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

Szilárd Páll pall.szilard at gmail.com
Tue Apr 9 20:36:11 CEST 2019


Dear Stefanie,

On Fri, Apr 5, 2019 at 11:48 AM Tafelmeier, Stefanie <
Stefanie.Tafelmeier at zae-bayern.de> wrote:

> Hi Szilárd,
>
> thanks for your advices.
> I performed the tests.
> Both performed without errors.
>

OK, that excludes simple and obvious issues.
Wild guess, but can you run those again, but this time prefix the command
with
"taskset -c 22-32"
? This makes the tests use cores 22-32 just to check if using a specific
set of cores may somehow trigger an error.

What CUDA version did you use to compiler the memtest tool -- was it the
same (CUDA 9.2) as the one used for building GROMACS?

Just to get it right; I have to ask in more detail, because the connection
> between is the CPU/GPU and calculation distribution is still a bit blurry
> to me:
>
> If the output of the regressiontests show that the test crashes after 1-2
> steps, this means there is an issue between the transfer between the CPU
> and GPU?
> As far as I got the short range calculation part is normally split into
> nonbonded -> GPU and bonded -> CPU?
>

The -nb/-pme/-bonded flags control which tasks executes where (if not
specified defaults control this); the output contains a report which
summarizes where the major force tasks are executed, e.g. this is from one
of your log files which tells that PP (i.e. particle tasks like short-range
nonbonded) and the full PME tasks are offloaded to a GPU with ID 0 (and to
check which GPU is that you can look at the "Hardware detection" section of
the log):

1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
  PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PME tasks will do all aspects on the GPU

For more details, please see
http://manual.gromacs.org/documentation/2019.1/user-guide/mdrun-performance.html#running-mdrun-with-gpus

We have seen two types of errors so far:
- "Asynchronous H2D copy failed: invalid argument" which is still
mysterious to me and has showed up both in your repeated manual runs as
well as the regressiontest; as this aborts the run
- Failing regressiontests with either invalid results or crashes (below
above abort): to be honest I do not know what causes these but given that
results

The latter errors indicate incorrect results, in your last "complex" tests
tarball I saw some tests failing with LINCS errors (and indicating NaN
values) and a good fraction of tests failing with a GPU-side assertions --
both of which suggest that things do go wrong on the GPU.

And does this mean that maybe also the calculation I do, have wrong
> energies? Can I trust my results?
>

At this point I can unfortunately not recommend running production
simulations on this machine.

Will try to continue exploring the possible errors and I hope you can help
out with some test:

- Please run the complex regressiontests (using the RelWithAssert binary)
by setting the CUDA_LAUNCH_BLOCKING environment variable. This may allow us
to reason better about the source of the errors. Also you can reconfigure
with cmake -DGMX_OPENMP_MAX_THREADS=128 to avoid the 88 OpenMP thread
errors in tests that you encountered yourself.

- Can you please update compiler GROMACS with CUDA 10 and check if either
of two kinds of errors does reproduce. (If it does, if you can upgrade the
driver I suggest upgrading to CUDA 10.1).



>
> Many thanks again for your support.
> Best wishes,
> Steffi
>
>
--
Szilárd


>
>
>
> -----Ursprüngliche Nachricht-----
> Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] Im Auftrag von Szilárd
> Páll
> Gesendet: Freitag, 29. März 2019 01:24
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs
>
> Hi,
>
> The standard output of the first set of runs is also something I was
> interested in, but I've found the equivalent in the
> complex/TESTDIR/mdrun.out files. What I see in the regresiontests output is
> that the forces/energies results are simply not correct; some tests simply
> crash after 1-2 steps, but others do complete (like the nbnxn-free-energy/)
> and the short-range energies a clearly far off.
>
> I suggest to try to check if there may be hardware issue:
>
> - run this memory testing tool:
> git clone
> https://github.com/ComputationalRadiationPhysics/cuda_memtest.git
> cd cuda_memtest
> make cuda_memtest CFLAGS='-arch sm_30 -DSM_20 -O3 -DENABLE_NVML=0'
> ./cuda_memtest
>
> - compile and run the gpu-burn tool:
> git clone https://github.com/wilicc/gpu-burn
> cd gpu-burn
> make
> then run
> gpu-burn 300
> to test for 5 minutes.
>
> --
> Szilárd
>
>
> On Thu, Mar 28, 2019 at 3:46 PM Tafelmeier, Stefanie <
> Stefanie.Tafelmeier at zae-bayern.de> wrote:
>
> > Hi Szilárd,
> >
> > Thanks again!
> >
> > Regarding the test:
> >   -ntmpi 1 -ntomp 22 -pin on -pinstride 1:      2 out of 5 run
> > https://it-service.zae-bayern.de/Team/index.php/s/XEQrYqq4pikGmMy  /
> > https://it-service.zae-bayern.de/Team/index.php/s/YBdKKJ9c7zQpEg9
> > Including:
> >   -nsteps 0 -nb gpu -pme cpu -bonded cpu:       0 run
> > https://it-service.zae-bayern.de/Team/index.php/s/YiByc7iXW5AW9ZX
> >   -nsteps 0 -nb gpu -pme gpu -bonded cpu:       2 out of 5 run
> > https://it-service.zae-bayern.de/Team/index.php/s/JNPXQnEgYtTAxGj   /
> > https://it-service.zae-bayern.de/Team/index.php/s/6aq6BQwwbBELqWe
> >   -nsteps 0 -nb gpu -pme gpu -bonded gpu:       0 run
> > https://it-service.zae-bayern.de/Team/index.php/s/yj4RAqPMFsDNgTc
> >
> > Including:
> >   -ntmpi 1 -ntomp 22 -pin on -pinstride 2:      1 out of 5 run
> > https://it-service.zae-bayern.de/Team/index.php/s/q5jHbdJ2EygtDaQ  /
> > https://it-service.zae-bayern.de/Team/index.php/s/sRPccwHRxojW9J8
> >   -nsteps 0 -nb gpu -pme cpu -bonded cpu:       0 run
> > https://it-service.zae-bayern.de/Team/index.php/s/GdKk5N68CY7BGxJ
> >   -nsteps 0 -nb gpu -pme gpu -bonded cpu:       1 out of 5 run
> > https://it-service.zae-bayern.de/Team/index.php/s/orwzKJMampWwDo5  /
> > https://it-service.zae-bayern.de/Team/index.php/s/JXApT4tFtxQWxG6
> >   -nsteps 0 -nb gpu -pme gpu -bonded gpu:       0 run
> > https://it-service.zae-bayern.de/Team/index.php/s/8YKK7Zxax22RfGQ
> >
> > Including:
> >   -ntmpi 1 -ntomp 22 -pin on -pinstride 4:      1 out of 5 run
> > https://it-service.zae-bayern.de/Team/index.php/s/szZjzaxmwfimrgB  /
> > https://it-service.zae-bayern.de/Team/index.php/s/QdTd2an9dbE9BSt
> >   -nsteps 0 -nb gpu -pme cpu -bonded cpu:       3 out of 5 run
> > https://it-service.zae-bayern.de/Team/index.php/s/DPoqKrgcWfF5PKM  /
> > https://it-service.zae-bayern.de/Team/index.php/s/3NbsGHtCPsf7zFS
> >   -nsteps 0 -nb gpu -pme gpu -bonded cpu:       3 out of 5 run
> > https://it-service.zae-bayern.de/Team/index.php/s/WqP4tXjrR8i3455  /
> > https://it-service.zae-bayern.de/Team/index.php/s/DACGc86xxKR6pWs
> >   -nsteps 0 -nb gpu -pme gpu -bonded gpu:       0 run
> > https://it-service.zae-bayern.de/Team/index.php/s/3nKdwA28KySLEdB
> >
> >
> > Regarding the regressiontest:
> > Here is the link to the tarball:
> > https://it-service.zae-bayern.de/Team/index.php/s/mMyt3MPEfRrn8Ge
> >
> >
> > Thanks again for all your support and fingers crossed!
> >
> > Best wishes,
> > Steffi
> >
> >
> >
> >
> >
> > -----Ursprüngliche Nachricht-----
> > Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] Im Auftrag von
> Szilárd
> > Páll
> > Gesendet: Mittwoch, 27. März 2019 20:27
> > An: Discussion list for GROMACS users
> > Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs
> >
> > Hi Steffi,
> >
> > On Wed, Mar 27, 2019 at 1:08 PM Tafelmeier, Stefanie <
> > Stefanie.Tafelmeier at 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-bounces at maillist.sys.kth.se [mailto:
> > > gromacs.org_gmx-users-bounces at 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.Tafelmeier at 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-bounces at maillist.sys.kth.se [mailto:
> > > > gromacs.org_gmx-users-bounces at 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.Tafelmeier at zae-bayern.de> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > Many thanks again.
> > > > >
> > > > > Regarding the tests:
> > > > > - ntmpi 1 -ntomp 22 -pin on
> > > > > >OK, so this suggests that your previously successful 22-thread
> runs
> > > did
> > > > > not
> > > > > turn on pinning, I assume?
> > > > > It seems so, yet it does not run successfully each time. But if
> done
> > > with
> > > > > 20-threads, which works usually without error, it does not look
> like
> > > the
> > > > > pinning is turned on.
> > > > >
> > > >
> > > > Pinning is only turned on if mdrun can safely assume that the cores
> of
> > > the
> > > > node are not shared by multiple applications. This assumption can
> only
> > be
> > > > made if all hardware threads of the entire node are used the run
> itself
> > > > (i.e. in your case 2x22 cores with HyperThreadince hence 2 threads
> > each =
> > > > 88 threads).
> > > >
> > > > -ntmpi 1 -ntomp 1 -pin on; runs
> > > > > -ntmpi 1 -ntomp 2 -pin on; runs
> > > > >
> > > > > - ntmpi 24 -ntomp 1 -pinstride 1 -pin on; runs
> > > > > - ntmpi 24 -ntomp 1 -pinstride 2 -pin on; runs
> > > > >
> > > > > After patch supplied:
> > > > > - ntmpi 1 -ntomp 22 -pin on; sometime runs - sometimes doesn't*
>  ->
> > > > > md_run.log at :
> > > > > https://it-service.zae-bayern.de/Team/index.php/s/ezXWnQ2pGNeFx6T
> > > > >
> > > > >  md_norun.log at:
> > > > > https://it-service.zae-bayern.de/Team/index.php/s/wYPY7dWEJdwmqJi
> > > > > - ntmpi 1 -ntomp 22 -pin off; sometime runs - sometimes doesn't*
> >  (ran
> > > > > before)
> > > > > - ntmpi 1 -ntomp 23 -pin off; doesn't work*  (ran before)
> > > > >
> > > > > - ntmpi 1 -ntomp 23 -pinstride 1 -pin on; doesn't work*
> > > > >
> > > > > - ntmpi 1 -ntomp 23 -pinstride 2 -pin on; doesn't work*  (ran
> before)
> > > > >
> > > >
> > > >
> > > > The suspicious thing is that the patch I made only improves the
> > verbosity
> > > > of the error reporting, it should have no impact on whether the error
> > is
> > > > triggered or not. Considering the above behavior it seems that
> pinning
> > > (at
> > > > least the patters tried) has no influence on whether the runs work.
> > > >
> > > > Can you please try:
> > > > -ntmpi 1 -ntomp 11 -pin on -pinstride 1
> > > > -ntmpi 1 -ntomp 11 -pin on -pinstride 2
> > > > -ntmpi 1 -ntomp 11 -pin on -pinstride 4
> > > > -ntmpi 1 -ntomp 11 -pin on -pinstride 8
> > > > and
> > > > -ntmpi 1 -ntomp 22 -pin on -pinstride 1
> > > > -ntmpi 1 -ntomp 22 -pin on -pinstride 2
> > > > -ntmpi 1 -ntomp 22 -pin on -pinstride 4
> > > >
> > > > And please run these 5 times each (-nsteps 0 is fine to make things
> > > quick).
> > > >
> > > > Also, please use this patch
> > > > https://termbin.com/r8kk
> > > > The same way as you did the one before, it adds another check that
> > might
> > > > shed some light on what's going on.
> > > >
> > > > - ntmpi 24 -ntomp 1 -pinstride 1 -pin on; runs
> > > > > - ntmpi 24 -ntomp 1 -pinstride 2 -pin on; runs
> > > > >
> > > > > * Fatal error:
> > > > > Asynchronous H2D copy failed: invalid argument
> > > > >
> > > > > When compiling, the make check shows that the
> regressiontest-complex
> > > and
> > > > > regressiontest-essential dynamics fail.
> > > > > I am not sure if this is correlated?
> > > > >
> > > >
> > > > It might be, please share the outputs of the regressiontests.
> > > >
> > > > --
> > > > Szilárd
> > > >
> > > >
> > > > > Many thanks in advance.
> > > > > Best wishes,
> > > > > Steffi
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > -----Ursprüngliche Nachricht-----
> > > > > Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> > > > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] Im Auftrag von
> > > > Szilárd
> > > > > Páll
> > > > > Gesendet: Freitag, 15. März 2019 17:57
> > > > > An: Discussion list for GROMACS users
> > > > > Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs
> > > > >
> > > > > On Fri, Mar 15, 2019 at 5:02 PM Tafelmeier, Stefanie <
> > > > > Stefanie.Tafelmeier at zae-bayern.de> wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > about the tests:
> > > > > > - ntmpi 1 -ntomp 22 -pin on; doesn't work*
> > > > > >
> > > > >
> > > > > OK, so this suggests that your previously successful 22-thread runs
> > did
> > > > not
> > > > > turn on pinning, I assume?
> > > > > Can you please try:
> > > > > -ntmpi 1 -ntomp 1 -pin on
> > > > > -ntmpi 1 -ntomp 2 -pin on
> > > > > that is to check does pinning work at all?
> > > > > Also, please try one/both of the above (assuming they fail with)
> same
> > > > > binary, but CPU-only run, i.e.
> > > > > -ntmpi 1 -ntomp 1 -pin on -nb cpu
> > > > >
> > > > >
> > > > > > - ntmpi 1 -ntomp 22 -pin off; runs
> > > > > > - ntmpi 1 -ntomp 23 -pin off; runs
> > > > > > - ntmpi 1 -ntomp 23 -pinstride 1 -pin on; doesn't work*
> > > > > > - ntmpi 1 -ntomp 23 -pinstride 2 -pin on; runs
> > > > > > - ntmpi 23 -ntomp 1 -pinstride 1 -pin on; doesn't work**
> > > > > > - ntmpi 23 -ntomp 1 -pinstride 2 -pin on; doesn't work**
> > > > > >
> > > > >
> > > > > Just to confirm, can you please run the **'s with either -ntmpi 24
> > (to
> > > > > avoid the DD error).
> > > > >
> > > > >
> > > > > >
> > > > > > *Error as known.
> > > > > >
> > > > > > **The number of ranks you selected (23) contains a large prime
> > factor
> > > > 23.
> > > > > > In
> > > > > > most cases this will lead to bad performance. Choose a number
> with
> > > > > smaller
> > > > > > prime factors or set the decomposition (option -dd) manually.
> > > > > >
> > > > > > The log file is at:
> > > > > >
> https://it-service.zae-bayern.de/Team/index.php/s/fypKB9iZJz8yXq8
> > > > > >
> > > > >
> > > > > Will have a look and get back with more later.
> > > > >
> > > > >
> > > > > >
> > > > > > Many thanks again,
> > > > > > Steffi
> > > > > >
> > > > > > -----Ursprüngliche Nachricht-----
> > > > > > Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> > > > > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] Im Auftrag
> von
> > > > > Szilárd
> > > > > > Páll
> > > > > > Gesendet: Freitag, 15. März 2019 16:27
> > > > > > An: Discussion list for GROMACS users
> > > > > > Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs
> > > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Please share log files with an external service attachments are
> not
> > > > > > accepted on the list.
> > > > > >
> > > > > > Also, when checking the error with the patch supplied, please run
> > the
> > > > > > following cases -- no long runs are needed just want to know
> which
> > of
> > > > > these
> > > > > > runs and which of these doesn't:
> > > > > > - ntmpi 1 -ntomp 22 -pin on
> > > > > > - ntmpi 1 -ntomp 22 -pin off
> > > > > > - ntmpi 1 -ntomp 23 -pin off
> > > > > > - ntmpi 1 -ntomp 23 -pinstride 1 -pin on
> > > > > > - ntmpi 1 -ntomp 23 -pinstride 2 -pin on
> > > > > > - ntmpi 23 -ntomp 1 -pinstride 1 -pin on
> > > > > > - ntmpi 23 -ntomp 1 -pinstride 2 -pin on
> > > > > >
> > > > > > Thanks,
> > > > > > --
> > > > > > Szilárd
> > > > > >
> > > > > >
> > > > > > On Fri, Mar 15, 2019 at 4:04 PM Tafelmeier, Stefanie <
> > > > > > Stefanie.Tafelmeier at zae-bayern.de> wrote:
> > > > > >
> > > > > > > Hi Szilárd,
> > > > > > >
> > > > > > > thanks for the quick reply.
> > > > > > > About the first suggestion, I'll try and give feedback soon.
> > > > > > >
> > > > > > > Regarding the second, I attached the log-file for the case of
> > > > > > > mdrun -v -nt 25
> > > > > > > Which ends in the known error message.
> > > > > > >
> > > > > > > Again, thanks a lot for your information and help.
> > > > > > >
> > > > > > > Best wishes,
> > > > > > > Steffi
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > -----Ursprüngliche Nachricht-----
> > > > > > > Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:
> > > > > > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] Im Auftrag
> > von
> > > > > > Szilárd
> > > > > > > Páll
> > > > > > > Gesendet: Freitag, 15. März 2019 15:30
> > > > > > > An: Discussion list for GROMACS users
> > > > > > > Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs
> > > > > > >
> > > > > > > Hi Stefanie,
> > > > > > >
> > > > > > > Unless and until the error and performance-related concerns
> prove
> > > to
> > > > be
> > > > > > > related, let's keep those separate.
> > > > > > >
> > > > > > > I'd first focus on the former. To be honest, I've never
> > encountered
> > > > > such
> > > > > > an
> > > > > > > issue where if you use more than a certain number of threads,
> the
> > > run
> > > > > > > aborts with that error. To investigate further can you please
> > apply
> > > > the
> > > > > > > following patch file which hopefully give more context to the
> > > error:
> > > > > > > https://termbin.com/uhgp
> > > > > > > (e.g. you can execute the following to accomplish that:
> > > > > > > curl https://termbin.com/uhgp > devicebuffer.cuh.patch &&
> patch
> > > -p0
> > > > <
> > > > > > > devicebuffer.cuh.patch)
> > > > > > >
> > > > > > > Regarding the performance-related questions, can you please
> > share a
> > > > > full
> > > > > > > log file of the runs so we can see the machine config,
> simulation
> > > > > > > system/settings, etc. Without that it is hard to judge what's
> > best
> > > > for
> > > > > > your
> > > > > > > case. However, if you only have a single GPU (which seems to be
> > the
> > > > > case
> > > > > > > based on the log excerpts) along those two rather beefy CPUs,
> > than
> > > > you
> > > > > > will
> > > > > > > likely not get much benefit from using all cores and it is
> normal
> > > > that
> > > > > > you
> > > > > > > see little to no improvement from using cores of a second CPU
> > > socket.
> > > > > > >
> > > > > > > Cheers,
> > > > > > > --
> > > > > > > Szilárd
> > > > > > >
> > > > > > >
> > > > > > > On Thu, Mar 14, 2019 at 12:47 PM Tafelmeier, Stefanie <
> > > > > > > Stefanie.Tafelmeier at zae-bayern.de> wrote:
> > > > > > >
> > > > > > > > Dear all,
> > > > > > > >
> > > > > > > > I was not sure if the email before reached you, but again
> many
> > > > thanks
> > > > > > for
> > > > > > > > your reply Szilárd.
> > > > > > > >
> > > > > > > > As written below we are still facing a problem with the
> > > performance
> > > > > of
> > > > > > > > your workstation.
> > > > > > > > I wrote before because of the error message when keeping
> > > occurring
> > > > > for
> > > > > > > > mdrun simulation:
> > > > > > > >
> > > > > > > > Assertion failed:
> > > > > > > > Condition: stat == cudaSuccess
> > > > > > > > Asynchronous H2D copy failed
> > > > > > > >
> > > > > > > > As I mentioned all Versions to install (Gormacs, Cuda, nvcc,
> > gcc)
> > > > are
> > > > > > the
> > > > > > > > newest once now.
> > > > > > > >
> > > > > > > > If I run mdrun without further settings it will lead to this
> > > error
> > > > > > > > message. If I run it and choose the thread amount directly
> the
> > > > mdrun
> > > > > is
> > > > > > > > performing well. But only for –nt numbers between 1 – 22.
> > Higher
> > > > ones
> > > > > > > again
> > > > > > > > lead to the before mentioned error message.
> > > > > > > >
> > > > > > > > In order to investigate in more detail, I tried different
> > > versions
> > > > > for
> > > > > > > > –nt, –ntmpi – ntomp also combined with –npme:
> > > > > > > > -       The best performance in the sense of ns/day is with
> –nt
> > > 22
> > > > > > > > respectively –ntomp 22 alone. But then only 22 threads are
> > > > involved.
> > > > > > > Which
> > > > > > > > is fine if I run more than one mdrun simultaneously, as I can
> > > > > > distribute
> > > > > > > > the other 66 threads. The GPU usage is then around 65%.
> > > > > > > > -       A similar good performance is reached with mdrun
> > -ntmpi
> > > 4
> > > > > > -ntomp
> > > > > > > > 18 -npme 1 -pme gpu -nb gpu. But then 44 threads are
> involved.
> > > The
> > > > > GPU
> > > > > > > > usage is then around 50%.
> > > > > > > >
> > > > > > > > I read the information on
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html
> > > > > > > > which was very helpful, bur some things are still not clear
> now
> > > to
> > > > > me:
> > > > > > > > I was wondering if there is any other enhancement of the
> > > > performance?
> > > > > > Or
> > > > > > > > what is the reason, that –nt maximum is at 22 threads? Could
> > this
> > > > be
> > > > > > > > connected to the sockets (see details below) of your
> > workstation?
> > > > > > > > It is not clear to me how a number of thread (-nt) higher 22
> > can
> > > > lead
> > > > > > to
> > > > > > > > the error regarding the Asynchronous H2D copy)
> > > > > > > >
> > > > > > > > Please excuse all these questions. I would appreciate a lot
> if
> > > you
> > > > > > might
> > > > > > > > have a hint for this problem as well.
> > > > > > > >
> > > > > > > > Best regards,
> > > > > > > > Steffi
> > > > > > > >
> > > > > > > > -----
> > > > > > > >
> > > > > > > > The workstation details are:
> > > > > > > > Running on 1 node with total 44 cores, 88 logical cores, 1
> > > > compatible
> > > > > > GPU
> > > > > > > > Hardware detected:
> > > > > > > >
> > > > > > > >   CPU info:
> > > > > > > >     Vendor: Intel
> > > > > > > >     Brand:  Intel(R) Xeon(R) Gold 6152 CPU @ 2.10GHz
> > > > > > > >     Family: 6   Model: 85   Stepping: 4
> > > > > > > >     Features: aes apic avx avx2 avx512f avx512cd avx512bw
> > > avx512vl
> > > > > > clfsh
> > > > > > > > cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc
> > > pcid
> > > > > > > pclmuldq
> > > > > > > > pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1
> > sse4.2
> > > > > ssse3
> > > > > > > tdt
> > > > > > > > x2apic
> > > > > > > >
> > > > > > > >     Number of AVX-512 FMA units: 2
> > > > > > > >   Hardware topology: Basic
> > > > > > > >     Sockets, cores, and logical processors:
> > > > > > > >       Socket  0: [   0  44] [   1  45] [   2  46] [   3  47]
> [
> > >  4
> > > > > > 48] [
> > > > > > > >  5  49] [   6  50] [   7  51] [   8  52] [   9  53] [  10
> 54]
> > [
> > > > 11
> > > > > > 55]
> > > > > > > > [  12  56] [  13  57] [  14  58] [  15  59] [  16  60] [  17
> > > 61] [
> > > > > 18
> > > > > > > > 62] [  19  63] [  20  64] [  21  65]
> > > > > > > >       Socket  1: [  22  66] [  23  67] [  24  68] [  25  69]
> [
> > > 26
> > > > > > 70] [
> > > > > > > > 27  71] [  28  72] [  29  73] [  30  74] [  31  75] [  32
> 76]
> > [
> > > > 33
> > > > > > 77]
> > > > > > > > [  34  78] [  35  79] [  36  80] [  37  81] [  38  82] [  39
> > > 83] [
> > > > > 40
> > > > > > > > 84] [  41  85] [  42  86] [  43  87]
> > > > > > > >   GPU info:
> > > > > > > >     Number of GPUs detected: 1
> > > > > > > >     #0: NVIDIA Quadro P6000, compute cap.: 6.1, ECC:  no,
> stat:
> > > > > > > compatible
> > > > > > > >
> > > > > > > > -----
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > -----Ursprüngliche Nachricht-----
> > > > > > > > Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> > [mailto:
> > > > > > > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] Im
> Auftrag
> > > von
> > > > > > > Szilárd
> > > > > > > > Páll
> > > > > > > > Gesendet: Donnerstag, 31. Januar 2019 17:15
> > > > > > > > An: Discussion list for GROMACS users
> > > > > > > > Betreff: Re: [gmx-users] WG: Issue with CUDA and gromacs
> > > > > > > >
> > > > > > > > On Thu, Jan 31, 2019 at 2:14 PM Szilárd Páll <
> > > > pall.szilard at gmail.com
> > > > > >
> > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > On Wed, Jan 30, 2019 at 5:15 PM Tafelmeier, Stefanie
> > > > > > > > > <Stefanie.Tafelmeier at zae-bayern.de> wrote:
> > > > > > > > > >
> > > > > > > > > > Dear all,
> > > > > > > > > >
> > > > > > > > > > We are facing an issue with the CUDA toolkit.
> > > > > > > > > > We tried several combinations of gromacs versions and
> CUDA
> > > > > > Toolkits.
> > > > > > > > No Toolkit older than 9.2 was possible to try as there are no
> > > > driver
> > > > > > for
> > > > > > > > nvidia available for a Quadro P6000.
> > > > > > > > > > Gromacs
> > > > > > > > >
> > > > > > > > > Install the latest 410.xx drivers and it will work; the
> > NVIDIA
> > > > > driver
> > > > > > > > > download website (
> https://www.nvidia.com/Download/index.aspx
> > )
> > > > > > > > > recommends 410.93.
> > > > > > > > >
> > > > > > > > > Here's a system with CUDA 10-compatible driver running o a
> > > system
> > > > > > with
> > > > > > > > > a P6000: https://termbin.com/ofzo
> > > > > > > >
> > > > > > > > Sorry, I misread that as "CUDA >=9.2 was not possible".
> > > > > > > >
> > > > > > > > Note that the driver is backward compatible, so you can use a
> > new
> > > > > > > > driver with older CUDA versions.
> > > > > > > >
> > > > > > > > Also note that the oldest driver NVIDIA claims to have P6000
> > > > support
> > > > > > > > is 390.59 which is, as far as I know, one gen older than the
> > 396
> > > > that
> > > > > > > > the CUDA 9.2 toolkit came with. This is however, not
> something
> > > I'd
> > > > > > > > recommend pursuing, use a new driver from the official site
> > with
> > > > any
> > > > > > > > CUDA version that GROMACS supports and it should be fine.
> > > > > > > >
> > > > > > > > >
> > > > > > > > > > CUDA
> > > > > > > > > >
> > > > > > > > > > Error message
> > > > > > > > > >
> > > > > > > > > > 2019
> > > > > > > > > >
> > > > > > > > > > 10.0
> > > > > > > > > >
> > > > > > > > > > gmx mdrun:
> > > > > > > > > > Assertion failed:
> > > > > > > > > > Condition: stat == cudaSuccess
> > > > > > > > > > Asynchronous H2D copy failed
> > > > > > > > > >
> > > > > > > > > > 2019
> > > > > > > > > >
> > > > > > > > > > 9.2
> > > > > > > > > >
> > > > > > > > > > gmx mdrun:
> > > > > > > > > > Assertion failed:
> > > > > > > > > > Condition: stat == cudaSuccess
> > > > > > > > > > Asynchronous H2D copy failed
> > > > > > > > > >
> > > > > > > > > > 2018.5
> > > > > > > > > >
> > > > > > > > > > 9.2
> > > > > > > > > >
> > > > > > > > > > gmx mdrun: Fatal error:
> > > > > > > > > > HtoD cudaMemcpyAsync failed: invalid argument
> > > > > > > > >
> > > > > > > > > Can we get some more details on these, please? complete log
> > > files
> > > > > > > > > would be a good start.
> > > > > > > > >
> > > > > > > > > > 5.1.5
> > > > > > > > > >
> > > > > > > > > > 9.2
> > > > > > > > > >
> > > > > > > > > > Installation make: nvcc fatal   : Unsupported gpu
> > > architecture
> > > > > > > > 'compute_20'*
> > > > > > > > > >
> > > > > > > > > > 2016.2
> > > > > > > > > >
> > > > > > > > > > 9.2
> > > > > > > > > >
> > > > > > > > > > Installation make: nvcc fatal   : Unsupported gpu
> > > architecture
> > > > > > > > 'compute_20'*
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > *We also tried to set the target CUDA architectures as
> > > > described
> > > > > in
> > > > > > > > the installation guide (
> > > > > > > >
> manual.gromacs.org/documentation/2019/install-guide/index.html
> > ).
> > > > > > > > Unfortunately it didn't work.
> > > > > > > > >
> > > > > > > > > What does it mean that it didn't work? Can you share the
> > > command
> > > > > you
> > > > > > > > > used and what exactly did not work?
> > > > > > > > >
> > > > > > > > > For the P6000 which is a "compute capability 6.1" device
> (for
> > > > > anyone
> > > > > > > > > who needs to look it up, go here:
> > > > > > > > > https://developer.nvidia.com/cuda-gpus), you should set
> > > > > > > > > cmake ../ -DGMX_CUDA_TARGET_SM="61"
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > Szilárd
> > > > > > > > >
> > > > > > > > > > Performing simulations on CPU only always works, yet of
> > cause
> > > > are
> > > > > > > more
> > > > > > > > slowly than they could be with additionally using the GPU.
> > > > > > > > > > The issue #2761 (https://redmine.gromacs.org/issues/2762
> )
> > > > seems
> > > > > > > > similar to our problem.
> > > > > > > > > > Even though this issue is still open, we wanted to ask if
> > you
> > > > can
> > > > > > > give
> > > > > > > > us any information about how to solve this problem?
> > > > > > > > > >
> > > > > > > > > > Many thanks in advance.
> > > > > > > > > > Best regards,
> > > > > > > > > > Stefanie Tafelmeier
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > Further details if necessary:
> > > > > > > > > > The workstation:
> > > > > > > > > > 2 x Xeon Gold 6152 @ 3,7Ghz (22 K, 44Th, AVX512)
> > > > > > > > > > Nvidia Quadro P6000 with 3840 Cuda-Cores
> > > > > > > > > >
> > > > > > > > > > The simulations system:
> > > > > > > > > > Long chain alkanes (previously used with gromacs 5.1.5
> and
> > > CUDA
> > > > > > 7.5 -
> > > > > > > > worked perfectly)
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > ZAE Bayern
> > > > > > > > > > Stefanie Tafelmeier
> > > > > > > > > > Bereich Energiespeicherung/Division Energy Storage
> > > > > > > > > > Thermische Energiespeicher/Thermal Energy Storage
> > > > > > > > > > Walther-Meißner-Str. 6
> > > > > > > > > > 85748 Garching
> > > > > > > > > >
> > > > > > > > > > Tel.: +49 89 329442-75
> > > > > > > > > > Fax: +49 89 329442-12
> > > > > > > > > > Stefanie.tafelmeier at zae-bayern.de<mailto:
> > > > > > > > Stefanie.tafelmeier at zae-bayern.de>
> > > > > > > > > > http://www.zae-bayern.de<http://www.zae-bayern.de/>
> > > > > > > > > >
> > > > > > > > > >
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> > > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > > > --
> > > > > > > > Gromacs Users mailing list
> > > > > > > >
> > > > > > > > * Please search the archive at
> > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > > before
> > > > > > > > posting!
> > > > > > > >
> > > > > > > > * Can't post? Read
> > http://www.gromacs.org/Support/Mailing_Lists
> > > > > > > >
> > > > > > > > * For (un)subscribe requests visit
> > > > > > > >
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > > > or
> > > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > > > --
> > > > > > > > Gromacs Users mailing list
> > > > > > > >
> > > > > > > > * Please search the archive at
> > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > > before
> > > > > > > > posting!
> > > > > > > >
> > > > > > > > * Can't post? Read
> > http://www.gromacs.org/Support/Mailing_Lists
> > > > > > > >
> > > > > > > > * For (un)subscribe requests visit
> > > > > > > >
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > > > or
> > > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > > --
> > > > > > > Gromacs Users mailing list
> > > > > > >
> > > > > > > * Please search the archive at
> > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > before
> > > > > > > posting!
> > > > > > >
> > > > > > > * Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
> > > > > > >
> > > > > > > * For (un)subscribe requests visit
> > > > > > >
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > > or
> > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > > --
> > > > > > > Gromacs Users mailing list
> > > > > > >
> > > > > > > * Please search the archive at
> > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > before
> > > > > > > posting!
> > > > > > >
> > > > > > > * Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
> > > > > > >
> > > > > > > * For (un)subscribe requests visit
> > > > > > >
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > > or
> > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at
> > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > > > > > posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or
> > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at
> > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > > > > > posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or
> > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.


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