Re: [gmx-users] GPU warnings

[Szilárd Páll]

On Tue, Dec 11, 2012 at 6:49 PM, Mirco Wahab <
mirco.wa...@chemie.tu-freiberg.de> wrote:

> Am 11.12.2012 16:04, schrieb Szilárd Páll:
>
>  It looks like some gcc 4.7-s don't work with CUDA, although I've been
>> using
>> various Ubuntu/Linaro versions, most recently 4.7.2 and had no
>> issues whatsoever. Some people seem to have bumped into the same problem
>> (see http://goo.gl/1onBz or http://goo.gl/JEnuk) and the suggested fix is
>> to put
>> #undef _GLIBCXX_ATOMIC_BUILTINS
>> #undef _GLIBCXX_USE_INT128
>> in a header and pre-include it for nvcc by calling it like this:
>> nvcc --pre-include undef_atomics_int128.h
>>
>
> The same problem occurs in SuSE 12.2/x64 with it's default 4.7.2
> (20120920).
>
> Another possible fix on SuSE 12.2: install the (older) gcc repository
> from 12.1/x64 (with lower priority), install the gcc/g++ 4.6 from there
> as an alternative compiler and select the "active gcc" through the
> "update-alternatives --config gcc" mechanism. This works very well.
>

Thanks for the info. The Ubuntu/Linaro version must have a fix for
this. Unfortunately, we can't do much about it and gcc 4.7 is anyway
blocked by the CUDA 5.0 headers.

FYI: Verlet scheme nonbonded kernels (and probably the group scheme as
well), especially with AVX, can be quite a bit slower with older gcc
versions.

I find it really annoying (and stupid) that NVIDIA did not fix their
compiler to work with gcc 4.7 which had already been out for almost a half
a year at the time of the CUDA 5.0 release.

--
Szilárd


>
> Regards
>
> M.
>
>
> --
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Re: [gmx-users] GPU warnings

[Mirco Wahab]

Am 11.12.2012 16:04, schrieb Szilárd Páll:

It looks like some gcc 4.7-s don't work with CUDA, although I've been using
various Ubuntu/Linaro versions, most recently 4.7.2 and had no
issues whatsoever. Some people seem to have bumped into the same problem
(see http://goo.gl/1onBz or http://goo.gl/JEnuk) and the suggested fix is
to put
#undef _GLIBCXX_ATOMIC_BUILTINS
#undef _GLIBCXX_USE_INT128
in a header and pre-include it for nvcc by calling it like this:
nvcc --pre-include undef_atomics_int128.h


The same problem occurs in SuSE 12.2/x64 with it's default 4.7.2
(20120920).

Another possible fix on SuSE 12.2: install the (older) gcc repository
from 12.1/x64 (with lower priority), install the gcc/g++ 4.6 from there
as an alternative compiler and select the "active gcc" through the
"update-alternatives --config gcc" mechanism. This works very well.

Regards

M.

--
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Re: [gmx-users] GPU warnings

[Szilárd Páll]

Hi Thomas,

It looks like some gcc 4.7-s don't work with CUDA, although I've been using
various Ubuntu/Linaro versions, most recently 4.7.2 and had no
issues whatsoever. Some people seem to have bumped into the same problem
(see http://goo.gl/1onBz or http://goo.gl/JEnuk) and the suggested fix is
to put
#undef _GLIBCXX_ATOMIC_BUILTINS
#undef _GLIBCXX_USE_INT128
in a header and pre-include it for nvcc by calling it like this:
nvcc --pre-include undef_atomics_int128.h

Cheers,

--
Szilárd



On Sun, Dec 9, 2012 at 12:18 PM, Thomas Evangelidis wrote:

> > > gcc 4.7.2 is not supported by any CUDA version.
> > >
> >
> > I suggest that you just fix it by editing the include/host_config.h and
> > changing the version check macro (line 82 AFAIK). I've never had real
> > problems with using new and officially not supported gcc-s, the version
> > check is more of a promise from NVIDIA that "we've tested thoroughly
> > internally and we more or less vouch for thins combination".
> >
> > Cheers,
> > --
> > Szilárd
> >
> > PS:
> > Disclamer: I don't take responsibility if your machine goes up in flames!
> > ;)
> >
> >
> Hi Szilárd,,
>
> I tried to compile gromacs-4.6beta1, is this the version you suggested? If
> not, please indicate how to download the source cause I am confused with
> all these development versions.
>
> Anyway, this is the error I get with 4.6beta1, gcc 4.7.2 and cuda 5:
>
> [  0%] Building NVCC (Device) object
>
> src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o
>
> /usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/ext/atomicity.h(48):
> error: identifier "__atomic_fetch_add" is undefined
>
>
> /usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/ext/atomicity.h(52):
> error: identifier "__atomic_fetch_add" is undefined
>
> 2 errors detected in the compilation of
> "/tmp/tmpxft_2394_-9_cudautils.compute_30.cpp1.ii".
> CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:252 (message):
>   Error generating file
>
>
> /home/thomas/Programs/gromacs-4.6-beta1_gnu_cuda5_build/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o
>
>
> gmake[3]: ***
>
> [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o]
> Error 1
> gmake[2]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
> Error 2
> gmake[1]: *** [src/programs/mdrun/CMakeFiles/mdrun.dir/rule] Error 2
> gmake: *** [mdrun] Error 2
>
>
> Unless I am missing something, cuda 5 does not support gcc 4.7.2.
>
>
>  Thomas
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] GPU warnings

[Thomas Evangelidis]

> > gcc 4.7.2 is not supported by any CUDA version.
> >
>
> I suggest that you just fix it by editing the include/host_config.h and
> changing the version check macro (line 82 AFAIK). I've never had real
> problems with using new and officially not supported gcc-s, the version
> check is more of a promise from NVIDIA that "we've tested thoroughly
> internally and we more or less vouch for thins combination".
>
> Cheers,
> --
> Szilárd
>
> PS:
> Disclamer: I don't take responsibility if your machine goes up in flames!
> ;)
>
>
Hi Szilárd,,

I tried to compile gromacs-4.6beta1, is this the version you suggested? If
not, please indicate how to download the source cause I am confused with
all these development versions.

Anyway, this is the error I get with 4.6beta1, gcc 4.7.2 and cuda 5:

[  0%] Building NVCC (Device) object
src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o
/usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/ext/atomicity.h(48):
error: identifier "__atomic_fetch_add" is undefined

/usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/ext/atomicity.h(52):
error: identifier "__atomic_fetch_add" is undefined

2 errors detected in the compilation of
"/tmp/tmpxft_2394_-9_cudautils.compute_30.cpp1.ii".
CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:252 (message):
  Error generating file

/home/thomas/Programs/gromacs-4.6-beta1_gnu_cuda5_build/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o


gmake[3]: ***
[src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o]
Error 1
gmake[2]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
Error 2
gmake[1]: *** [src/programs/mdrun/CMakeFiles/mdrun.dir/rule] Error 2
gmake: *** [mdrun] Error 2


Unless I am missing something, cuda 5 does not support gcc 4.7.2.


 Thomas
--
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Re: [gmx-users] GPU warnings

[Szilárd Páll]

On Sun, Nov 25, 2012 at 8:47 PM, Thomas Evangelidis wrote:

> Hi Szilárd,
>
> I was able to run code compiled with icc 13 on Fedora 17, but as I don't
> > have Intel Compiler v13 on this machine I can't check it now.
> >
> > Please check if it works for you with gcc 4.7.2 (which is the default)
> and
> > let me know if you succeed. The performance difference between icc and
> gcc
> > on your processor should be negligible with GPU runs and at most 5-10%
> with
> > CPU-only runs.
> >
> > As the issue is quite annoying, I'll try to have a look later, probably
> > after the beta is out.
> >
> >
> gcc 4.7.2 is not supported by any CUDA version.
>

I suggest that you just fix it by editing the include/host_config.h and
changing the version check macro (line 82 AFAIK). I've never had real
problems with using new and officially not supported gcc-s, the version
check is more of a promise from NVIDIA that "we've tested thoroughly
internally and we more or less vouch for thins combination".

Cheers,
--
Szilárd

PS:
Disclamer: I don't take responsibility if your machine goes up in flames! ;)


>
> Thomas
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>
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Re: [gmx-users] GPU warnings

[Thomas Evangelidis]

Hi Szilárd,

I was able to run code compiled with icc 13 on Fedora 17, but as I don't
> have Intel Compiler v13 on this machine I can't check it now.
>
> Please check if it works for you with gcc 4.7.2 (which is the default) and
> let me know if you succeed. The performance difference between icc and gcc
> on your processor should be negligible with GPU runs and at most 5-10% with
> CPU-only runs.
>
> As the issue is quite annoying, I'll try to have a look later, probably
> after the beta is out.
>
>
gcc 4.7.2 is not supported by any CUDA version.

Thomas
--
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Re: [gmx-users] GPU warnings

[Szilárd Páll]

On Mon, Nov 19, 2012 at 6:25 PM, Szilárd Páll wrote:

> On Mon, Nov 19, 2012 at 4:09 PM, Thomas Evangelidis wrote:
>
>> Hi Szilárd,
>>
>> I compiled with the Intel compilers, not gcc. In case I am missing
>> something, these are the versions I have:
>>
>
> Indeed, I see it now in the log file. Let me try with icc 13 and will get
> back to you.
>

I was able to run code compiled with icc 13 on Fedora 17, but as I don't
have Intel Compiler v13 on this machine I can't check it now.

Please check if it works for you with gcc 4.7.2 (which is the default) and
let me know if you succeed. The performance difference between icc and gcc
on your processor should be negligible with GPU runs and at most 5-10% with
CPU-only runs.

As the issue is quite annoying, I'll try to have a look later, probably
after the beta is out.

Cheers,
Sz.


>
>> glibc.i6862.15-57.fc17
>> @updates
>> glibc.x86_64  2.15-57.fc17
>> @updates
>> glibc-common.x86_64   2.15-57.fc17
>> @updates
>> glibc-devel.i686  2.15-57.fc17
>> @updates
>> glibc-devel.x86_642.15-57.fc17
>> @updates
>> glibc-headers.x86_64  2.15-57.fc17   @updates
>>
>> gcc.x86_644.7.2-2.fc17
>> @updates
>> gcc-c++.x86_644.7.2-2.fc17
>> @updates
>> gcc-gfortran.x86_64   4.7.2-2.fc17
>> @updates
>> libgcc.i686   4.7.2-2.fc17
>> @updates
>> libgcc.x86_64 4.7.2-2.fc17   @updates
>>
>>
>> Thomas
>>
>>
>>
>> On 19 November 2012 16:57, Szilárd Páll  wrote:
>>
>> > Thomas & Albert,
>> >
>> > We are unable to reproduce the issue on FC 17 with glibc 2.15-58 and gcc
>> > 4.7.2.
>> >
>> > Please try to update your packages (you should have updates available
>> for
>> > glibc), try recompiling with the latest 4.6 code and report back whether
>> > you succeed.
>> >
>> > Cheers,
>> >
>> > --
>> > Szilárd
>> >
>> >
>> > On Fri, Nov 16, 2012 at 4:31 PM, Szilárd Páll > > >wrote:
>> >
>> > > Hi Albert,
>> > >
>> > > Apologies for hijacking your thread. Do you happen to have Fedora 17
>> as
>> > > well?
>> > >
>> > > --
>> > > Szilárd
>> > >
>> > >
>> > >
>> > > On Sun, Nov 4, 2012 at 10:55 AM, Albert  wrote:
>> > >
>> > >> hello:
>> > >>
>> > >>  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti
>> (2 x
>> > >> 1344 CUDA cores), and I got the following warnings:
>> > >>
>> > >> thank you very much.
>> > >>
>> > >> ---**messages--**
>> > >> -
>> > >>
>> > >> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
>> > per
>> > >> node with 2 MPI processes.
>> > >>  This will cause considerable performance loss!
>> > >>
>> > >> 2 GPUs detected on host boreas:
>> > >>   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> > >> compatible
>> > >>   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> > >> compatible
>> > >>
>> > >> 2 GPUs auto-selected to be used for this run: #0, #1
>> > >>
>> > >> Using CUDA 8x8x8 non-bonded kernels
>> > >> Making 1D domain decomposition 1 x 2 x 1
>> > >>
>> > >> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
>> > >> We have just committed the new CPU detection code in this branch,
>> > >> and will commit new SSE/AVX kernels in a few days. However, this
>> > >> means that currently only the NxN kernels are accelerated!
>> > >> In the mean time, you might want to avoid production runs in 4.6.
>> > >>
>> > >> --
>> > >> gmx-users mailing listgmx-users@gromacs.org
>> > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> > >> * Please search the archive at http://www.gromacs.org/**
>> > >> Support/Mailing_Lists/Search<
>> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> > >> * Please don't post (un)subscribe requests to the list. Use the www
>> > >> interface or send it to gmx-users-requ...@gromacs.org.
>> > >> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>> > http://www.gromacs.org/Support/Mailing_Lists>
>> > >>
>> > >
>> > >
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > * Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>>
>>
>>
>> --
>>
>> ==
>>
>> Thomas Evangelidis
>>
>> PhD student
>> University of Athens
>> Faculty of Pharmacy
>> Department of Pharmaceutical Chemistry
>> Panepistimioupoli-Zografou
>> 157 71 Athens
>> GREECE
>>
>> email: tev...@pharm.uo

Re: [gmx-users] GPU warnings

[Szilárd Páll]

On Mon, Nov 19, 2012 at 4:09 PM, Thomas Evangelidis wrote:

> Hi Szilárd,
>
> I compiled with the Intel compilers, not gcc. In case I am missing
> something, these are the versions I have:
>

Indeed, I see it now in the log file. Let me try with icc 13 and will get
back to you.

>
> glibc.i6862.15-57.fc17
> @updates
> glibc.x86_64  2.15-57.fc17
> @updates
> glibc-common.x86_64   2.15-57.fc17
> @updates
> glibc-devel.i686  2.15-57.fc17
> @updates
> glibc-devel.x86_642.15-57.fc17
> @updates
> glibc-headers.x86_64  2.15-57.fc17   @updates
>
> gcc.x86_644.7.2-2.fc17
> @updates
> gcc-c++.x86_644.7.2-2.fc17
> @updates
> gcc-gfortran.x86_64   4.7.2-2.fc17
> @updates
> libgcc.i686   4.7.2-2.fc17
> @updates
> libgcc.x86_64 4.7.2-2.fc17   @updates
>
>
> Thomas
>
>
>
> On 19 November 2012 16:57, Szilárd Páll  wrote:
>
> > Thomas & Albert,
> >
> > We are unable to reproduce the issue on FC 17 with glibc 2.15-58 and gcc
> > 4.7.2.
> >
> > Please try to update your packages (you should have updates available for
> > glibc), try recompiling with the latest 4.6 code and report back whether
> > you succeed.
> >
> > Cheers,
> >
> > --
> > Szilárd
> >
> >
> > On Fri, Nov 16, 2012 at 4:31 PM, Szilárd Páll  > >wrote:
> >
> > > Hi Albert,
> > >
> > > Apologies for hijacking your thread. Do you happen to have Fedora 17 as
> > > well?
> > >
> > > --
> > > Szilárd
> > >
> > >
> > >
> > > On Sun, Nov 4, 2012 at 10:55 AM, Albert  wrote:
> > >
> > >> hello:
> > >>
> > >>  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2
> x
> > >> 1344 CUDA cores), and I got the following warnings:
> > >>
> > >> thank you very much.
> > >>
> > >> ---**messages--**
> > >> -
> > >>
> > >> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
> > per
> > >> node with 2 MPI processes.
> > >>  This will cause considerable performance loss!
> > >>
> > >> 2 GPUs detected on host boreas:
> > >>   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> > >> compatible
> > >>   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> > >> compatible
> > >>
> > >> 2 GPUs auto-selected to be used for this run: #0, #1
> > >>
> > >> Using CUDA 8x8x8 non-bonded kernels
> > >> Making 1D domain decomposition 1 x 2 x 1
> > >>
> > >> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
> > >> We have just committed the new CPU detection code in this branch,
> > >> and will commit new SSE/AVX kernels in a few days. However, this
> > >> means that currently only the NxN kernels are accelerated!
> > >> In the mean time, you might want to avoid production runs in 4.6.
> > >>
> > >> --
> > >> gmx-users mailing listgmx-users@gromacs.org
> > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > >> * Please search the archive at http://www.gromacs.org/**
> > >> Support/Mailing_Lists/Search<
> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > >> * Please don't post (un)subscribe requests to the list. Use the www
> > >> interface or send it to gmx-users-requ...@gromacs.org.
> > >> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> > http://www.gromacs.org/Support/Mailing_Lists>
> > >>
> > >
> > >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
>
> ==
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tev...@pharm.uoa.gr
>
>   teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] GPU warnings

[Thomas Evangelidis]

Hi Szilárd,

I compiled with the Intel compilers, not gcc. In case I am missing
something, these are the versions I have:

glibc.i6862.15-57.fc17
@updates
glibc.x86_64  2.15-57.fc17
@updates
glibc-common.x86_64   2.15-57.fc17
@updates
glibc-devel.i686  2.15-57.fc17
@updates
glibc-devel.x86_642.15-57.fc17
@updates
glibc-headers.x86_64  2.15-57.fc17   @updates

gcc.x86_644.7.2-2.fc17
@updates
gcc-c++.x86_644.7.2-2.fc17
@updates
gcc-gfortran.x86_64   4.7.2-2.fc17
@updates
libgcc.i686   4.7.2-2.fc17
@updates
libgcc.x86_64 4.7.2-2.fc17   @updates


Thomas



On 19 November 2012 16:57, Szilárd Páll  wrote:

> Thomas & Albert,
>
> We are unable to reproduce the issue on FC 17 with glibc 2.15-58 and gcc
> 4.7.2.
>
> Please try to update your packages (you should have updates available for
> glibc), try recompiling with the latest 4.6 code and report back whether
> you succeed.
>
> Cheers,
>
> --
> Szilárd
>
>
> On Fri, Nov 16, 2012 at 4:31 PM, Szilárd Páll  >wrote:
>
> > Hi Albert,
> >
> > Apologies for hijacking your thread. Do you happen to have Fedora 17 as
> > well?
> >
> > --
> > Szilárd
> >
> >
> >
> > On Sun, Nov 4, 2012 at 10:55 AM, Albert  wrote:
> >
> >> hello:
> >>
> >>  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 x
> >> 1344 CUDA cores), and I got the following warnings:
> >>
> >> thank you very much.
> >>
> >> ---**messages--**
> >> -
> >>
> >> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
> per
> >> node with 2 MPI processes.
> >>  This will cause considerable performance loss!
> >>
> >> 2 GPUs detected on host boreas:
> >>   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> >> compatible
> >>   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> >> compatible
> >>
> >> 2 GPUs auto-selected to be used for this run: #0, #1
> >>
> >> Using CUDA 8x8x8 non-bonded kernels
> >> Making 1D domain decomposition 1 x 2 x 1
> >>
> >> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
> >> We have just committed the new CPU detection code in this branch,
> >> and will commit new SSE/AVX kernels in a few days. However, this
> >> means that currently only the NxN kernels are accelerated!
> >> In the mean time, you might want to avoid production runs in 4.6.
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >> * Please search the archive at http://www.gromacs.org/**
> >> Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> >> * Please don't post (un)subscribe requests to the list. Use the www
> >> interface or send it to gmx-users-requ...@gromacs.org.
> >> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >>
> >
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 

==

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [gmx-users] GPU warnings

[Szilárd Páll]

Thomas & Albert,

We are unable to reproduce the issue on FC 17 with glibc 2.15-58 and gcc
4.7.2.

Please try to update your packages (you should have updates available for
glibc), try recompiling with the latest 4.6 code and report back whether
you succeed.

Cheers,

--
Szilárd


On Fri, Nov 16, 2012 at 4:31 PM, Szilárd Páll wrote:

> Hi Albert,
>
> Apologies for hijacking your thread. Do you happen to have Fedora 17 as
> well?
>
> --
> Szilárd
>
>
>
> On Sun, Nov 4, 2012 at 10:55 AM, Albert  wrote:
>
>> hello:
>>
>>  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 x
>> 1344 CUDA cores), and I got the following warnings:
>>
>> thank you very much.
>>
>> ---**messages--**
>> -
>>
>> WARNING: On node 0: oversubscribing the available 0 logical CPU cores per
>> node with 2 MPI processes.
>>  This will cause considerable performance loss!
>>
>> 2 GPUs detected on host boreas:
>>   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> compatible
>>   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> compatible
>>
>> 2 GPUs auto-selected to be used for this run: #0, #1
>>
>> Using CUDA 8x8x8 non-bonded kernels
>> Making 1D domain decomposition 1 x 2 x 1
>>
>> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
>> We have just committed the new CPU detection code in this branch,
>> and will commit new SSE/AVX kernels in a few days. However, this
>> means that currently only the NxN kernels are accelerated!
>> In the mean time, you might want to avoid production runs in 4.6.
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>
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Re: [gmx-users] GPU warnings

[Szilárd Páll]

Hi Albert,

Apologies for hijacking your thread. Do you happen to have Fedora 17 as
well?

--
Szilárd


On Sun, Nov 4, 2012 at 10:55 AM, Albert  wrote:

> hello:
>
>  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 x
> 1344 CUDA cores), and I got the following warnings:
>
> thank you very much.
>
> ---**messages--**-
>
> WARNING: On node 0: oversubscribing the available 0 logical CPU cores per
> node with 2 MPI processes.
>  This will cause considerable performance loss!
>
> 2 GPUs detected on host boreas:
>   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> compatible
>   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> compatible
>
> 2 GPUs auto-selected to be used for this run: #0, #1
>
> Using CUDA 8x8x8 non-bonded kernels
> Making 1D domain decomposition 1 x 2 x 1
>
> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
> We have just committed the new CPU detection code in this branch,
> and will commit new SSE/AVX kernels in a few days. However, this
> means that currently only the NxN kernels are accelerated!
> In the mean time, you might want to avoid production runs in 4.6.
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Re: [gmx-users] GPU warnings

[Szilárd Páll]

Hi Thomas,

The output you get means that you don't have any of the macros we try to
use although your man pages seem to be referring to them. Hence, I'm really
clueless why is this happening. Could you please file a bug report on
redmine.gromacs.org and add both the initial output as well as my patch and
the resulting output. Don't forget to specify version of software you were
using.

Thanks,
--
Szilárd

On Thu, Nov 15, 2012 at 3:53 PM, Thomas Evangelidis wrote:

> Hi Szilárd,
>
> This is the warning message I get this time:
>
> WARNING: Oversubscribing the available -66 logical CPU cores with 1
> thread-MPI threads.
>
>  This will cause considerable performance loss!
>
> I have also attached the md.log file.
>
> thanks,
> Thomas
>
>
>
> On 14 November 2012 19:48, Szilárd Páll  wrote:
>
>> Hi Thomas,
>>
>> Could you please try applying the attached patch (git apply
>> hardware_detect.patch in the 4.6 source root) and let me know what the
>> output is?
>>
>> This should show which sysconf macro is used and what its return value is
>> as well as indicate if none of the macros are in fact defined by your
>> headers.
>>
>> Thanks,
>>
>> --
>> Szilárd
>>
>>
>>
>> On Sat, Nov 10, 2012 at 5:24 PM, Thomas Evangelidis wrote:
>>
>>>
>>>
>>> On 10 November 2012 03:21, Szilárd Páll  wrote:
>>>
 Hi,

 You must have an odd sysconf version! Could you please check what is
 the sysconf system variable's name in the sysconf man page (man sysconf)
 where it says something like:

 _SC_NPROCESSORS_ONLN
  The number of processors currently online.

 The first line should be one of the
 following: _SC_NPROCESSORS_ONLN, _SC_NPROC_ONLN,
 _SC_NPROCESSORS_CONF, _SC_NPROC_CONF, but I guess yours is something
 different.

>>>
>>> The following text is taken from man sysconf:
>>>
>>>These values also exist, but may not be standard.
>>>
>>> - _SC_PHYS_PAGES
>>>   The number of pages of physical memory.  Note that it is
>>> possible for the product of this value and the value of _SC_PAGE_SIZE to
>>> overflow.
>>>
>>> - _SC_AVPHYS_PAGES
>>>   The number of currently available pages of physical memory.
>>>
>>> - _SC_NPROCESSORS_CONF
>>>   The number of processors configured.
>>>
>>> - _SC_NPROCESSORS_ONLN
>>>   The number of processors currently online (available).
>>>
>>>
>>>
>>>
 Can you also check what your glibc version is?

>>>
>>> $ yum list installed | grep glibc
>>> glibc.i6862.15-57.fc17
>>> @updates
>>> glibc.x86_64  2.15-57.fc17
>>> @updates
>>> glibc-common.x86_64   2.15-57.fc17
>>> @updates
>>> glibc-devel.i686  2.15-57.fc17
>>> @updates
>>> glibc-devel.x86_642.15-57.fc17
>>> @updates
>>> glibc-headers.x86_64  2.15-57.fc17
>>> @updates
>>>
>>>
>>>


 On Fri, Nov 9, 2012 at 5:51 PM, Thomas Evangelidis 
 wrote:

>
>
>
> > I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench
>> > benchmark with the following command line:
>> >
>> > mdrun_intel_cuda5 -v -s topol.tpr -testverlet
>> >
>> > "WARNING: Oversubscribing the available 0 logical CPU cores with 1
>> > thread-MPI threads."
>> >
>> > 0 logical CPU cores? Isn't this bizarre? My CPU is Intel Core
>> i7-3610QM
>> >
>>
>> That is bizzarre. Could you run with "-debug 1" and have a look at the
>> mdrun.debug output which should contain a message like:
>> "Detected N processors, will use this as the number of supported
>> hardware
>> threads."
>>
>> I'm wondering, is N=0 in your case!?
>>
>> It says "Detected 0 processors, will use this as the number of
> supported hardware threads."
>
>
>>
>> > (2.3 GHz). Unlike Albert, I don't see any performance loss, I get
>> 13.4
>> > ns/day on a single core with 1 GPU and 13.2 ns/day with GROMACS
>> v4.5.5 on 4
>> > cores (8 threads) without the GPU. Yet, I don't see any performance
>> gain
>> > with more that 4 -nt threads.
>> >
>> > mdrun_intel_cuda5 -v -nt 2 -s topol.tpr -testverlet : 15.4 ns/day
>> > mdrun_intel_cuda5 -v -nt 3 -s topol.tpr -testverlet : 16.0 ns/day
>> > mdrun_intel_cuda5 -v -nt 4 -s topol.tpr -testverlet : 16.3 ns/day
>> > mdrun_intel_cuda5 -v -nt 6 -s topol.tpr -testverlet : 16.2 ns/day
>> > mdrun_intel_cuda5 -v -nt 8 -s topol.tpr -testverlet : 15.4 ns/day
>> >
>>
>> I guess there is not much point in not using all cores, is it? Note
>> that
>> the performance drops after 4 threads because Hyper-Threading with
>> OpenMP
>> doesn't always help.
>>
>>
>> >
>> > I have also attached my log file (from "mdrun_intel_cuda5 -v -s
>> topol.tpr
>> > -testverlet") in case you find it helpf

Re: [gmx-users] GPU warnings

[Justin Lemkul]

On 11/15/12 9:53 AM, Thomas Evangelidis wrote:

Hi Szilárd,

This is the warning message I get this time:

WARNING: Oversubscribing the available -66 logical CPU cores with 1
thread-MPI threads.
  This will cause considerable performance loss!

I have also attached the md.log file.



Attachments are rejected by the mailing list.  They either have to be copied and 
pasted, linked, or sent to an individual specifically off-list.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] GPU warnings

[Szilárd Páll]

Hi Thomas,

Could you please try applying the attached patch (git apply
hardware_detect.patch in the 4.6 source root) and let me know what the
output is?

This should show which sysconf macro is used and what its return value is
as well as indicate if none of the macros are in fact defined by your
headers.

Thanks,

--
Szilárd


On Sat, Nov 10, 2012 at 5:24 PM, Thomas Evangelidis wrote:

>
>
> On 10 November 2012 03:21, Szilárd Páll  wrote:
>
>> Hi,
>>
>> You must have an odd sysconf version! Could you please check what is the
>> sysconf system variable's name in the sysconf man page (man sysconf) where
>> it says something like:
>>
>> _SC_NPROCESSORS_ONLN
>>  The number of processors currently online.
>>
>> The first line should be one of the
>> following: _SC_NPROCESSORS_ONLN, _SC_NPROC_ONLN,
>> _SC_NPROCESSORS_CONF, _SC_NPROC_CONF, but I guess yours is something
>> different.
>>
>
> The following text is taken from man sysconf:
>
>These values also exist, but may not be standard.
>
> - _SC_PHYS_PAGES
>   The number of pages of physical memory.  Note that it is
> possible for the product of this value and the value of _SC_PAGE_SIZE to
> overflow.
>
> - _SC_AVPHYS_PAGES
>   The number of currently available pages of physical memory.
>
> - _SC_NPROCESSORS_CONF
>   The number of processors configured.
>
> - _SC_NPROCESSORS_ONLN
>   The number of processors currently online (available).
>
>
>
>
>> Can you also check what your glibc version is?
>>
>
> $ yum list installed | grep glibc
> glibc.i6862.15-57.fc17
> @updates
> glibc.x86_64  2.15-57.fc17
> @updates
> glibc-common.x86_64   2.15-57.fc17
> @updates
> glibc-devel.i686  2.15-57.fc17
> @updates
> glibc-devel.x86_642.15-57.fc17
> @updates
> glibc-headers.x86_64  2.15-57.fc17   @updates
>
>
>
>>
>>
>> On Fri, Nov 9, 2012 at 5:51 PM, Thomas Evangelidis wrote:
>>
>>>
>>>
>>>
>>> > I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench
 > benchmark with the following command line:
 >
 > mdrun_intel_cuda5 -v -s topol.tpr -testverlet
 >
 > "WARNING: Oversubscribing the available 0 logical CPU cores with 1
 > thread-MPI threads."
 >
 > 0 logical CPU cores? Isn't this bizarre? My CPU is Intel Core
 i7-3610QM
 >

 That is bizzarre. Could you run with "-debug 1" and have a look at the
 mdrun.debug output which should contain a message like:
 "Detected N processors, will use this as the number of supported
 hardware
 threads."

 I'm wondering, is N=0 in your case!?

 It says "Detected 0 processors, will use this as the number of
>>> supported hardware threads."
>>>
>>>

 > (2.3 GHz). Unlike Albert, I don't see any performance loss, I get 13.4
 > ns/day on a single core with 1 GPU and 13.2 ns/day with GROMACS
 v4.5.5 on 4
 > cores (8 threads) without the GPU. Yet, I don't see any performance
 gain
 > with more that 4 -nt threads.
 >
 > mdrun_intel_cuda5 -v -nt 2 -s topol.tpr -testverlet : 15.4 ns/day
 > mdrun_intel_cuda5 -v -nt 3 -s topol.tpr -testverlet : 16.0 ns/day
 > mdrun_intel_cuda5 -v -nt 4 -s topol.tpr -testverlet : 16.3 ns/day
 > mdrun_intel_cuda5 -v -nt 6 -s topol.tpr -testverlet : 16.2 ns/day
 > mdrun_intel_cuda5 -v -nt 8 -s topol.tpr -testverlet : 15.4 ns/day
 >

 I guess there is not much point in not using all cores, is it? Note that
 the performance drops after 4 threads because Hyper-Threading with
 OpenMP
 doesn't always help.


 >
 > I have also attached my log file (from "mdrun_intel_cuda5 -v -s
 topol.tpr
 > -testverlet") in case you find it helpful.
 >

 I don't see it attached.



>>> I have attached both mdrun_intel_cuda5.debug and md.log files.  They
>>> will possibly be filtered by the mailing list but will be delivered to your
>>> email.
>>>
>>> thanksm
>>> Thomas
>>>
>>
>>
>
>
> --
>
> ==
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tev...@pharm.uoa.gr
>
>   teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
>
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Re: [gmx-users] GPU warnings

[Thomas Evangelidis]

On 10 November 2012 03:21, Szilárd Páll  wrote:

> Hi,
>
> You must have an odd sysconf version! Could you please check what is the
> sysconf system variable's name in the sysconf man page (man sysconf) where
> it says something like:
>
> _SC_NPROCESSORS_ONLN
>  The number of processors currently online.
>
> The first line should be one of the
> following: _SC_NPROCESSORS_ONLN, _SC_NPROC_ONLN,
> _SC_NPROCESSORS_CONF, _SC_NPROC_CONF, but I guess yours is something
> different.
>

The following text is taken from man sysconf:

   These values also exist, but may not be standard.

- _SC_PHYS_PAGES
  The number of pages of physical memory.  Note that it is
possible for the product of this value and the value of _SC_PAGE_SIZE to
overflow.

- _SC_AVPHYS_PAGES
  The number of currently available pages of physical memory.

- _SC_NPROCESSORS_CONF
  The number of processors configured.

- _SC_NPROCESSORS_ONLN
  The number of processors currently online (available).




> Can you also check what your glibc version is?
>

$ yum list installed | grep glibc
glibc.i6862.15-57.fc17
@updates
glibc.x86_64  2.15-57.fc17
@updates
glibc-common.x86_64   2.15-57.fc17
@updates
glibc-devel.i686  2.15-57.fc17
@updates
glibc-devel.x86_642.15-57.fc17
@updates
glibc-headers.x86_64  2.15-57.fc17   @updates



>
>
> On Fri, Nov 9, 2012 at 5:51 PM, Thomas Evangelidis wrote:
>
>>
>>
>>
>> > I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench
>>> > benchmark with the following command line:
>>> >
>>> > mdrun_intel_cuda5 -v -s topol.tpr -testverlet
>>> >
>>> > "WARNING: Oversubscribing the available 0 logical CPU cores with 1
>>> > thread-MPI threads."
>>> >
>>> > 0 logical CPU cores? Isn't this bizarre? My CPU is Intel Core i7-3610QM
>>> >
>>>
>>> That is bizzarre. Could you run with "-debug 1" and have a look at the
>>> mdrun.debug output which should contain a message like:
>>> "Detected N processors, will use this as the number of supported hardware
>>> threads."
>>>
>>> I'm wondering, is N=0 in your case!?
>>>
>>> It says "Detected 0 processors, will use this as the number of supported
>> hardware threads."
>>
>>
>>>
>>> > (2.3 GHz). Unlike Albert, I don't see any performance loss, I get 13.4
>>> > ns/day on a single core with 1 GPU and 13.2 ns/day with GROMACS v4.5.5
>>> on 4
>>> > cores (8 threads) without the GPU. Yet, I don't see any performance
>>> gain
>>> > with more that 4 -nt threads.
>>> >
>>> > mdrun_intel_cuda5 -v -nt 2 -s topol.tpr -testverlet : 15.4 ns/day
>>> > mdrun_intel_cuda5 -v -nt 3 -s topol.tpr -testverlet : 16.0 ns/day
>>> > mdrun_intel_cuda5 -v -nt 4 -s topol.tpr -testverlet : 16.3 ns/day
>>> > mdrun_intel_cuda5 -v -nt 6 -s topol.tpr -testverlet : 16.2 ns/day
>>> > mdrun_intel_cuda5 -v -nt 8 -s topol.tpr -testverlet : 15.4 ns/day
>>> >
>>>
>>> I guess there is not much point in not using all cores, is it? Note that
>>> the performance drops after 4 threads because Hyper-Threading with OpenMP
>>> doesn't always help.
>>>
>>>
>>> >
>>> > I have also attached my log file (from "mdrun_intel_cuda5 -v -s
>>> topol.tpr
>>> > -testverlet") in case you find it helpful.
>>> >
>>>
>>> I don't see it attached.
>>>
>>>
>>>
>> I have attached both mdrun_intel_cuda5.debug and md.log files.  They will
>> possibly be filtered by the mailing list but will be delivered to your
>> email.
>>
>> thanksm
>> Thomas
>>
>
>


-- 

==

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [gmx-users] GPU warnings

[Szilárd Páll]

Hi,

You must have an odd sysconf version! Could you please check what is the
sysconf system variable's name in the sysconf man page (man sysconf) where
it says something like:

_SC_NPROCESSORS_ONLN
 The number of processors currently online.

The first line should be one of the
following: _SC_NPROCESSORS_ONLN, _SC_NPROC_ONLN,
_SC_NPROCESSORS_CONF, _SC_NPROC_CONF, but I guess yours is something
different.

Can you also check what your glibc version is?

Thanks,

--
Szilárd


On Fri, Nov 9, 2012 at 5:51 PM, Thomas Evangelidis wrote:

>
>
>
> > I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench
>> > benchmark with the following command line:
>> >
>> > mdrun_intel_cuda5 -v -s topol.tpr -testverlet
>> >
>> > "WARNING: Oversubscribing the available 0 logical CPU cores with 1
>> > thread-MPI threads."
>> >
>> > 0 logical CPU cores? Isn't this bizarre? My CPU is Intel Core i7-3610QM
>> >
>>
>> That is bizzarre. Could you run with "-debug 1" and have a look at the
>> mdrun.debug output which should contain a message like:
>> "Detected N processors, will use this as the number of supported hardware
>> threads."
>>
>> I'm wondering, is N=0 in your case!?
>>
>> It says "Detected 0 processors, will use this as the number of supported
> hardware threads."
>
>
>>
>> > (2.3 GHz). Unlike Albert, I don't see any performance loss, I get 13.4
>> > ns/day on a single core with 1 GPU and 13.2 ns/day with GROMACS v4.5.5
>> on 4
>> > cores (8 threads) without the GPU. Yet, I don't see any performance gain
>> > with more that 4 -nt threads.
>> >
>> > mdrun_intel_cuda5 -v -nt 2 -s topol.tpr -testverlet : 15.4 ns/day
>> > mdrun_intel_cuda5 -v -nt 3 -s topol.tpr -testverlet : 16.0 ns/day
>> > mdrun_intel_cuda5 -v -nt 4 -s topol.tpr -testverlet : 16.3 ns/day
>> > mdrun_intel_cuda5 -v -nt 6 -s topol.tpr -testverlet : 16.2 ns/day
>> > mdrun_intel_cuda5 -v -nt 8 -s topol.tpr -testverlet : 15.4 ns/day
>> >
>>
>> I guess there is not much point in not using all cores, is it? Note that
>> the performance drops after 4 threads because Hyper-Threading with OpenMP
>> doesn't always help.
>>
>>
>> >
>> > I have also attached my log file (from "mdrun_intel_cuda5 -v -s
>> topol.tpr
>> > -testverlet") in case you find it helpful.
>> >
>>
>> I don't see it attached.
>>
>>
>>
> I have attached both mdrun_intel_cuda5.debug and md.log files.  They will
> possibly be filtered by the mailing list but will be delivered to your
> email.
>
> thanksm
> Thomas
>
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Re: [gmx-users] GPU warnings

[Szilárd Páll]

Hi,

On Tue, Nov 6, 2012 at 12:03 AM, Thomas Evangelidis wrote:

> Hi,
>
> I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench
> benchmark with the following command line:
>
> mdrun_intel_cuda5 -v -s topol.tpr -testverlet
>
> "WARNING: Oversubscribing the available 0 logical CPU cores with 1
> thread-MPI threads."
>
> 0 logical CPU cores? Isn't this bizarre? My CPU is Intel Core i7-3610QM
>

That is bizzarre. Could you run with "-debug 1" and have a look at the
mdrun.debug output which should contain a message like:
"Detected N processors, will use this as the number of supported hardware
threads."

I'm wondering, is N=0 in your case!?


> (2.3 GHz). Unlike Albert, I don't see any performance loss, I get 13.4
> ns/day on a single core with 1 GPU and 13.2 ns/day with GROMACS v4.5.5 on 4
> cores (8 threads) without the GPU. Yet, I don't see any performance gain
> with more that 4 -nt threads.
>
> mdrun_intel_cuda5 -v -nt 2 -s topol.tpr -testverlet : 15.4 ns/day
> mdrun_intel_cuda5 -v -nt 3 -s topol.tpr -testverlet : 16.0 ns/day
> mdrun_intel_cuda5 -v -nt 4 -s topol.tpr -testverlet : 16.3 ns/day
> mdrun_intel_cuda5 -v -nt 6 -s topol.tpr -testverlet : 16.2 ns/day
> mdrun_intel_cuda5 -v -nt 8 -s topol.tpr -testverlet : 15.4 ns/day
>

I guess there is not much point in not using all cores, is it? Note that
the performance drops after 4 threads because Hyper-Threading with OpenMP
doesn't always help.


>
> I have also attached my log file (from "mdrun_intel_cuda5 -v -s topol.tpr
> -testverlet") in case you find it helpful.
>

I don't see it attached.

--
Szilárd


>
> Thanks,
> Thomas
>
>
>
> On 5 November 2012 18:54, Szilárd Páll  wrote:
>
> > The first warning indicates that you are starting more threads than the
> > hardware supports which would explain the poor performance.
> >
> > Could share a log file of the suspiciously slow run as well as the
> command
> > line you used to start mdrun?
> >
> > Cheers,
> >
> > --
> > Szilárd
> >
> >
> > On Sun, Nov 4, 2012 at 5:32 PM, Albert  wrote:
> >
> > > well, IC.
> > > the performance is rather poor than GTX590. 32ns/day vs 4 ns/day
> > > probably that's also something related to the warnings?
> > >
> > > THX
> > >
> > >
> > >
> > > On 11/04/2012 01:59 PM, Justin Lemkul wrote:
> > >
> > >>
> > >>
> > >> On 11/4/12 4:55 AM, Albert wrote:
> > >>
> > >>> hello:
> > >>>
> > >>>   I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti
> (2
> > x
> > >>> 1344
> > >>> CUDA cores), and I got the following warnings:
> > >>>
> > >>> thank you very much.
> > >>>
> > >>> ---**messages--**
> > >>> -
> > >>>
> > >>> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
> > >>> per node
> > >>> with 2 MPI processes.
> > >>>   This will cause considerable performance loss!
> > >>>
> > >>> 2 GPUs detected on host boreas:
> > >>>#0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> > >>> compatible
> > >>>#1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> > >>> compatible
> > >>>
> > >>> 2 GPUs auto-selected to be used for this run: #0, #1
> > >>>
> > >>> Using CUDA 8x8x8 non-bonded kernels
> > >>> Making 1D domain decomposition 1 x 2 x 1
> > >>>
> > >>> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
> > >>> We have just committed the new CPU detection code in this branch,
> > >>> and will commit new SSE/AVX kernels in a few days. However, this
> > >>> means that currently only the NxN kernels are accelerated!
> > >>> In the mean time, you might want to avoid production runs in 4.6.
> > >>>
> > >>>
> > >> I can't address the first warning, but the second is fairly obvious.
> > >>  You're not using an official release, you're using the development
> > version
> > >> - let the user beware.  The code is not yet production-ready.
> > >>
> > >> -Justin
> > >>
> > >>
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > > * Please search the archive at http://www.gromacs.org/**
> > > Support/Mailing_Lists/Search<
> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the www
> > > interface or send it to gmx-users-requ...@gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> > http://www.gromacs.org/Support/Mailing_Lists>
> > >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
>
> 

Re: [gmx-users] GPU warnings

[Thomas Evangelidis]

Hi,

I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench
benchmark with the following command line:

mdrun_intel_cuda5 -v -s topol.tpr -testverlet

"WARNING: Oversubscribing the available 0 logical CPU cores with 1
thread-MPI threads."

0 logical CPU cores? Isn't this bizarre? My CPU is Intel Core i7-3610QM
(2.3 GHz). Unlike Albert, I don't see any performance loss, I get 13.4
ns/day on a single core with 1 GPU and 13.2 ns/day with GROMACS v4.5.5 on 4
cores (8 threads) without the GPU. Yet, I don't see any performance gain
with more that 4 -nt threads.

mdrun_intel_cuda5 -v -nt 2 -s topol.tpr -testverlet : 15.4 ns/day
mdrun_intel_cuda5 -v -nt 3 -s topol.tpr -testverlet : 16.0 ns/day
mdrun_intel_cuda5 -v -nt 4 -s topol.tpr -testverlet : 16.3 ns/day
mdrun_intel_cuda5 -v -nt 6 -s topol.tpr -testverlet : 16.2 ns/day
mdrun_intel_cuda5 -v -nt 8 -s topol.tpr -testverlet : 15.4 ns/day

I have also attached my log file (from "mdrun_intel_cuda5 -v -s topol.tpr
-testverlet") in case you find it helpful.

Thanks,
Thomas



On 5 November 2012 18:54, Szilárd Páll  wrote:

> The first warning indicates that you are starting more threads than the
> hardware supports which would explain the poor performance.
>
> Could share a log file of the suspiciously slow run as well as the command
> line you used to start mdrun?
>
> Cheers,
>
> --
> Szilárd
>
>
> On Sun, Nov 4, 2012 at 5:32 PM, Albert  wrote:
>
> > well, IC.
> > the performance is rather poor than GTX590. 32ns/day vs 4 ns/day
> > probably that's also something related to the warnings?
> >
> > THX
> >
> >
> >
> > On 11/04/2012 01:59 PM, Justin Lemkul wrote:
> >
> >>
> >>
> >> On 11/4/12 4:55 AM, Albert wrote:
> >>
> >>> hello:
> >>>
> >>>   I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2
> x
> >>> 1344
> >>> CUDA cores), and I got the following warnings:
> >>>
> >>> thank you very much.
> >>>
> >>> ---**messages--**
> >>> -
> >>>
> >>> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
> >>> per node
> >>> with 2 MPI processes.
> >>>   This will cause considerable performance loss!
> >>>
> >>> 2 GPUs detected on host boreas:
> >>>#0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> >>> compatible
> >>>#1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> >>> compatible
> >>>
> >>> 2 GPUs auto-selected to be used for this run: #0, #1
> >>>
> >>> Using CUDA 8x8x8 non-bonded kernels
> >>> Making 1D domain decomposition 1 x 2 x 1
> >>>
> >>> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
> >>> We have just committed the new CPU detection code in this branch,
> >>> and will commit new SSE/AVX kernels in a few days. However, this
> >>> means that currently only the NxN kernels are accelerated!
> >>> In the mean time, you might want to avoid production runs in 4.6.
> >>>
> >>>
> >> I can't address the first warning, but the second is fairly obvious.
> >>  You're not using an official release, you're using the development
> version
> >> - let the user beware.  The code is not yet production-ready.
> >>
> >> -Justin
> >>
> >>
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 

==

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
-- 
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Re: [gmx-users] GPU warnings

[Szilárd Páll]

The first warning indicates that you are starting more threads than the
hardware supports which would explain the poor performance.

Could share a log file of the suspiciously slow run as well as the command
line you used to start mdrun?

Cheers,

--
Szilárd


On Sun, Nov 4, 2012 at 5:32 PM, Albert  wrote:

> well, IC.
> the performance is rather poor than GTX590. 32ns/day vs 4 ns/day
> probably that's also something related to the warnings?
>
> THX
>
>
>
> On 11/04/2012 01:59 PM, Justin Lemkul wrote:
>
>>
>>
>> On 11/4/12 4:55 AM, Albert wrote:
>>
>>> hello:
>>>
>>>   I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 x
>>> 1344
>>> CUDA cores), and I got the following warnings:
>>>
>>> thank you very much.
>>>
>>> ---**messages--**
>>> -
>>>
>>> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
>>> per node
>>> with 2 MPI processes.
>>>   This will cause considerable performance loss!
>>>
>>> 2 GPUs detected on host boreas:
>>>#0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>>> compatible
>>>#1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>>> compatible
>>>
>>> 2 GPUs auto-selected to be used for this run: #0, #1
>>>
>>> Using CUDA 8x8x8 non-bonded kernels
>>> Making 1D domain decomposition 1 x 2 x 1
>>>
>>> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
>>> We have just committed the new CPU detection code in this branch,
>>> and will commit new SSE/AVX kernels in a few days. However, this
>>> means that currently only the NxN kernels are accelerated!
>>> In the mean time, you might want to avoid production runs in 4.6.
>>>
>>>
>> I can't address the first warning, but the second is fairly obvious.
>>  You're not using an official release, you're using the development version
>> - let the user beware.  The code is not yet production-ready.
>>
>> -Justin
>>
>>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Re: [gmx-users] GPU warnings

[Albert]

well, IC.
the performance is rather poor than GTX590. 32ns/day vs 4 ns/day
probably that's also something related to the warnings?

THX


On 11/04/2012 01:59 PM, Justin Lemkul wrote:



On 11/4/12 4:55 AM, Albert wrote:

hello:

  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti 
(2 x 1344

CUDA cores), and I got the following warnings:

thank you very much.

---messages---

WARNING: On node 0: oversubscribing the available 0 logical CPU cores 
per node

with 2 MPI processes.
  This will cause considerable performance loss!

2 GPUs detected on host boreas:
   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat: 
compatible
   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat: 
compatible


2 GPUs auto-selected to be used for this run: #0, #1

Using CUDA 8x8x8 non-bonded kernels
Making 1D domain decomposition 1 x 2 x 1

* WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
We have just committed the new CPU detection code in this branch,
and will commit new SSE/AVX kernels in a few days. However, this
means that currently only the NxN kernels are accelerated!
In the mean time, you might want to avoid production runs in 4.6.



I can't address the first warning, but the second is fairly obvious.  
You're not using an official release, you're using the development 
version - let the user beware.  The code is not yet production-ready.


-Justin



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Re: [gmx-users] GPU warnings

[Thomas Evangelidis]

I 'm also get the first warning ("oversubscribing the available...") and
see no obvious performance gain. Do you know how to avoid that?

thanks,
Thomas



On 4 November 2012 14:59, Justin Lemkul  wrote:

>
>
> On 11/4/12 4:55 AM, Albert wrote:
>
>> hello:
>>
>>   I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 x
>> 1344
>> CUDA cores), and I got the following warnings:
>>
>> thank you very much.
>>
>> ---**messages--**
>> -
>>
>> WARNING: On node 0: oversubscribing the available 0 logical CPU cores per
>> node
>> with 2 MPI processes.
>>   This will cause considerable performance loss!
>>
>> 2 GPUs detected on host boreas:
>>#0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> compatible
>>#1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> compatible
>>
>> 2 GPUs auto-selected to be used for this run: #0, #1
>>
>> Using CUDA 8x8x8 non-bonded kernels
>> Making 1D domain decomposition 1 x 2 x 1
>>
>> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
>> We have just committed the new CPU detection code in this branch,
>> and will commit new SSE/AVX kernels in a few days. However, this
>> means that currently only the NxN kernels are accelerated!
>> In the mean time, you might want to avoid production runs in 4.6.
>>
>>
> I can't address the first warning, but the second is fairly obvious.
>  You're not using an official release, you're using the development version
> - let the user beware.  The code is not yet production-ready.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 

==

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
-- 
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Re: [gmx-users] GPU warnings

[Justin Lemkul]

On 11/4/12 4:55 AM, Albert wrote:

hello:

  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 x 1344
CUDA cores), and I got the following warnings:

thank you very much.

---messages---

WARNING: On node 0: oversubscribing the available 0 logical CPU cores per node
with 2 MPI processes.
  This will cause considerable performance loss!

2 GPUs detected on host boreas:
   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat: compatible
   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat: compatible

2 GPUs auto-selected to be used for this run: #0, #1

Using CUDA 8x8x8 non-bonded kernels
Making 1D domain decomposition 1 x 2 x 1

* WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
We have just committed the new CPU detection code in this branch,
and will commit new SSE/AVX kernels in a few days. However, this
means that currently only the NxN kernels are accelerated!
In the mean time, you might want to avoid production runs in 4.6.



I can't address the first warning, but the second is fairly obvious.  You're not 
using an official release, you're using the development version - let the user 
beware.  The code is not yet production-ready.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] GPU warnings

[Albert]

hello:

 I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 x 
1344 CUDA cores), and I got the following warnings:


thank you very much.

---messages---

WARNING: On node 0: oversubscribing the available 0 logical CPU cores 
per node with 2 MPI processes.

 This will cause considerable performance loss!

2 GPUs detected on host boreas:
  #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat: 
compatible
  #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat: 
compatible


2 GPUs auto-selected to be used for this run: #0, #1

Using CUDA 8x8x8 non-bonded kernels
Making 1D domain decomposition 1 x 2 x 1

* WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
We have just committed the new CPU detection code in this branch,
and will commit new SSE/AVX kernels in a few days. However, this
means that currently only the NxN kernels are accelerated!
In the mean time, you might want to avoid production runs in 4.6.

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