[gmx-users] mdrun-gpu error

[Roland Schulz]

You should use the latest GROMACS version also for the GPU. Thus compile the
4.5.1 for the GPU and run this.

On Fri, Oct 15, 2010 at 4:16 PM, Renato Freitas <renatoffs at gmail.com> wrote:

> Hi there,
> I have installed the gromacs-4.5.1 and it was running without
> problems. Also I installed the GPU version of GROMACS
> (gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and
> NVIDIA driver are installed. Then I tried to run the test provided by
> Alan with the mdrun-gpu and I got an error.
>
> ##### To test mdrun-gpu
>
> cat << EOF >| em.mdp
> define                   = -DFLEXIBLE
> integrator               = cg ; steep
> nsteps                   = 200
> constraints              = none
> emtol                    = 1000.0
> nstcgsteep               = 10 ; do a steep every 10 steps of cg
> emstep                   = 0.01 ; used with steep
> nstcomm                  = 1
> coulombtype              = PME
> ns_type                  = grid
> rlist                    = 1.0
> rcoulomb                 = 1.0
> rvdw                     = 1.4
> Tcoupl                   = no
> Pcoupl                   = no
> gen_vel                  = no
> nstxout                  = 0 ; write coords every # step
> optimize_fft             = yes
> EOF
>
> cat << EOF >| md.mdp
> integrator               = md-vv
> nsteps                   = 1000
> dt                       = 0.002
> constraints              = all-bonds
> constraint-algorithm     = shake
> nstcomm                  = 1
> nstcalcenergy            = 1
> ns_type                  = grid
> rlist                    = 1.3
> rcoulomb                 = 1.3
> rvdw                     = 1.3
> vdwtype                  = cut-off
> coulombtype              = PME
> Tcoupl                   = Andersen
> nsttcouple               = 1
> tau_t                    = 0.1
> tc-grps                  = system
> ref_t                    = 300
> Pcoupl                   = mttk
> Pcoupltype               = isotropic
> nstpcouple               = 1
> tau_p                    = 0.5
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> gen_vel                  = yes
> nstxout                  = 2 ; write coords every # step
> lincs-iter               = 2
> DispCorr                 = EnerPres
> optimize_fft             = yes
> EOF
>
> wget -c "http://www.pdbe.org/download/1brv"; -O 1brv.pdb
>
> pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh
>
> editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0
>
> genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs
>
> grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr
>
> echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p
> Prot.top -norandom
>
> grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr
>
> mdrun -v -deffnm em
>
> grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr
>
> mdrun-gpu -v -deffnm md -device
> "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"
>
> -------------------------------------------------------
> Getting Loaded...
> Reading file md.tpr, VERSION 4.5 (single precision)
>
> -------------------------------------------------------
> Program mdrun-gpu, VERSION 4.5-GPU-beta2
> Source code file:
> /home/rossen/Research/Projects/Gromacs-dev/gromacs/src/gmxlib/tpxio.c,
> line: 1971
>
> Fatal error:
> reading tpx file (md.tpr) version 73 with version 71 program
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> I also have tried to use my own system to test the mdrun-gpu and I got
> the same error.
> Any ideas?
>
> Thanks,
>
> Renato
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