72      200     0.07     0.07  constraints_rattle_
 7.01    119.03    13.18      200     0.07     0.07  constraints_shake_vv_
 6.23    130.73    11.70     1200     0.01     0.01  deport_atomic_data_
 3.69    137.66     6.93      201     0.03     0.03  bspgen_
 3.17    143.61     5.95      201     0.03     0.24  ewald_spme_forces_
 2.65    148.59     4.98  2367053     0.00     0.00  images_
 2.45    153.19     4.60 39319511     0.00     0.00  local_index_
 2.25    157.41     4.23 328218229     0.00     0.00  match_
 2.14    161.43     4.02      201     0.02     0.02  ewald_spme_forces_IP_spme_forces_
 1.81    164.84     3.41                             spec_dexp2
 1.59    167.82     2.98      201     0.01     0.66  two_body_forces_
 1.30    170.26     2.44      201     0.01     0.01  parallel_fft_mp_forward_3d_fft_z_
 0.80    171.76     1.50      201     0.01     0.01  parallel_fft_mp_back_3d_fft_x_

Test4:

Intel 

time   seconds   seconds    calls   s/call   s/call  name
18.66     29.94    29.94  1604385     0.00     0.00  vdw_forces_
15.84     55.35    25.41       31     0.82     0.98  link_cell_pairs_
13.21     76.55    21.20  1604385     0.00     0.00  ewald_real_forces_
12.69     96.92    20.37       30     0.68     0.71  constraints_shake_vv_
 7.68    109.24    12.32       30     0.41     0.44  constraints_rattle_
 7.32    120.99    11.75      180     0.07     0.07  deport_atomic_data_
 3.79    127.07     6.08  2880181     0.00     0.00  images_
 3.23    132.25     5.18 40320168     0.00     0.00  local_index_
 3.10    137.22     4.98 364097691     0.00     0.00  match_
 2.72    141.58     4.36       31     0.14     0.14  ewald_spme_forces_IP_spme_forces_
 2.16    145.05     3.47       31     0.11     3.38  two_body_forces_
 2.05    148.34     3.29     4092     0.00     0.00  gpfa_module_mp_gpfa2f_
 1.95    151.47     3.13       31     0.10     0.42  ewald_spme_forces_
 0.67    152.54     1.07       31     0.03     0.03  bspgen_

AMD 

time   seconds   seconds    calls   s/call   s/call  name
18.03     33.20    33.20  1603402     0.00     0.00  vdw_forces_
13.13     57.37    24.17       31     0.78     0.90  link_cell_pairs_
12.76     80.87    23.50       30     0.78     0.81  constraints_shake_vv_
11.25    101.59    20.72  1603402     0.00     0.00  ewald_real_forces_
 9.40    118.90    17.31       30     0.58     0.60  constraints_rattle_
 7.53    132.76    13.86      180     0.08     0.08  deport_atomic_data_
 3.27    138.78     6.02  2878846     0.00     0.00  images_
 2.65    143.65     4.87       31     0.16     0.16  bspgen_
 2.60    148.44     4.79 40437733     0.00     0.00  local_index_
 2.45    152.96     4.52                             spec_dexp2
 2.36    157.31     4.35       31     0.14     0.14  ewald_spme_forces_IP_spme_forces_
 2.07    161.13     3.82       62     0.06     1.77  two_body_forces_
 2.02    164.84     3.72 363897922     0.00     0.00  match_
 1.87    168.28     3.44       31     0.11     0.55  ewald_spme_forces_
 1.82    171.64     3.36     4092     0.00     0.00  gpfa_module_mp_gpfa2f_
 0.75    173.03     1.39      150     0.01     0.30  nve_0_vv_


Test5: 

time   seconds   seconds    calls   s/call   s/call  name
44.99     50.53    50.53      101     0.50     0.50  three_body_forces_
16.21     68.74    18.21   873523     0.00     0.00  ewald_real_forces_
15.19     85.80    17.06      101     0.17     0.17  link_cell_pairs_
10.25     97.31    11.51   873523     0.00     0.00  vdw_forces_
 3.71    101.48     4.17   873523     0.00     0.00  images_
 3.33    105.22     3.74      101     0.04     0.59  two_body_forces_
 2.08    107.56     2.34      101     0.02     0.02  ewald_spme_forces_IP_spme_forces_
 1.41    109.14     1.58      101     0.02     0.05  ewald_spme_forces_
 0.97    110.23     1.09      101     0.01     0.01  bspgen_

Test7: 

time   seconds   seconds    calls   s/call   s/call  name
16.97     13.50    13.50      101     0.13     0.15  link_cell_pairs_
16.75     26.82    13.32     1326     0.01     0.01  constraints_shake_vv_
11.59     36.04     9.22      600     0.02     0.02  deport_atomic_data_
10.69     44.54     8.50  1249646     0.00     0.00  ewald_real_forces_
10.59     52.96     8.42  1249646     0.00     0.00  vdw_forces_
 4.39     56.45     3.49  2122099     0.00     0.00  images_
 4.34     59.91     3.46 23122212     0.00     0.00  local_index_
 4.14     63.20     3.29      101     0.03     0.03  ewald_spme_forces_IP_spme_forces_
 3.34     65.86     2.66      200     0.01     0.11  npt_b0_vv_
 2.87     68.14     2.28      101     0.02     0.09  ewald_spme_forces_
 2.78     70.35     2.21      100     0.02     0.03  constraints_rattle_
 2.21     72.11     1.76      101     0.02     0.46  two_body_forces_
 1.89     73.61     1.51 154519604     0.00     0.00  match_
 1.85     75.08     1.47      101     0.01     0.01  bspgen_
 0.65     75.60     0.52      202     0.00     0.00  shellsort2_

Test9: 

95.21     75.98    75.98      401     0.19     0.19  tersoff_forces_
 1.09     76.85     0.87     2400     0.00     0.00  deport_atomic_data_
 0.96     77.62     0.77      402     0.00     0.00  shellsort2_

Test11: 

36.75     52.13    52.13  4004908     0.00     0.00  metal_forces_
22.05     83.41    31.28     1001     0.03     0.03  link_cell_pairs_
21.82    114.36    30.95  4004908     0.00     0.00  metal_ld_collect_fst_
10.26    128.91    14.55  8009816     0.00     0.00  images_
 2.59    132.59     3.68     1001     0.00     0.14  two_body_forces_
 2.44    136.05     3.46     1001     0.00     0.04  metal_ld_compute_
 1.35    137.97     1.92     1002     0.00     0.00  shellsort2_
 0.62    138.85     0.88     6000     0.00     0.00  deport_atomic_data_

Test13: 

18.91     22.56    22.56    22348     0.00     0.00  gpfa_module_mp_gpfa2f_
12.43     37.39    14.83      900     0.02     0.02  deport_atomic_data_
11.80     51.47    14.08     1950     0.01     0.01  constraints_shake_vv_
 8.38     61.47    10.00      151     0.07     0.08  link_cell_pairs_
 5.49     68.02     6.55      300     0.02     0.09  npt_b0_vv_
 5.02     74.01     5.99      302     0.02     0.02  gpfa_module_mp_gpfa3f_
 4.86     79.81     5.80      151     0.04     0.33  ewald_spme_forces_
 4.38     85.04     5.23      151     0.03     0.04  ewald_spme_forces_IP_spme_forces_
 3.53     89.26     4.22 34695506     0.00     0.00  local_index_
 3.47     93.40     4.14      150     0.03     0.03  constraints_rattle_
 2.94     96.91     3.51  2364786     0.00     0.00  ewald_real_forces_
 2.84    100.30     3.39  4097851     0.00     0.00  images_
 2.36    103.11     2.81  2364786     0.00     0.00  vdw_forces_
 1.32    104.68     1.57      151     0.01     0.01  bspgen_
 1.27    106.19     1.51      151     0.01     0.01  parallel_fft_mp_forward_3d_fft_z_
 1.18    107.60     1.41      151     0.01     0.01  parallel_fft_mp_back_3d_fft_x_
 1.16    108.98     1.38      151     0.01     0.10  parallel_fft_mp_forward_3d_fft_y_
 1.14    110.34     1.36      151     0.01     0.48  two_body_forces_
 1.11    111.66     1.33 92125754     0.00     0.00  match_
 1.09    112.96     1.30      151     0.01     0.01  parallel_fft_mp_forward_3d_fft_x_
 0.99    114.14     1.18      151     0.01     0.10  parallel_fft_mp_back_3d_fft_y_

Test14: 

21.33     16.80    16.80      130     0.13     0.13  constraints_shake_vv_
10.48     25.05     8.25       60     0.14     0.14  deport_atomic_data_
 7.24     30.75     5.70       11     0.52     0.60  link_cell_pairs_
 6.41     35.80     5.05     3014     0.00     0.00  gpfa_module_mp_gpfa3f_
 5.75     40.33     4.53       20     0.23     1.35  npt_b0_vv_
 5.30     44.50     4.17       10     0.42     0.43  constraints_rattle_
 5.27     48.65     4.15       11     0.38     2.20  ewald_spme_forces_
 5.13     52.69     4.04     2992     0.00     0.00  gpfa_module_mp_gpfa2f_
 4.28     56.06     3.37       11     0.31     0.31  ewald_spme_forces_IP_spme_forces_
 3.19     58.57     2.51 20333039     0.00     0.00  local_index_
 2.79     60.77     2.20  1534827     0.00     0.00  ewald_real_forces_
 2.78     62.96     2.19  2646191     0.00     0.00  images_
 2.30     64.77     1.81  1534827     0.00     0.00  vdw_forces_
 2.29     66.57     1.80       11     0.16     0.16  bspgen_
 1.92     68.08     1.51       22     0.07     0.07  gpfa_module_mp_gpfa5f_
 1.80     69.50     1.42       11     0.13     0.60  parallel_fft_mp_forward_3d_fft_y_
 1.79     70.91     1.41       11     0.13     0.60  parallel_fft_mp_back_3d_fft_y_
 1.09     71.77     0.86 57924127     0.00     0.00  match_
 0.95     72.52     0.75        1     0.75     0.75  dihedrals_14_check_

Test17: 

20.71     10.65    10.65      201     0.05     0.06  link_cell_pairs_
13.88     17.79     7.14   984116     0.00     0.00  ewald_real_forces_
11.43     23.67     5.88   984116     0.00     0.00  vdw_forces_
 9.72     28.67     5.00     3200     0.00     0.00  constraints_shake_vv_
 6.68     32.11     3.44  2260717     0.00     0.00  images_
 5.84     35.11     3.01 23232840     0.00     0.00  local_index_
 5.06     37.71     2.60      201     0.01     0.01  ewald_spme_forces_IP_spme_forces_
 4.53     40.04     2.33      200     0.01     0.02  constraints_rattle_
 3.46     41.82     1.78      201     0.01     0.03  ewald_spme_forces_
 2.51     43.11     1.29     4235     0.00     0.00  pmf_coms_
 2.25     44.27     1.16 118620664     0.00     0.00  match_
 2.18     45.39     1.12     1200     0.00     0.00  deport_atomic_data_
 2.10     46.47     1.08      201     0.01     0.17  two_body_forces_
 2.10     47.55     1.08      201     0.01     0.01  bspgen_
 1.50     48.32     0.77      400     0.00     0.03  npt_b0_vv_
 1.11     48.89     0.57      402     0.00     0.00  shellsort2_
 0.80     49.30     0.41      201     0.00     0.00  pass_shared_units_

Test18: 

34.45     69.38    69.38     1800     0.04     0.04  constraints_shake_vv_
 9.78     89.07    19.69      101     0.19     0.22  link_cell_pairs_
 8.63    106.45    17.38      100     0.17     0.20  constraints_rattle_
 6.61    119.77    13.32  2041857     0.00     0.00  ewald_real_forces_
 5.95    131.75    11.98  2041857     0.00     0.00  vdw_forces_
 5.38    142.59    10.84     2718     0.00     0.01  pmf_coms_
 5.29    153.24    10.65  4883071     0.00     0.00  images_
 4.95    163.22     9.98 66656800     0.00     0.00  local_index_
 3.18    169.62     6.40      200     0.03     0.60  npt_b0_vv_
 2.74    175.14     5.52      101     0.05     0.06  ewald_spme_forces_IP_spme_forces_
 1.84    178.84     3.70      101     0.04     0.16  ewald_spme_forces_
 1.71    182.28     3.44      600     0.01     0.01  deport_atomic_data_
 1.51    185.33     3.05      101     0.03     0.03  bspgen_
 1.44    188.24     2.91      101     0.03     0.74  two_body_forces_
 1.18    190.61     2.38 231279151     0.00     0.00  match_
 0.76    192.14     1.53    25304     0.00     0.00  update_shared_units_

Test27: 

38.45     91.00    91.00 12076288     0.00     0.00  metal_forces_
24.32    148.56    57.56     3501     0.02     0.02  link_cell_pairs_
17.06    188.93    40.37 12076288     0.00     0.00  metal_ld_collect_eam_
 8.90    210.00    21.07 24152576     0.00     0.00  images_
 2.64    216.24     6.24     3501     0.00     0.06  two_body_forces_
 2.39    221.90     5.66     3501     0.00     0.02  metal_ld_compute_
 1.46    225.35     3.45     3502     0.00     0.00  shellsort2_
 1.11    227.98     2.63    21000     0.00     0.00  deport_atomic_data_
 0.90    230.11     2.13    21006     0.00     0.00  export_atomic_data_

Test31: 

31.17     66.30    66.30 12004000     0.00     0.00  metal_forces_
29.18    128.38    62.08     3001     0.02     0.02  link_cell_pairs_
13.22    156.50    28.12 12004000     0.00     0.00  metal_ld_collect_eam_
10.09    177.96    21.46 24008000     0.00     0.00  images_
 5.35    189.35    11.39    18000     0.00     0.00  deport_atomic_data_
 2.99    195.71     6.36     3001     0.00     0.06  two_body_forces_
 2.77    201.60     5.89     3001     0.00     0.02  metal_ld_compute_
 1.29    204.34     2.75     3002     0.00     0.00  shellsort2_
 0.70    205.83     1.49     6000     0.00     0.00  npt_b0_vv_

Test35: 

27.22     27.64    27.64      562     0.05     0.06  link_cell_pairs_
19.94     47.89    20.25  1878757     0.00     0.00  ewald_real_forces_
 9.75     57.79     9.90  1878757     0.00     0.00  vdw_forces_
 5.52     63.40     5.61  3227549     0.00     0.00  images_
 5.46     68.95     5.55     2008     0.00     0.00  constraints_shake_vv_
 4.44     73.46     4.51      562     0.01     0.01  ewald_spme_forces_IP_spme_forces_
 3.43     76.95     3.49 354007894     0.00     0.00  match_
 3.38     80.38     3.43      562     0.01     0.15  two_body_forces_
 3.30     83.73     3.35      562     0.01     0.01  bspgen_
 3.23     87.01     3.29 28441741     0.00     0.00  local_index_
 2.87     89.92     2.91      500     0.01     0.01  constraints_rattle_
 2.85     92.81     2.89      562     0.01     0.02  ewald_spme_forces_
 2.05     94.89     2.08     3366     0.00     0.00  deport_atomic_data_
 1.71     96.63     1.74     1124     0.00     0.00  shellsort2_
 1.44     98.09     1.46     1000     0.00     0.01  npt_m1_vv_
 0.49     98.59     0.50      562     0.00     0.00  set_halo_particles_

From the above data, we can clearly see that the FFT dependence of the code is very tiny (in some cases where it shows up, it's about a percent), so there is no need to try different FFT libraries for the purpose of efficiency.

Shared vs Exclusive run on AMD servers (4 x 6378 @ 2.4 GHz)

We descirbe the effect of shared FPU and L2-cache of the AMD server. The results are summarized in the following table (# processes=8):

Run Scheme Test1 Test3 Test4 Test5 Test7 Test9 Test11 Test13 Test14 Test17 Test18 Test27 Test31 Test35
Shared
time(s)		 95 221 213 142 300 144 158 247 186 190 356 323 269 228
Exclusive
time (s)		 90 168 161 109 226 116 128 185 157 151 282 265 209 173

In the above table, "shared" represents cores that share resources such as L2-Cache and FPU, while "exclusive" stands for cores which do not share any resources.

Performance Comparison

Following is a table for performance comparison of Intel and AMD servers when the job was run using 8 processors:

Server Test1 Test3 Test4 Test5 Test7 Test9 Test11 Test13 Test14 Test17 Test18 Test27 Test31 Test35 Notes
Intel 62 65 87 65 88 57 61 58 114 65 89 131 96 81 1
Scaled Intel 85 89 120 89 121 78 84 80 157 89 122 180 132 111 2
AMD (Shared) 95 221 213 142 300 144 158 247 186 190 356 323 269 228 1,3
AMD(Exclusive) 90 168 161 109 226 116 128 185 157 151 282 265 209 173 1,4
AMD Shared/AMD Exc. 1.05 1.31 1.32 1.30 1.33 1.24 1.23 1.34 1.18 1.26 1.26 1.22 1.29 1.32 -
AMD Exc./Intel (scaled) 1.06 1.89 1.34 1.22 1.87 1.49 1.52 2.31 1.00 1.70 2.31 1.47 1.58 1.56 -
AMD Shared/Intel (scaled) 1.12 2.48 1.78 1.60 2.48 1.85 1.88 3.09 1.18 2.13 2.92 1.79 2.03 2.05 -
AMD (16 proc)/
Intel(8 proc)		 1.06 1.43 0.93 0.88 1.38 .95 1.07 2.14 0.74 1.63 1.58 1.07 1.15 1.53 3

1 Intel: E5 2643 @ 3.3 GHz, AMD: Opetron 6378 @ 2.4 GHz
2 Scaling was done by the factor of 3.3/2.4=1.375
3 "Shared" represents cores that share resources such as L2-Cache and FPU
4 "Exclusive" represents cores that don't share resources such as L2-Cache and FPU


BLAST

A couple of things before we dive into the benchmarking-

1. NCBI-BLAST is not an MPI enabled code. Only parallelization that is available is intranode which can be achieved through OpenMP. If you would like parallel BLAST, MPIBLAST is an option but upon doing some internet search I found people reporting it to be unstable.

2. Compilation of BLAST with OpenMP must be done using thread safety otherwise the code would crash for more than one thread. This can be enabled with the use of "--with-mt" in the configure script.


Comparison of Intel, Open64 and GNU Builds

Intel compiler: 

module load intel
export CFLAGS="-Wall -O2 -msse2 "
export CXXFLAGS="-Wall -O2 -msse2 "
export CPPFLAGS="-Wall -O2 -msse2 "
./configure --with-bin-release --without-debug --with-mt


GNU compiler: 

module load gcc/.4.7.2 
export CFLAGS="-Wall -O2 -msse2 "
export CXXFLAGS="-Wall -O2 -msse2 "
export CPPFLAGS="-Wall -O2 -msse2 "
./configure --with-bin-release --without-debug --with-mt --with-64


Open64 compiler: 

module load open64/.4.5.2
export CFLAGS="-Wall -O2 -msse2 "
export CXXFLAGS="-Wall -O2 -msse2 "
export CPPFLAGS="-Wall -O2 -msse2 "
./configure --with-bin-release --without-debug --with-mt --with-64

Following is a comparison of test case for blastx executable of BLAST.

Wall Time on Intel Sandy-Bridge
#processor Intel-Basic
Time(s)		 Intel-Fancy
Time(s)		 GNU-Basic
Time(s)		 GNU-Fancy
Time(s)		 Open64-Basic
Time(s)		 Open64-Fancy
Time(s)
1 400 412 416 451 475 -
2 209 216 219 235 251 -
4 115 120 122 130 137 -
8 67 69 73 77 79 -

The executable built with Open64 and fancy flags crashes on the Intel Sandy-Bridge server.

Clearly, intel compiler with basic flags has better performance with other compiler+flag combinations. Interestingly, the fancy flags suffer for both intel and gcc case.


On the AMD server, we got (these runs share resources (FPU, L2-Cache))-

Wall Time on AMD Abu-Dhabi
#processor Intel
Time(s)		 Open64
Time(s)
1 557 615
2 348 380
4 199 216
8 126 136
16 83 88


1 Basic Flags:
Intel:-Wall -O2 -msse2
Open64:-Wall -O2 -msse2
GNU: -Wall -O2 -msse2

2 Fancy Flags:
Intel: -Wall -O3 -mavx -unroll-aggresive -opt-prefetch -use-intel-optimized-headers
GNU: CCFLAGS= -Wall -O3 -mavx -fsched-pressure -flto -funroll-all-loops -fprefetch-loop-arrays -minline-all-stringops -fno-tree-pre -ftree-vectorize
Open64 -Wall -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

Scaling

In the following table, we compare scaling of different executables of BLAST on Intel Sandy-Bridge server:

Scaling on Intel Sandy-Bridge
#processor blastx tblastx blastp
1 412 768 -
2 216 574 -
4 120 268 -
8 69 98 -


Scaling on AMD Abu Dhabi
#processor blastx tblastx blastp
1 557 - -
2 348 267 -
4 199 -
8 126 - -
16 83 - -

With boost and python Libraries

I read online that boost libraries might increase the efficiency. So, compiled the code using boost to see if there is any performance improvement. 

module load boost
./configure --with-bin-release --without-debug --with-mt --with-boost=/apps/boost/1.53.0
Server with
boost		 without
boost
Intel 70 67
AMD 125 126

I tried python libraries as well 

module load python
./configure --with-bin-release --without-debug --with-mt --with-python=/apps/python/2.7.3

The table below depicts the performance:

Server with
python		 without
python
Intel 70 67
AMD 126 126

None of these libraries seem to improve the performance of BLAST.

Profiling

For the blastx executable, we found- 


 %   cumulative   self              self     total
time   seconds   seconds    calls   s/call   s/call  name
48.33    206.29   206.29  6838800     0.00     0.00  s_BlastAaWordFinder_TwoHit
17.73    281.95    75.66 12644388     0.00     0.00  s_BlastSmallAaScanSubject
11.13    329.45    47.50 801659273    0.00     0.00  BSearchContextInfo
 7.16    360.00    30.55 800757705    0.00     0.00  s_BlastAaExtendLeft
 4.90    380.92    20.92 800757705    0.00     0.00  s_BlastAaExtendTwoHit
 2.47    391.47    10.55 2311127628   0.00     0.00  ComputeTableIndexIncremental
 1.77    399.01     7.54    48008     0.00     0.00  BlastKarlinLHtoK
 1.43    405.12     6.12 211437430    0.00     0.00  s_BlastAaExtendRight
 1.19    410.21     5.09  1835792     0.00     0.00  Blast_SemiGappedAlign


In the "s_BlastAaWordFinder_TwoHit" subroutine, we have 

index % time    self  children    called     name
              206.29  191.90 6838800/6838800     BlastAaWordFinder [9]
[10]    93.3  206.29  191.90 6838800             s_BlastAaWordFinder_TwoHit [10]
              75.66   11.13 12644388/12644388   s_BlastSmallAaScanSubject [15]
              20.92   36.67 800757705/800757705 s_BlastAaExtendTwoHit [16]
              47.44    0.00 800757705/801659273 BSearchContextInfo [17]
               0.08    0.00 6838800/6838800     Blast_UngappedStatsUpdate [194]
               0.00    0.01  901568/901568      BlastSaveInitHsp [880]
               0.01    0.00 6838800/6838800     Blast_ExtendWordExit [1357]

It seems that the blastx excutable uses mostly inside routines, not any library routines such as FFT.

Shared vs Exclusive run on AMD servers (4 x 6378 @ 2.4 GHz)

We descirbe the effect of shared FPU and L2-cache of the AMD server. The results are summarized in the following table (# processes=8):

Run Scheme blastx
Shared
time(s)		 127
Exclusive
time (s)		 112

In the above table, "shared" represents cores that share resources such as L2-Cache and FPU, while "exclusive" stands for cores which do not share any resources.

Performance Comparison

Server blastx Notes
Intel 67 1
Scaled Intel 92 2
AMD (Shared) 127 1,3
AMD(Exclusive) 112 1,4
AMD Shared/AMD Exc. 1.13 -
AMD Exc./Intel (scaled) 1.22 -
AMD Shared/Intel (scaled) 1.38 -
AMD (16 proc)/
Intel(8 proc)		 0.90

1 Intel: E5 2643 @ 3.3 GHz, AMD: Opetron 6378 @ 2.4 GHz
2 Scaling was done by the factor of 3.3/2.4=1.375
3 "Shared" represents cores that share resources such as L2-Cache and FPU
4 "Exclusive" represents cores that don't share resources such as L2-Cache and FPU

QUANTUM ESPRESSO

Quantum Espresso is a plane wave density functional theory code used for the electronic structure calculations of materials.

Intel (2 x E5-2643 @ 3.30GHz)

The test case for these runs is a self consistent calculation for energy of bulk copper. (For input file please ask Manoj Srivastava) Following table demonstrates the scaling of the code with number of processors:

8
processors		 4 proc
numanode=0		 4 proc
numanode=0,1
156 293 289

Clearly, we can see that there is no shared cache effect on the intel machine. From our experience with VASP as well as profiling we know that the code spends most of its time in FFT libraries. Following table captures result of variation of FFT libraries:

FFTW-FFT MKL-FFT
156 140

AMD (2 x 6220 @ 3.0 GHz)

16
processors		 8 proc
Non-shared		 8 proc
Shared
252 250 345
FFTW-FFT MKL-FFT
250 232

Compilation Table

This table instructs number of different compiler options that can be used to build the code.

Package Intel GNU Open64
VASP Y - -
LAMMPS Y Y Y
GROMACS Y Y Y
QE Y - -
DL_POLY Y Y Y
BLAST Y Y N
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