[gmx-users] mdrun-gpu error

[Renato Freitas]

Hi Roland,

I did as you suggested and it worked fine!

Thanks,

Renato


2010/10/15 Roland Schulz <roland at utk.edu>:
> 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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