Hi there,<div><br></div><div>I am testing on a MBP 17" SL 10.6.4 64 bits and nvidia GeForce 9600M GT <br><div><br></div><div>So I got mdrun-gpu compiled and apparently running, but when I try to run 'mdrun' to compare I have a segment fault.</div>
<div><br></div><div>Any other comments to the md.mdp and em.mdp are very welcome too.</div><div><br></div><div><div>##### To test mdrun-gpu</div><div><br></div><div><div>cat << EOF >| em.mdp</div><div>define = -DFLEXIBLE</div>
<div>integrator = cg ; steep</div><div>nsteps = 200</div><div>constraints = none</div><div>emtol = 1000.0</div><div>nstcgsteep = 10 ; do a steep every 10 steps of cg</div>
<div>emstep = 0.01 ; used with steep</div><div>nstcomm = 1</div><div>coulombtype = PME</div><div>ns_type = grid</div><div>rlist = 1.0</div>
<div>rcoulomb = 1.0</div><div>rvdw = 1.4</div><div>Tcoupl = no</div><div>Pcoupl = no</div><div>gen_vel = no</div><div>nstxout = 0 ; write coords every # step</div>
<div>optimize_fft = yes</div><div>EOF</div><div><br></div><div>cat << EOF >| md.mdp</div><div>integrator = md-vv</div><div>nsteps = 1000</div><div>dt = 0.002</div>
<div>constraints = all-bonds</div><div>constraint-algorithm = shake</div><div>nstcomm = 1</div><div>nstcalcenergy = 1</div><div>ns_type = grid</div><div>rlist = 1.3</div>
<div>rcoulomb = 1.3</div><div>rvdw = 1.3</div><div>vdwtype = cut-off</div><div>coulombtype = PME</div><div>Tcoupl = Andersen</div><div>nsttcouple = 1</div>
<div>tau_t = 0.1</div><div>tc-grps = system</div><div>ref_t = 300</div><div>Pcoupl = mttk</div><div>Pcoupltype = isotropic</div><div>
nstpcouple = 1</div>
<div>tau_p = 0.5</div><div>compressibility = 4.5e-5</div><div>ref_p = 1.0</div><div>gen_vel = yes</div><div>nstxout = 2 ; write coords every # step</div>
<div>lincs-iter = 2</div><div>DispCorr = EnerPres</div><div>optimize_fft = yes</div><div>EOF</div><div><br></div><div>wget -c "<a href="http://www.pdbe.org/download/1brv">http://www.pdbe.org/download/1brv</a>" -O 1brv.pdb</div>
<div><br></div><div>pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh</div><div><br></div><div>editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0</div><div><br></div><div>genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs</div>
<div><br></div><div>grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr</div><div><br></div><div>echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p Prot.top -norandom</div><div><br></div><div>grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr</div>
<div><br></div><div>mdrun -v -deffnm em</div><div><br></div><div>grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr</div><div><br></div><div>mdrun-gpu -v -deffnm md -device "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"</div>
<div><br></div><div>[snip]</div><div>Reading file md.tpr, VERSION 4.5.1-dev-20100913-9342b (single precision)</div><div>Loaded with Money</div><div><br></div><div><br></div><div>Back Off! I just backed up md.trr to ./#md.trr.7#</div>
<div><br></div><div>Back Off! I just backed up md.edr to ./#md.edr.7#</div><div><br></div><div>WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators.</div><div><br></div><div><br></div>
<div>WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.</div><div><br></div><div><br></div><div>WARNING: Non-supported GPU selected (#0, GeForce 9600M GT), forced continuing.Note, that the simulation can be slow or it migth even crash.</div>
<div><br></div><div><br></div><div>Pre-simulation ~15s memtest in progress...done, no errors detected</div><div>starting mdrun 'PROTEIN G in water'</div><div>1000 steps, 2.0 ps.</div><div>step 900, remaining runtime: 4 s</div>
<div>Writing final coordinates.</div><div><br></div><div>step 1000, remaining runtime: 0 s</div><div>Post-simulation ~15s memtest in progress...done, no errors detected</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>OpenMM run - timing based on wallclock.</div>
<div><br></div><div> NODE (s) Real (s) (%)</div><div> Time: 44.556 44.556 100.0</div><div> (Mnbf/s) (MFlops) (ns/day) (hour/ns)</div><div>Performance: 0.000 0.027 3.882 6.182</div>
</div><div><br></div><div><br></div><div>But if I try:</div><div>mdrun -v -deffnm md -nt 1</div><div>[snip]</div><div><div>starting mdrun 'PROTEIN G in water'</div><div>1000 steps, 2.0 ps.</div><div>[1] 75786 segmentation fault mdrun -v -deffnm md -nt 1</div>
</div><div><br></div><div>Note: using -nt 1 because SHAKE is not supported with domain decomposition.</div><div><br></div><div>If using Tcoupl and Pcoupl = no and then I can compare mdrun x mdrun-gpu, being my gpu ~2 times slower than only one core. Well, I definitely don't intended to use mdrun-gpu but I am surprised that it performed that bad (OK, I am using a low-end GPU, but sander_openmm seems to work fine and very fast on my mbp).</div>
<div><br></div><div>BTW, in gmx 4.5 manual, there's reference to Andersen thermostat only at section 6.9 GROMACS on GPUs. Is it supposed to be used only with mdrun-gpu?</div><div><br></div><div>Any ideas? Thanks,</div>
<div><br></div><div>Alan</div><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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