Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

[Szilárd Páll]

Hi Steffi,

On Wed, Mar 27, 2019 at 1:08 PM Tafelmeier, Stefanie <
stefanie.tafelme...@zae-bayern.de> wrote:

> Hi Szilárd,
>
> thanks again!
> Here are the links for the log files, that didn't run:
> Old patch:
>  -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran*
> https://it-service.zae-bayern.de/Team/index.php/s/b4AYiMCoHeNgJH3
>  -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran*
> https://it-service.zae-bayern.de/Team/index.php/s/JEP2iwFFZCebZLF
>  -ntmpi 1 -ntomp 22 -pin on -pinstride 4:one out of 5 ran
> https://it-service.zae-bayern.de/Team/index.php/s/apra2zS7FHdqDQy
>
> New patch:
>  -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran*
> https://it-service.zae-bayern.de/Team/index.php/s/jAD52jBgNddrS3w
>  -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran*
> https://it-service.zae-bayern.de/Team/index.php/s/bcRjtz7r9NekzKB
>  -ntmpi 1 -ntomp 22 -pin on -pinstride 4:none ran*
> https://it-service.zae-bayern.de/Team/index.php/s/b3zp8DNztjE6ssF
>

This still doesn't tell much more unfortunately.

Two more things to try (can be combined)
- please set build with setting first
cmake . -DCMAKE_BUILD_TYPE=RelWithAssert
this may give us some extra debugging information during runs
- please use this patch now -- it will print some additional stuff to the
standard error output so please grab that and share it:
https://termbin.com/zq4q
(you can redirect the output e.g. by gmx mdrun > mdrun.out 2>&1)
- try running (with the above binary build + patch) the above failing case
repeasted a few times:
  -nsteps 0 -nb gpu -pme cpu -bonded cpu
  -nsteps 0 -nb gpu -pme gpu -bonded cpu
  -nsteps 0 -nb gpu -pme gpu -bonded gpu



> Regarding the Regressiontest:
>
> Sorry I didn't get it at the first time.
> If the md.log files are enough here is a folder for the failed parts of
> the complex regression test:
> https://it-service.zae-bayern.de/Team/index.php/s/64KAQBgNoPm4rJ2
>
> If you need any other files or the full directories please let me know.
>

Hmmm, looks like there are more issues here, some log files look truncated
others indicate termination by LINCS errors. Yes, the mdrun.out and
checkpot* files would be useful. How about just making a tarball of the
whole complex directory and sharing that?

Hopefully these tests will shed some light on what the issue is.

Cheers,
--
Szilard

Again, a lot of thank for your support.


> Best wishes,
> Steffi
>
>
>
>
>
>
>
>
>
>
> -Ursprüngliche Nachricht-
> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Szilárd
> Páll
> Gesendet: Dienstag, 26. März 2019 16:57
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs
>
> Hi Steffi,
>
> Thanks for running the tests; yes, the patch file was meant to be applied
> to the unchanged GROMACS 2019 code.
>
> Please also share the log files from thr failed runs, not just the
> copy-paste of the fatal error -- as a result of the additional check there
> might have been a note printed which I was after.
>
> Regarding the regression tests, what I would like to have is the actual
> directories of the tests that failed, i.e. as your log indicates a few of
> the complex tests at least.
>
> Cheers,
> --
> Szilárd
>
> On Tue, Mar 26, 2019 at 1:44 PM Tafelmeier, Stefanie <
> stefanie.tafelme...@zae-bayern.de> wrote:
>
> > Hi Szilárd,
> >
> > thanks again for your answer.
> > Regarding the tests:
> > without the new patch:
> >
> > -ntmpi 1 -ntomp 11 -pin on -pinstride 1:all ran
> > -ntmpi 1 -ntomp 11 -pin on -pinstride 2:all ran
> > -ntmpi 1 -ntomp 11 -pin on -pinstride 4:all ran
> > -ntmpi 1 -ntomp 11 -pin on -pinstride 8:all ran
> > and
> > -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran*
> > -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran*
> > -ntmpi 1 -ntomp 22 -pin on -pinstride 4:one out of 5 ran
> >
> >
> > With the new patch (devicebuffer.cuh had to be the original, right? The
> > already patched didn't work as the lines didn't fit, as far as I
> > understood.):
> >
> > -ntmpi 1 -ntomp 11 -pin on -pinstride 1:all ran
> > -ntmpi 1 -ntomp 11 -pin on -pinstride 2:all ran
> > -ntmpi 1 -ntomp 11 -pin on -pinstride 4:all ran
> > -ntmpi 1 -ntomp 11 -pin on -pinstride 8:all ran
> > and
> > -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran*
> > -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran*
> > -ntmpi 1 -ntomp 22 -pin on -pinstride 4:none ran*
> >
> > * Fatal error:
> > Asynchronous H2D copy failed: invalid argument
> >
> >
> > Regarding the regressiontest:
> > The LastTest.log is available here:
> > https://it-service.zae-bayern.de/Team/index.php/s/3sdki7Cf2x2CEQi
> > this was not given in the log:
> > The following tests FAILED:
> >  42 - regressiontests/complex (Timeout)
> >  46 - regressiontests/essentialdynamics (Failed)
> > 

Re: [gmx-users] (no subject)

[Dallas Warren]

In molecular dynamics things move around.

The fact that the molecules aren't in the starting position shows that it
isn't a stable configuration, the interactions between the protein and the
molecules are insufficient to keep them together in that spot.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 28 Mar 2019 at 05:50, saranya  wrote:

> Hi users,
>
>   I have simulated a protein with gas molecules (CO2,NO2 and SO2) for
> 100ns. I have followed the  protein ligand tutorial. I have applied
> position constraints. After equilibrium the gas molecules are at the docked
> position but at the 60ns simulation the gas molecules are far away from the
> protein. I have applied pBC and sure this is not an visualisatuin error.
> How can I rectify this, Kindly give your valuable suggestions in this
> regard.
>
>
>
> --
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*
> --
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[gmx-users] (no subject)

[saranya]

Hi users,

  I have simulated a protein with gas molecules (CO2,NO2 and SO2) for
100ns. I have followed the  protein ligand tutorial. I have applied
position constraints. After equilibrium the gas molecules are at the docked
position but at the 60ns simulation the gas molecules are far away from the
protein. I have applied pBC and sure this is not an visualisatuin error.
How can I rectify this, Kindly give your valuable suggestions in this
regard.



-- 

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
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Re: [gmx-users] Zsh completion behaves differently from bash completion

[Mark Abraham]

Hi,

Only bash is supported. I imagine zsh could be supported, but if someone is
keen to help out, then https://redmine.gromacs.org/issues/1410 would be a
great place to talk about it!

Mark

On Wed, 27 Mar 2019 at 13:22 Lorenzo Gaifas 
wrote:

> Dear gromacs users,
>
> I recently tried for the first time to use gromacs in zshell, instead of
> bash as I was used to. I very quickly realised that tab completion is
> behaving differently than I expected.
> When I write for example:
> `gmx editconf'
> and press tab, as expected a `-' is suggested, and I get suggestions for
> all the possible options. However, If I write:
> `gmx ediconf -f',
> when I press tab, another `-' is added and again I get offered all the
> options. In bash, instead, completion suggests possible filenames that
> match the option.
> Why is that? Can it be fixed and, if yes, how?
>
> Best regards,
> LG
> --
> Gromacs Users mailing list
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[gmx-users] Zsh completion behaves differently from bash completion

[Lorenzo Gaifas]

Dear gromacs users,

I recently tried for the first time to use gromacs in zshell, instead of
bash as I was used to. I very quickly realised that tab completion is
behaving differently than I expected.
When I write for example:
`gmx editconf'
and press tab, as expected a `-' is suggested, and I get suggestions for
all the possible options. However, If I write:
`gmx ediconf -f',
when I press tab, another `-' is added and again I get offered all the
options. In bash, instead, completion suggests possible filenames that
match the option.
Why is that? Can it be fixed and, if yes, how?

Best regards,
LG
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Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

[Tafelmeier, Stefanie]

Hi Szilárd,

thanks again!
Here are the links for the log files, that didn't run:
Old patch:
 -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran*  
https://it-service.zae-bayern.de/Team/index.php/s/b4AYiMCoHeNgJH3 
 -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran*  
https://it-service.zae-bayern.de/Team/index.php/s/JEP2iwFFZCebZLF 
 -ntmpi 1 -ntomp 22 -pin on -pinstride 4:one out of 5 ran   
https://it-service.zae-bayern.de/Team/index.php/s/apra2zS7FHdqDQy 

New patch:
 -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran*  
https://it-service.zae-bayern.de/Team/index.php/s/jAD52jBgNddrS3w 
 -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran*  
https://it-service.zae-bayern.de/Team/index.php/s/bcRjtz7r9NekzKB 
 -ntmpi 1 -ntomp 22 -pin on -pinstride 4:none ran*  
https://it-service.zae-bayern.de/Team/index.php/s/b3zp8DNztjE6ssF 


Regarding the Regressiontest:

Sorry I didn't get it at the first time.
If the md.log files are enough here is a folder for the failed parts of the 
complex regression test:
https://it-service.zae-bayern.de/Team/index.php/s/64KAQBgNoPm4rJ2 

If you need any other files or the full directories please let me know.

Again, a lot of thank for your support.

Best wishes,
Steffi 










-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von 
Szilárd Páll
Gesendet: Dienstag, 26. März 2019 16:57
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

Hi Steffi,

Thanks for running the tests; yes, the patch file was meant to be applied
to the unchanged GROMACS 2019 code.

Please also share the log files from thr failed runs, not just the
copy-paste of the fatal error -- as a result of the additional check there
might have been a note printed which I was after.

Regarding the regression tests, what I would like to have is the actual
directories of the tests that failed, i.e. as your log indicates a few of
the complex tests at least.

Cheers,
--
Szilárd

On Tue, Mar 26, 2019 at 1:44 PM Tafelmeier, Stefanie <
stefanie.tafelme...@zae-bayern.de> wrote:

> Hi Szilárd,
>
> thanks again for your answer.
> Regarding the tests:
> without the new patch:
>
> -ntmpi 1 -ntomp 11 -pin on -pinstride 1:all ran
> -ntmpi 1 -ntomp 11 -pin on -pinstride 2:all ran
> -ntmpi 1 -ntomp 11 -pin on -pinstride 4:all ran
> -ntmpi 1 -ntomp 11 -pin on -pinstride 8:all ran
> and
> -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran*
> -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran*
> -ntmpi 1 -ntomp 22 -pin on -pinstride 4:one out of 5 ran
>
>
> With the new patch (devicebuffer.cuh had to be the original, right? The
> already patched didn't work as the lines didn't fit, as far as I
> understood.):
>
> -ntmpi 1 -ntomp 11 -pin on -pinstride 1:all ran
> -ntmpi 1 -ntomp 11 -pin on -pinstride 2:all ran
> -ntmpi 1 -ntomp 11 -pin on -pinstride 4:all ran
> -ntmpi 1 -ntomp 11 -pin on -pinstride 8:all ran
> and
> -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran*
> -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran*
> -ntmpi 1 -ntomp 22 -pin on -pinstride 4:none ran*
>
> * Fatal error:
> Asynchronous H2D copy failed: invalid argument
>
>
> Regarding the regressiontest:
> The LastTest.log is available here:
> https://it-service.zae-bayern.de/Team/index.php/s/3sdki7Cf2x2CEQi
> this was not given in the log:
> The following tests FAILED:
>  42 - regressiontests/complex (Timeout)
>  46 - regressiontests/essentialdynamics (Failed)
> Errors while running CTest
> CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
> 'CMakeFiles/run-ctest-nophys' failed
> make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
> CMakeFiles/Makefile2:1397: recipe for target
> 'CMakeFiles/run-ctest-nophys.dir/all'failed
> make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
> CMakeFiles/Makefile2:1177: recipe for target
> 'CMakeFiles/check.dir/rule' failed
> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> Makefile:626: recipe for target 'check' failed
> make: *** [check] Error 2
>
> Many thanks again.
> Best wishes,
> Steffi
>
>
>
>
>
> -Ursprüngliche Nachricht-
> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Szilárd
> Páll
> Gesendet: Montag, 25. März 2019 20:13
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs
>
> Hi,
>
>
>
> --
> Szilárd
>
>
> On Mon, Mar 18, 2019 at 2:34 PM Tafelmeier, Stefanie <
> stefanie.tafelme...@zae-bayern.de> wrote:
>
> > Hi,
> >
> > Many thanks again.
> >
> > Regarding the tests:
> > - ntmpi 1 -ntomp 22 -pin on
> > >OK, so this suggests that your previ

Re: [gmx-users] NVT equilibration in vacuum

[Erik Marklund]

Additionally, be aware of the tumbling ice cube effect and set comm-mode to 
angular to avoid it.

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor  of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se

On 27 Mar 2019, at 00:53, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 3/26/19 5:43 PM, Neena Susan Eappen wrote:
Hello gromacs users,

I am using gromacs to simulate a peptide in vacuum. I was wondering for the NVT 
equilibration step, are there any particular parameters to be changed for 
vacuum conditions as there is no position restraining on solvent molecules?

Preparing a vacuum system is not like a condensed-phase system. To do a 
simulation in vacuum, turn off PBC and set all cutoffs to zero (rlist, rvdw, 
rcoulomb).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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