[gmx-users] Affinity setting for 1/16 threads failed. Version 5.0.2

Siva Dasetty sdasett at g.clemson.edu
Wed Nov 18 15:28:06 CET 2015

Dear all,

I am running simulations using version 5.0.2 (default in gordon) and I am
having a performance loss from 180 ns/day to 8 ns/day compared to the same
simulations that I previously ran in a different cluster.

In both the clusters I am using a single node and 16 cpus (no gpus) and the
following is the command line I used:

mdrun_mpi -s <tpr file> -v -deffnm <output file> -nb cpu -cpi <cpt file>
-append -pin on

Following is reported in the log file:

WARNING: Affinity setting for 1/16 threads failed.

         This can cause performance degradation! If you think your setting
are correct, contact the GROMACS developers.

I even tried running a simulation without the flag -pin on and there is no
change in the performance.

Are there any other options that I can try to recover the performance?

Additional Information:

The other difference I could see is in the compilers:

In gordon (8ns/day):

C compiler: /opt/mvapich2/intel/ib/bin/mpicc Intel

C compiler flags:    -mavx    -std=gnu99 -w3 -wd111 -wd177 -wd181 -wd193
-wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418
-wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346
-wd11074 -wd11076  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const

C++ compiler:       /opt/mvapich2/intel/ib/bin/mpicxx Intel

C++ compiler flags:  -mavx    -w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304
-wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572
-wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076
-wd1782 -wd2282  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const

In our cluster (180 ns/day):

C compiler: /software/openmpi/bin/mpicc GNU 4.8.1

C compiler flags:    -msse4.1    -Wno-maybe-uninitialized -Wextra -Wno-miss

ing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused

-Wunused-value -Wunused-parameter  -O3 -DNDEBUG -fomit-frame-pointer -funro

ll-all-loops -fexcess-precision=fast  -Wno-array-bounds

C++ compiler: /software/openmpi/bin/mpicxx GNU 4.8.1

C++ compiler flags:  -msse4.1    -Wextra -Wno-missing-field-initializers -W

pointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG -fomit-frame-pointer

 -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds

Thanks in advance for your help,

Siva Dasetty

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