You should use the latest GROMACS version also for the GPU. Thus compile the 4.5.1 for the GPU and run this.<br><br><div class="gmail_quote">On Fri, Oct 15, 2010 at 4:16 PM, Renato Freitas <span dir="ltr"><<a href="mailto:renatoffs@gmail.com">renatoffs@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi there,<br>
I have installed the gromacs-4.5.1 and it was running without<br>
problems. Also I installed the GPU version of GROMACS<br>
(gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and<br>
NVIDIA driver are installed. Then I tried to run the test provided by<br>
Alan with the mdrun-gpu and I got an error.<br>
<br>
##### To test mdrun-gpu<br>
<br>
cat << EOF >| em.mdp<br>
define = -DFLEXIBLE<br>
integrator = cg ; steep<br>
nsteps = 200<br>
constraints = none<br>
emtol = 1000.0<br>
nstcgsteep = 10 ; do a steep every 10 steps of cg<br>
emstep = 0.01 ; used with steep<br>
nstcomm = 1<br>
coulombtype = PME<br>
ns_type = grid<br>
rlist = 1.0<br>
rcoulomb = 1.0<br>
rvdw = 1.4<br>
Tcoupl = no<br>
Pcoupl = no<br>
gen_vel = no<br>
nstxout = 0 ; write coords every # step<br>
optimize_fft = yes<br>
EOF<br>
<br>
cat << EOF >| md.mdp<br>
integrator = md-vv<br>
nsteps = 1000<br>
dt = 0.002<br>
constraints = all-bonds<br>
constraint-algorithm = shake<br>
nstcomm = 1<br>
nstcalcenergy = 1<br>
ns_type = grid<br>
rlist = 1.3<br>
rcoulomb = 1.3<br>
rvdw = 1.3<br>
vdwtype = cut-off<br>
coulombtype = PME<br>
Tcoupl = Andersen<br>
nsttcouple = 1<br>
tau_t = 0.1<br>
tc-grps = system<br>
ref_t = 300<br>
Pcoupl = mttk<br>
Pcoupltype = isotropic<br>
nstpcouple = 1<br>
tau_p = 0.5<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
gen_vel = yes<br>
nstxout = 2 ; write coords every # step<br>
lincs-iter = 2<br>
DispCorr = EnerPres<br>
optimize_fft = yes<br>
EOF<br>
<br>
wget -c "<a href="http://www.pdbe.org/download/1brv" target="_blank">http://www.pdbe.org/download/1brv</a>"; -O 1brv.pdb<br>
<br>
pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh<br>
<br>
editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0<br>
<br>
genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs<br>
<br>
grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr<br>
<br>
echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p<br>
Prot.top -norandom<br>
<br>
grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr<br>
<br>
mdrun -v -deffnm em<br>
<br>
grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr<br>
<br>
mdrun-gpu -v -deffnm md -device<br>
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"<br>
<br>
-------------------------------------------------------<br>
Getting Loaded...<br>
Reading file md.tpr, VERSION 4.5 (single precision)<br>
<br>
-------------------------------------------------------<br>
Program mdrun-gpu, VERSION 4.5-GPU-beta2<br>
Source code file:<br>
/home/rossen/Research/Projects/Gromacs-dev/gromacs/src/gmxlib/tpxio.c,<br>
line: 1971<br>
<br>
Fatal error:<br>
reading tpx file (md.tpr) version 73 with version 71 program<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
I also have tried to use my own system to test the mdrun-gpu and I got<br>
the same error.<br>
Any ideas?<br>
<br>
Thanks,<br>
<br>
Renato<br>
<font color="#888888">--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>