[gmx-users] Intel vs gcc compilers

[Djurre de Jong-Bruinink]

Dear Gromacs developers/users,

After suggestions on this mailing list to use intel over gcc compilers, we recently obtained the newest intel compilers (2013.4.183). I was kind of disappointed to find that there is no speed-up at all when comparing a gcc and intel compiled g4.6.2. Is this expected for our hardware, would the speed-up only become apparent when using specific functions (OMP, group-scheme) or am I doing something wrong in the compilation?

An exert fromboth log files is below, the complete logfiles can be found there: 

http://md.chem.rug.nl/~djurre/logs/N6intel.log
http://md.chem.rug.nl/~djurre/logs/N6gcc.log


Thanks in advance,
Djurre de Jong


Log file opened on Tue Jun 25 11:33:25 2013
Host: node041  pid: 13590  nodeid: 0  nnodes:  72
Gromacs version:    VERSION 4.6.2
Precision:          single
Memory model:       64 bit
MPI library:        MPI
OpenMP support:     enabled
GPU support:        disabled
invsqrt routine:    gmx_software_invsqrt(x)
CPU acceleration:   SSE2
FFT library:        fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage:       enabled
Built on:           Mon Jun 24 20:54:51 CEST 2013
Built by:           p238199 at login01 [CMAKE]
Build OS/arch:      Linux 2.6.18-308.11.1.el5 x86_64
Build CPU vendor:   AuthenticAMD
Build CPU brand:    Six-Core AMD Opteron(tm) Processor 2435
Build CPU family:   16   Model: 8   Stepping: 0
Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm misalignsse mmx msr nonstop_tsc pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a
C compiler:         /cm/shared/apps/openmpi/intel/64/1.4.5/bin/mpicc Intel icc (ICC) 13.1.2 20130514
C compiler flags:   -msse2    -std=gnu99 -Wall   -ip -funroll-all-loops  -O3 -DNDEBUG


               Core t (s)   Wall t (s)        (%)
       Time:    10651.270      222.008     4797.7
                 (ns/day)    (hour/ns)
Performance:       77.836        0.308


######################################################################################

Host: node041  pid: 13728  nodeid: 0  nnodes:  72
Gromacs version:    VERSION 4.6.2
Precision:          single
Memory model:       64 bit
MPI library:        MPI
OpenMP support:     enabled
GPU support:        disabled
invsqrt routine:    gmx_software_invsqrt(x)
CPU acceleration:   SSE2
FFT library:        fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage:       enabled
Built on:           Tue Jun 25 10:25:13 CEST 2013
Built by:           p238199 at login01 [CMAKE]
Build OS/arch:      Linux 2.6.18-308.11.1.el5 x86_64
Build CPU vendor:   AuthenticAMD
Build CPU brand:    Six-Core AMD Opteron(tm) Processor 2435
Build CPU family:   16   Model: 8   Stepping: 0
Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm misalignsse mmx msr nonstop_tsc pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a
C compiler:         /cm/shared/apps/openmpi/gcc/64/1.4.5/bin/mpicc GNU gcc (GCC) 4.7.2
C compiler flags:   -msse2    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value   -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3 -DNDEBUG


               Core t (s)   Wall t (s)        (%)
       Time:    10516.210      219.223     4797.0
                 (ns/day)    (hour/ns)
Performance:       78.825        0.304