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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear all,
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<div>For a system with 32267 atoms (metalloprotein with bound ligand, using a parametrized bonded model, with Amber FF14SB; force field solvated in a cubic water box and with a few Na+ ions as counterions), run on 4 nodes with:</div>
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<div>1. Intel(R) Xeon(R) CPU X5650 @ 2.67GHz (12 cores per node)</div>
<div>2. NVIDIA Tesla M2090 (2 per node)</div>
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<div>performance is about 73 ns/day.</div>
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<div>Performance on one node is about 25~30 ns/day. MD is run as such (<span style="font-size: 13.3333px;">LSB_DJOB_NUMPROC=48)</span><span style="font-size: 10pt;">:</span></div>
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<div>mpirun -f ${LSB_DJOB_HOSTFILE} -np ${LSB_DJOB_NUMPROC} mdrun_mpi -nice 0 -ntomp 1 -nb gpu -npme 24 -v -s ./Output/MD_01_200/MD_011.tpr -cpo ./Output/MD_01_20/MD_011.cpt -c ./Output/MD_01_200/MD_011.gro -e ./Output/MD_01_200/MD_011.edr -g./Output/MD_01_200/MD_011.log
-x ./Output/MD_01_200/MD_011.xtc</div>
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<div>Gromacs version is: 5.1.1.; openMPI version is: 1.8.8; CUDA driver version is: 7.50; CUDA runtime version is: 6.50.</div>
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<div>Is this a reasonable performance for this setup or it could be improved considering the specifications?</div>
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<div>Thank you.</div>
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<div>Best regards,</div>
<div>Petar Žuvela<br>
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<font size="3"><a name="m_513990452533906962_UNIQUE_ID_SafeHtmlFilter_UNIQUE_ID_SafeHtmlFilter_UNIQUE_ID_SafeHtmlFilter_UNIQUE_ID_SafeHtmlFilter_UNIQUE_ID_SafeHtmlFilter_UNIQUE_ID_SafeHtmlFilter_UNIQUE_ID_SafeHtmlFilter_UNIQUE_ID_SafeH" style="color:rgb(17,85,204)"><b><u><span lang="HR">Petar
Žuvela</span></u></b></a><u><span lang="HR">, Ph.D</span></u></font><font face="arial, sans-serif" style="font-size:small"><span lang="EN-US" style="font-size:10.5pt; font-size:10.5pt"></span></font></p>
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<span lang="HR" style="font-size:9.5pt">Postdoctoral Research Fellow</span></p>
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<div style="font-size:13.3333px">Room 0503, <span style="font-size:10pt">MD1 Building</span></div>
<div style="font-size:13.3333px"><span style="font-size:10pt">National University of Singapore</span></div>
<div style="font-size:13.3333px">12 Science Drive 2</div>
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