Date: Tue, 6 Feb 2024 14:37:03 -0500
Hi,
I would like to add to the above problem that the co-ordinates I
receive are quite weird too. I am attaching an image of the NPT simulation
result (The NVT MD runs fine) and NPT runs fine on other GPUs too.
On Tue, Feb 6, 2024 at 1:04 PM Abhilash J <md.scfbio.gmail.com> wrote:
> Hi
>
> We recently bought a machine with RTX 4500 ada GPUs. I tried running a
> MD of a system on it. The system was stable and gave expected results for
> minimization, heating and NVT ensemble parts of the simulation. As soon as
> the NPT part of the simulation started, the volume started increasing and
> density decreased. I checked all 4 GPUs, all are giving this weird result.
> I ran the same system (same parameters and input files) on a different
> machine with a different GPU and it was stable throughout the MD process
> including NPT ensemble. We use a centralized NFS mounted AMBER and CUDA
> installation so AMBER 22 and drivers are identical for both workstations
> (software environment is the same). I also tried changing the nVidia driver
> version (updated it to the latest) but it did not help.
> Some specifications of the machines used are as follows:
>
> Machine1 ( issues with AMBER NPT simulation):
> AMBER: 22
> CUDA Version: 12.2
> Driver Version: 535.154.05
> GPU: RTX 4500 ada
>
> Machine1 ( no issues with AMBER NPT simulation):
> AMBER: 22
> CUDA Version: 12.2
> Driver Version: 535.154.05
> GPU: RTX A5000
>
>
> parts of out file
>
>
> machine 1 ( issues with AMBER NPT simulation) :
>
> | GPU memory information (estimate):
> | KB of GPU memory in use: 185835
> | KB of CPU memory in use: 47794
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
>
> NSTEP = 10000 TIME(PS) = 970.000 TEMP(K) = 300.55 PRESS =
> 1003.8
> Etot = -59652.2123 EKtot = 15095.9219 EPtot =
> -74748.1342
> BOND = 530.0636 ANGLE = 1419.4192 DIHED =
> 2233.8609
> 1-4 NB = 598.4804 1-4 EEL = 5438.5408 VDWAALS =
> 12496.7320
> EELEC = -97467.3075 EHBOND = 0.0000 RESTRAINT =
> 2.0765
> EAMBER (non-restraint) = -74750.2107
> EKCMT = 6557.7921 VIRIAL = -8320.9621 VOLUME =
> 686501.3298
> Density =
> 0.3683
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 2.077 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 20000 TIME(PS) = 990.000 TEMP(K) = 300.21 PRESS =
> 619.3
> Etot = -59713.4773 EKtot = 15078.5977 EPtot =
> -74792.0750
> BOND = 529.0326 ANGLE = 1403.8229 DIHED =
> 2246.4463
> 1-4 NB = 636.9275 1-4 EEL = 5440.7277 VDWAALS =
> 11846.0918
> EELEC = -96896.7219 EHBOND = 0.0000 RESTRAINT =
> 1.5979
> EAMBER (non-restraint) = -74793.6729
> EKCMT = 6612.6035 VIRIAL = -6254.1426 VOLUME =
> 962301.5478
> Density =
> 0.2627
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 1.598 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 30000 TIME(PS) = 1010.000 TEMP(K) = 302.59 PRESS =
> 303.7
> Etot = -59975.6763 EKtot = 15198.1543 EPtot =
> -75173.8306
> BOND = 521.5358 ANGLE = 1441.4137 DIHED =
> 2246.0128
> 1-4 NB = 626.2191 1-4 EEL = 5474.6381 VDWAALS =
> 11213.3314
> EELEC = -96699.2187 EHBOND = 0.0000 RESTRAINT =
> 2.2373
> EAMBER (non-restraint) = -75176.0680
> EKCMT = 6596.2709 VIRIAL = -1137.6617 VOLUME =
> 1179278.5515
> Density =
> 0.2144
>
> ------------------------------------------------------------------------------
>
> machine 2 ( no issues with AMBER NPT simulation) :
>
> | GPU memory information (estimate):
> | KB of GPU memory in use: 186315
> | KB of CPU memory in use: 48274
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
>
> NSTEP = 10000 TIME(PS) = 970.000 TEMP(K) = 304.42 PRESS =
> -11.8
> Etot = -66741.5838 EKtot = 15290.2188 EPtot =
> -82031.8025
> BOND = 520.2152 ANGLE = 1397.4144 DIHED =
> 2220.0926
> 1-4 NB = 599.0232 1-4 EEL = 5483.1949 VDWAALS =
> 9096.1249
> EELEC = -101349.2543 EHBOND = 0.0000 RESTRAINT =
> 1.3866
> EAMBER (non-restraint) = -82033.1891
> EKCMT = 6657.3725 VIRIAL = 6719.7680 VOLUME =
> 245140.6328
> Density =
> 1.0314
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 1.387 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 20000 TIME(PS) = 990.000 TEMP(K) = 302.79 PRESS =
> -94.9
> Etot = -66585.9186 EKtot = 15208.2480 EPtot =
> -81794.1666
> BOND = 522.4272 ANGLE = 1383.3173 DIHED =
> 2227.6762
> 1-4 NB = 631.6681 1-4 EEL = 5516.0293 VDWAALS =
> 8863.7857
> EELEC = -100940.5729 EHBOND = 0.0000 RESTRAINT =
> 1.5023
> EAMBER (non-restraint) = -81795.6689
> EKCMT = 6524.4404 VIRIAL = 7026.5906 VOLUME =
> 244951.3800
> Density =
> 1.0322
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 1.502 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 30000 TIME(PS) = 1010.000 TEMP(K) = 301.92 PRESS =
> 179.5
> Etot = -66469.6425 EKtot = 15164.4678 EPtot =
> -81634.1103
> BOND = 564.3909 ANGLE = 1401.1754 DIHED =
> 2224.0596
> 1-4 NB = 611.9704 1-4 EEL = 5449.2322 VDWAALS =
> 8904.6288
> EELEC = -100790.7116 EHBOND = 0.0000 RESTRAINT =
> 1.1441
> EAMBER (non-restraint) = -81635.2543
> EKCMT = 6571.8746 VIRIAL = 5621.0052 VOLUME =
> 245413.6457
> Density =
> 1.0303
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 1.144 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
>
> Regards
> Abhilash
>
>
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(image/png attachment: weird_NPT_issue_RTX4500ada.png)
