[gmx-developers] Oversubscribing on 4.62 with MPI / OpenMP

Jochen Hub jhub at gwdg.de
Wed Apr 24 20:46:52 CEST 2013


I have a problem related to the oversubscribing issue reported on Feb 5 
in the user list - yet it seems different.

I use the latest git 4.62 with icc13 and MVAPICH2/1.8.

I run on 2 nodes with, each with 2 Xeon Harpertowns (E5472).

mpiexec -np 16 mdrun

everyhting is fine - reasonable performance. With

mpiexec -np 2 mdrun

I get the warning:

WARNING: Oversubscribing the available 8 logical CPU cores with 16 
threads. This will cause considerable performance loss!

And the simulation is indeed very slow.

According to Berk's suggestion in the thread "MPI oversubscription" in 
the user list I have added print statements into 
src/gmxlib/gmx_detect_hardware.c to check for the sysconf(...) 
functions. I receive 8 in each MPI process:


Here, some more information from the log file (the two nodes are 
apparently detected) - so I am a bit lost.

Can someone give a hint how to solve this?

Many thanks,

Host: r104i1n8  pid: 12912  nodeid: 0  nnodes:  2
Gromacs version:    VERSION 4.6.2-dev
Precision:          single
Memory model:       64 bit
MPI library:        MPI
OpenMP support:     enabled
GPU support:        disabled
invsqrt routine:    gmx_software_invsqrt(x)
CPU acceleration:   SSE4.1
FFT library:        fftw-3.3.1-sse2
Large file support: enabled
RDTSCP usage:       disabled
Built on:           Wed Apr 24 17:07:56 CEST 2013
Built by:           nicjohub at r104i1n0 [CMAKE]
Build OS/arch:      Linux x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:    Intel(R) Xeon(R) CPU           E5472  @ 3.00GHz
Build CPU family:   6   Model: 23   Stepping: 6
Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse 
sse2 sse3 sse4.1 ssse3
C compiler:         /sw/comm/mvapich2/1.8-intel/bin/mpicc Intel icc 
(ICC) 13.0.1 20121010
C compiler flags:   -msse4.1   -std=gnu99 -Wall   -ip -funroll-all-loops 

Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU           E5472  @ 3.00GHz
Family:  6  Model: 23  Stepping:  6
Features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse sse2 sse3 
sse4.1 ssse3
Acceleration most likely to fit this hardware: SSE4.1
Acceleration selected at GROMACS compile time: SSE4.1

Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189

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