Hi Stephan,
The workstation administration is controlled by a different entity
(SBGrid, if you know about them). They installed AMBER 22 before ( in Q2 of
2023) we bought the 4500 ada workstation. Hence the compile version and
current CUDA version might differ.
The result of issuing "ldd $(which pmemd.cuda)"is "not a dynamic
executable".
As the compiled binaries are the same for both 4500 ada workstation
and A5000 workstation, I was hoping either AMBER would work for both or
none. Additionally only NPT MD displayed this issue. Maybe I am missing
some factor here.
Regards
Abhilash
On Wed, Feb 14, 2024 at 2:25 PM Stephan Schott <
s.schott-verdugo.fz-juelich.de> wrote:
> Hi again,
>
> Did you have to modify the cmake files at compilation time then? Or it
> worked without modifying anything? If the latter, you are probably using a
> different CUDA Toolkit. Can you double check the binaries are compiled
> using the proper libraries? You can double check the cmake log files, or
> "ldd $(which pmemd.cuda)" should give you the paths. If you indeed used
> CUDA 12.2.2, I am not sure, but you have to consider that, AFAIK, > 12.1
> hasn't been tested nor officially released in the AMBER community.
>
> Best regards,
> Stephan Schott Verdugo
> Biochemist
>
>
> Computational Biophysical Chemistry
> Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
> Forschungszentrum Jülich GmbH
> Wilhelm-Johnen-Straße, 52425 Jülich
> Germany
>
>
> ---------------------------------------------------------------------------------------------
>
> ---------------------------------------------------------------------------------------------
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Sitz der Gesellschaft: Jülich
> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
>
> ---------------------------------------------------------------------------------------------
>
> ---------------------------------------------------------------------------------------------
>
>
> El mié, 14 feb 2024 a la(s) 7:52 p.m., Abhilash J (md.scfbio.gmail.com)
> escribió:
>
>> Hi Stephan,
>>
>> I am using CUDA 12.2.2 and the latest driver version 535.154.05. I
>> also tried the previous driver version but that also did not help.
>>
>> Regards
>> Abhilash
>>
>>
>> On Wed, Feb 14, 2024 at 12:00 PM Stephan Schott <
>> s.schott-verdugo.fz-juelich.de> wrote:
>>
>>> Hi,
>>>
>>> Which CUDA version are you using? Try compiling with CUDA 12, if you are
>>> using an older version.
>>>
>>> Best regards,
>>>
>>> Stephan Schott Verdugo
>>> Biochemist
>>>
>>>
>>> Computational Biophysical Chemistry
>>> Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
>>> Forschungszentrum Jülich GmbH
>>> Wilhelm-Johnen-Straße, 52425 Jülich
>>> Germany
>>>
>>>
>>> ---------------------------------------------------------------------------------------------
>>>
>>> ---------------------------------------------------------------------------------------------
>>> Forschungszentrum Jülich GmbH
>>> 52425 Jülich
>>> Sitz der Gesellschaft: Jülich
>>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>>> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
>>>
>>> ---------------------------------------------------------------------------------------------
>>>
>>> ---------------------------------------------------------------------------------------------
>>>
>>>
>>> El mié, 14 feb 2024 a la(s) 5:38 p.m., Abhilash J via AMBER (
>>> amber.ambermd.org) escribió:
>>>
>>>> Hi David,
>>>>
>>>> I am already using barostat=2, the issue arises in spite of using
>>>> barostat=2. I tested the system on A5000, A100, 3090, 2080ti, A40, V100,
>>>> RTX8000, even the GTX 1080ti, M40 and K80. Only 4500 ada gives this
>>>> behaviour. Keeping barostat=1 (Berendsen) does not solve the issue.
>>>> My input file is attached below.
>>>>
>>>>
>>>> ==============================================
>>>> Production at NPT
>>>> &cntrl
>>>> imin=0, ! No minimization
>>>> irest=1, ! This IS a restart of an old MD simulation
>>>> ntx=5, ! So our inpcrd file has velocities
>>>>
>>>> ! Temperature control
>>>> ntt=3, ! Langevin dynamics
>>>> ig=-1, ! Random number seed
>>>> gamma_ln=1.0, ! Friction coefficient (ps^-1)
>>>> temp0=300.00, ! Target temperature
>>>>
>>>> ! Potential energy control
>>>> cut=10.0, ! nonbonded cutoff, in Angstroms
>>>>
>>>> ! MD settings
>>>> nstlim=5000000, ! 10 ns total
>>>> dt=0.002, ! time step (ps)
>>>>
>>>> ! SHAKE
>>>> ntc=2, ! Constrain bonds containing hydrogen
>>>> ntf=2, ! Do not calculate forces of bonds containing
>>>> hydrogen
>>>>
>>>> ! Control how often information is printed
>>>> ntpr=10000, ! Print energies every 10000 steps
>>>> ntwx=10000, ! Print coordinates every 10000 steps to the
>>>> trajectory
>>>> ntwr=500000, ! Print a restart file every 500K steps (can be less
>>>> frequent)
>>>> ! ntwv=-1, ! Uncomment to also print velocities to trajectory
>>>> ! ntwf=-1, ! Uncomment to also print forces to trajectory
>>>> ntxo=2, ! Write NetCDF format
>>>> ioutfm=1, ! Write NetCDF format (always do this!)
>>>> nscm=50000,
>>>>
>>>> ! Wrap coordinates when printing them to the same unit cell
>>>> ! iwrap=1,
>>>>
>>>> ! Constant pressure control.
>>>> barostat=2, ! MC barostat... change to 1 for Berendsen
>>>> ntp=1, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/
>>>> surften
>>>> pres0=1.0, ! Target external pressure, in bar
>>>>
>>>> ! Restraint options
>>>> nmropt=1,
>>>>
>>>> /
>>>> &wt type='REST', istep1=0,istep2=1500,value1=1.0, value2=1.0, /
>>>> &wt type='REST', istep1=1501,istep2=2500000,value1=1.0, value2=1.0, /
>>>> &wt type='END' /
>>>> LISTOUT=POUT
>>>> DISANG=restraints
>>>> &end
>>>> END
>>>> END
>>>>
>>>>
>>>> ==============================================
>>>>
>>>> On Sun, Feb 11, 2024 at 11:16 AM David A Case <dacase1.gmail.com>
>>>> wrote:
>>>>
>>>> > On Tue, Feb 06, 2024, Abhilash J via AMBER wrote:
>>>> > >
>>>> > > 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.
>>>> >
>>>> > It's possible that there is some RTX 4500 specific bug. Try some
>>>> parallel
>>>> > simulations (RTX 4500 vs A5000) setting barostat=2. This skips some
>>>> very
>>>> > complex code involved in computing virials and the internal pressure.
>>>> >
>>>> > ....dac
>>>> >
>>>> >
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------------------------
>>>>
>>>> ------------------------------------------------------------------------------------------------
>>>> Forschungszentrum Jülich GmbH
>>>> 52425 Jülich
>>>> Sitz der Gesellschaft: Jülich
>>>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>>>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>>>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>>>> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
>>>>
>>>> ------------------------------------------------------------------------------------------------
>>>>
>>>> ------------------------------------------------------------------------------------------------
>>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------------------------
>>>
>>> ------------------------------------------------------------------------------------------------
>>> Forschungszentrum Jülich GmbH
>>> 52425 Jülich
>>> Sitz der Gesellschaft: Jülich
>>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>>> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
>>>
>>> ------------------------------------------------------------------------------------------------
>>>
>>> ------------------------------------------------------------------------------------------------
>>>
>>
>>
>>
>> ------------------------------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------------------------
>> Forschungszentrum Jülich GmbH
>> 52425 Jülich
>> Sitz der Gesellschaft: Jülich
>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
>>
>> ------------------------------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------------------------
>>
>
>
>
> ------------------------------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------------------------
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Sitz der Gesellschaft: Jülich
> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
>
> ------------------------------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------------------------
>
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Received on Wed Feb 14 2024 - 12:30:02 PST
