[gmx-users] Gromacs 2019.4 - cudaStreamSynchronize failed issue
Chenou Zhang
czhan178 at asu.edu
Wed Dec 4 21:35:12 CET 2019
We did test that.
Our cluster has total 11 GPU nodes and I ran 20 tests over all of them. 7
out of the 20 tests did have the potential energy jump issue and they were
running on 5 different nodes.
So I tend to believe this issue happens on any of those nodes.
On Wed, Dec 4, 2019 at 1:14 PM Szilárd Páll <pall.szilard at gmail.com> wrote:
> The fact that you are observing errors alo the energies to be off by so
> much and that it reproduces with multiple inputs suggest that this may not
> a code issue. Did you do all runs that failed on the same hardware? Have
> you excluded the option that one of those GeForce cards may be flaky?
>
> --
> Szilárd
>
>
> On Wed, Dec 4, 2019 at 7:47 PM Chenou Zhang <czhan178 at asu.edu> wrote:
>
> > We tried the same gmx settings in 2019.4 with different protein systems.
> > And we got the same weird potential energy jump within 1000 steps.
> >
> > ```
> >
> > Step Time
> > 0 0.00000
> > Energies (kJ/mol)
> > Bond U-B Proper Dih. Improper Dih. CMAP
> Dih.
> > 2.08204e+04 9.92358e+04 6.53063e+04 1.06706e+03
> -2.75672e+02
> > LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul.
> recip.
> > 1.50031e+04 -4.86857e+04 3.10386e+04 -1.09745e+06
> 4.81832e+03
> > Potential Kinetic En. Total Energy Conserved En.
> Temperature
> > -9.09123e+05 2.80635e+05 -6.28487e+05 -6.28428e+05
> 3.04667e+02
> > Pressure (bar) Constr. rmsd
> > -1.56013e+00 3.60634e-06
> >
> > DD step 999 load imb.: force 14.6% pme mesh/force 0.581
> > Step Time
> > 1000 2.00000
> >
> > Energies (kJ/mol)
> > Bond U-B Proper Dih. Improper Dih. CMAP
> Dih.
> > 2.04425e+04 9.92768e+04 6.52873e+04 1.02016e+03
> -2.45851e+02
> > LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul.
> recip.
> > 1.49863e+04 -4.91092e+04 3.10572e+04 -1.09508e+06
> 4.97942e+03
> > Potential Kinetic En. Total Energy Conserved En.
> Temperature
> > 1.35726e+35 2.77598e+05 1.35726e+35 1.35726e+35
> 3.01370e+02
> > Pressure (bar) Constr. rmsd
> > -7.55250e+01 3.63239e-06
> >
> > DD step 1999 load imb.: force 16.1% pme mesh/force 0.598
> > Step Time
> > 2000 4.00000
> >
> > Energies (kJ/mol)
> > Bond U-B Proper Dih. Improper Dih. CMAP
> Dih.
> > 1.99521e+04 9.97482e+04 6.49595e+04 1.00798e+03
> -2.42567e+02
> > LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul.
> recip.
> > 1.50156e+04 -4.85324e+04 3.01944e+04 -1.09620e+06
> 4.82958e+03
> > Potential Kinetic En. Total Energy Conserved En.
> Temperature
> > 1.35726e+35 2.79206e+05 1.35726e+35 1.35726e+35
> 3.03115e+02
> > Pressure (bar) Constr. rmsd
> > -5.50508e+01 3.64353e-06
> >
> > DD step 2999 load imb.: force 16.6% pme mesh/force 0.602
> > Step Time
> > 3000 6.00000
> >
> >
> > Energies (kJ/mol)
> > Bond U-B Proper Dih. Improper Dih. CMAP
> Dih.
> > 1.98590e+04 9.88100e+04 6.50934e+04 1.07048e+03
> -2.38831e+02
> > LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul.
> recip.
> > 1.49609e+04 -4.93079e+04 3.12273e+04 -1.09582e+06
> 4.83209e+03
> > Potential Kinetic En. Total Energy Conserved En.
> Temperature
> > 1.35726e+35 2.79438e+05 1.35726e+35 1.35726e+35
> 3.03367e+02
> > Pressure (bar) Constr. rmsd
> > 7.62438e+01 3.61574e-06
> >
> > ```
> >
> > On Mon, Dec 2, 2019 at 2:13 PM Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > What driver version is reported in the respective log files? Does the
> > error
> > > persist if mdrun -notunepme is used?
> > >
> > > Mark
> > >
> > > On Mon., 2 Dec. 2019, 21:18 Chenou Zhang, <czhan178 at asu.edu> wrote:
> > >
> > > > Hi Gromacs developers,
> > > >
> > > > I'm currently running gromacs 2019.4 on our university's HPC cluster.
> > To
> > > > fully utilize the GPU nodes, I followed notes on
> > > >
> > > >
> > >
> >
> http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html
> > > > .
> > > >
> > > >
> > > > And here is the command I used for my runs.
> > > > ```
> > > > gmx mdrun -v -s $TPR -deffnm md_seed_fixed -ntmpi 8 -pin on -nb gpu
> > > -ntomp
> > > > 3 -pme gpu -pmefft gpu -npme 1 -gputasks 00112233 -maxh $HOURS -cpt
> 60
> > > -cpi
> > > > -noappend
> > > > ```
> > > >
> > > > And for some of those runs, they might fail with the following error:
> > > > ```
> > > > -------------------------------------------------------
> > > >
> > > > Program: gmx mdrun, version 2019.4
> > > >
> > > > Source file: src/gromacs/gpu_utils/cudautils.cuh (line 229)
> > > >
> > > > MPI rank: 3 (out of 8)
> > > >
> > > >
> > > >
> > > > Fatal error:
> > > >
> > > > cudaStreamSynchronize failed: an illegal memory access was
> encountered
> > > >
> > > >
> > > >
> > > > For more information and tips for troubleshooting, please check the
> > > GROMACS
> > > >
> > > > website at http://www.gromacs.org/Documentation/Errors
> > > > ```
> > > >
> > > > we also had a different error from slurm system:
> > > > ```
> > > > ^Mstep 4400: timed with pme grid 96 96 60, coulomb cutoff 1.446:
> 467.9
> > > > M-cycles
> > > > ^Mstep 4600: timed with pme grid 96 96 64, coulomb cutoff 1.372:
> 451.4
> > > > M-cycles
> > > > /var/spool/slurmd/job2321134/slurm_script: line 44: 29866
> Segmentation
> > > > fault gmx mdrun -v -s $TPR -deffnm md_seed_fixed -ntmpi 8 -pin
> on
> > > -nb
> > > > gpu -ntomp 3 -pme gpu -pmefft gpu -npme 1 -gputasks 00112233 -maxh
> > $HOURS
> > > > -cpt 60 -cpi -noappend
> > > > ```
> > > >
> > > > We first thought this could due to compiler issue and tried different
> > > > settings as following:
> > > > ===test1===
> > > > <source>
> > > > module load cuda/9.2.88.1
> > > > module load gcc/7.3.0
> > > > . /home/rsexton2/Library/gromacs/2019.4/test1/bin/GMXRC
> > > > </source>
> > > > ===test2===
> > > > <source>
> > > > module load cuda/9.2.88.1
> > > > module load gcc/6x
> > > > . /home/rsexton2/Library/gromacs/2019.4/test2/bin/GMXRC
> > > > </source>
> > > > ===test3===
> > > > <source>
> > > > module load cuda/9.2.148
> > > > module load gcc/7.3.0
> > > > . /home/rsexton2/Library/gromacs/2019.4/test3/bin/GMXRC
> > > > </source>
> > > > ===test4===
> > > > <source>
> > > > module load cuda/9.2.148
> > > > module load gcc/6x
> > > > . /home/rsexton2/Library/gromacs/2019.4/test4/bin/GMXRC
> > > > </source>
> > > > ===test5===
> > > > <source>
> > > > module load cuda/9.1.85
> > > > module load gcc/6x
> > > > . /home/rsexton2/Library/gromacs/2019.4/test5/bin/GMXRC
> > > > </source>
> > > > ===test6===
> > > > <source>
> > > > module load cuda/9.0.176
> > > > module load gcc/6x
> > > > . /home/rsexton2/Library/gromacs/2019.4/test6/bin/GMXRC
> > > > </source>
> > > > ===test7===
> > > > <source>
> > > > module load cuda/9.2.88.1
> > > > module load gccgpu/7.4.0
> > > > . /home/rsexton2/Library/gromacs/2019.4/test7/bin/GMXRC
> > > > </source>
> > > >
> > > > However we still ended up with the same errors showed above. Does
> > anyone
> > > > know where does the cudaStreamSynchronize come in? Or am I wrongly
> > using
> > > > those gmx gpu commands?
> > > >
> > > > Any input will be appreciated!
> > > >
> > > > Thanks!
> > > > Chenou
> > > > --
> > > > Gromacs Users mailing list
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