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

Szilárd Páll pall.szilard at gmail.com
Fri Mar 15 17:57:23 CET 2019 

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
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> > > Stefanie.tafelmeier at zae-bayern.de>
> > > > > http://www.zae-bayern.de<http://www.zae-bayern.de/>
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