[gmx-developers] freeenergy/simtemp and freeenergy/vdwalone fail on rhel6/sandy bridge

[Mark Dixon]

Hi,

Possibly related to Friday's "freeenergy.relative unstable?" thread...

A source install of gromacs 4.6.3 passes the regression tests on one of 
our clusters, but the serial double-precision and MPI double-precision 
builds fail for a couple of freeenergy tests (simtemp and vdwalone) on a 
second cluster.

We used the same recent compiler (intel/13.1.3.192), the same method 
(below) and the same MPI (openmpi/1.6.5) on both machines; however, one 
machine is running RHEL5 and is based on Intel Nehalem processors, whereas 
the other is running CentOS6 and is based on Intel Sandy Bridge 
processors.

I wondered if anyone here had noticed this?

The failed numbers are only right to ~2 sig figs. Should I be concerned 
with the build on the sandy bridge machine?

Thanks,

Mark
-- 
-----------------------------------------------------------------
Mark Dixon                       Email    : m.c.dixon at leeds.ac.uk
HPC/Grid Systems Support         Tel (int): 35429
Information Systems Services     Tel (ext): +44(0)113 343 5429
University of Leeds, LS2 9JT, UK
-----------------------------------------------------------------

# Serial, double-precision build method

cmake -DGMX_DOUBLE=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_X11=ON -DCMAKE_INSTALL_PREFIX=$prefix ../gromacs-4.6.3
make
make check


# simtemp checkpot.out on centos6/sandy bridge machine

comparing energy file reference_d.edr and ener.edr

There are 33 terms in the energy files

There are 6 terms to compare in the energy files

LJ (SR)          step  20:       5620.37,  step  20:      5609.04
LJ (SR)          step  40:       5650.96,  step  40:      5628.03
Angle            step  60:       8.55224,  step  60:      8.65452
LJ (SR)          step  60:       5674.57,  step  60:      5643.39
Angle            step  80:       7.04247,  step  80:      6.98253
LJ (SR)          step  80:       5697.85,  step  80:      5658.71
LJ (SR)          step 100:       5789.57,  step 100:      5748.48
Coulomb (SR)     step 100:      -31075.7,  step 100:     -31043.8

Files read successfully

# vdwalone checkpot.out on centos6/sandy bridge machine

comparing energy file reference_d.edr and ener.edr

There are 40 terms in the energy files

There are 11 terms to compare in the energy files

LJ (SR)          step  20:       4318.48,  step  20:      4307.94
LJ (SR)          step  30:       4320.84,  step  30:       4302.5
LJ (SR)          step  40:       4340.35,  step  40:      4315.17
LJ (SR)          step  50:       4371.42,  step  50:      4339.86
LJ (SR)          step  60:       4409.49,  step  60:      4370.77
Coulomb (SR)     step  60:      -28193.8,  step  60:     -28158.5

Files read successfully


# MPI, double-precision build method

cmake -DGMX_DOUBLE=ON -DGMX_MPI=ON -DGMX_OPENMP=OFF -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_X11=ON -DCMAKE_INSTALL_PREFIX=$prefix ../gromacs-4.6.3
make
make check


# simtemp checkpot.out on centos6/sandy bridge machine

comparing energy file reference_d.edr and ener.edr

There are 33 terms in the energy files

There are 6 terms to compare in the energy files

LJ (SR)          step  20:       5620.37,  step  20:      5607.86
LJ (SR)          step  40:       5650.96,  step  40:       5625.5
LJ (SR)          step  60:       5674.57,  step  60:      5643.92
LJ (SR)          step  80:       5697.85,  step  80:      5659.46
Coulomb (SR)     step  80:        -30834,  step  80:     -30801.7
LJ (SR)          step 100:       5789.57,  step 100:      5747.16
Coulomb (SR)     step 100:      -31075.7,  step 100:     -31038.9

Files read successfully

# vdwalone checkpot.out on centos6/sandy bridge machine

comparing energy file reference_d.edr and ener.edr

There are 40 terms in the energy files

There are 11 terms to compare in the energy files

LJ (SR)          step  20:       4318.48,  step  20:      4307.03
LJ (SR)          step  30:       4320.84,  step  30:      4301.78
LJ (SR)          step  40:       4340.35,  step  40:      4313.95
LJ (SR)          step  50:       4371.42,  step  50:      4338.84
LJ (SR)          step  60:       4409.49,  step  60:      4371.53
Coulomb (SR)     step  60:      -28193.8,  step  60:     -28158.6

Files read successfully