[gmx-users] mdrun-gpu error

[Osmair Oliveira]

Hi Renato,
 >Fatal error:
> reading tpx file (md.tpr) version 73 with version 71 program

This error occur because you are using different version of the gromacs.
Are you sure that the version of the grompp is the same of the mdrun

I hope this help.

Prof. Dr. Osmair V. Oliveira
Federal Institute of Espirito Santo
Brazil

> Date: Fri, 15 Oct 2010 17:16:00 -0300
> From: renatoffs at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] mdrun-gpu error
> 
> 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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