Ruxi,
Sorry, but our cluster is having some issues right now so I can't actually
do anything at the moment from the command line. And class is starting in
a few minutes, so I probably won't be able to actually look around for
quite awhlie.
I was able to find the file you are talking about. Are you suggesting that
I comment out just the #error line? I'm afraid I have not used this kind
of #if compiler directive -- can I just remove that line -- or does that
screw up the logic of the if above and/or below as well. Should I change
the if statement that goes along with it instead?
Thanks,
Brent
On Fri, Apr 7, 2017 at 1:33 PM, Ruxi Qi <ruxiq.uci.edu> wrote:
> Hi Brent,
>
> Sorry for my jumping to the conclusion. I just realized it's impossible
> to fully remove <cuda_runtime.h>. As we used other libraries cublas and
> cusparse which also include that header file. I am afraid this option
> doesn't work, and we have to go back tweaking the configure to fix this
> issue.
>
> Right now If you want, you can comment out the #error line in you
> cuda/include/host_config.h to see whether it gets fixed. Thanks!
>
> Best,
>
> Ruxi
>
> On 04/07/2017 05:32 AM, Brent Krueger wrote:
> > Thank you Ruxi for identifying the source of this issue.
> >
> > I've commented out the cuda_rutime.h line from the file
> cuda_cg_wrapper.cu
> > in AmberTools/src/pbsa, did a make clean, reran configure -cuda intel and
> > that build also seemed to fail in the same spot. I've done a make
> > uninstall and am now building again.
> >
> > I'm afraid I've got to run to a meeting now and I've got meetings/class
> > pretty much all day so I'm not sure when I'll be able to get to testing,
> > but I should at least be able to verify whether this build worked for me
> or
> > not in a couple hours...
> >
> >
> > Cheers,
> > Brent
> >
> >
> > On Fri, Apr 7, 2017 at 2:42 AM, Ruxi Qi <ruxiq.uci.edu> wrote:
> >
> >> Just found a similar story with GCC in pmemd.cuda of Amber12. See
> >> http://archive.ambermd.org/201307/0456.html
> >>
> >> Best,
> >>
> >> Ruxi
> >>
> >> On 04/06/2017 11:38 PM, Ruxi Qi wrote:
> >>> Hi All,
> >>>
> >>> I found the real cause. It is the <cuda_runtime.h> included in our
> >>> cuda wrapper code (not cusp) that triggered the ICC version checking
> >>> in host_config.h. In contrast, pmemd.cuda doesn't use this header,
> >>> thus won't trigger the runtime compiler checking. A quick "fix" is
> >>> just removing the <cuda_runtime.h> inclusion in our code as long as we
> >>> use nvcc to compile.
> >>>
> >>> Two concerns:
> >>>
> >>> 1) As shown by those OS/Compiler/CUDA compatibility matrices from
> >>> Nvidia, allowing the use of the compiler not officially supported
> >>> (tested) by CUDA is of risk. I don't know to what extent this effect
> >>> will be, maybe not a big deal?
> >>>
> >>> 2) For now, we can fix this compiler error either through a) Add a
> >>> logic checking on the icc version to configure as suggested
> >>> previously, or b) I remove the <cuda_rutime.h> inclusion in our code -
> >>> this will need another round combination tests. Also just mention
> >>> again, user manually commenting out the #error line in host_config.h
> >>> will also be a workaround (not recommended?).
> >>>
> >>> Thanks!
> >>>
> >>> Ruxi
> >>>
> >>>
> >>>
> >>> On 04/06/2017 07:55 PM, Daniel Roe wrote:
> >>>> Hi,
> >>>>
> >>>> On Thu, Apr 6, 2017 at 6:59 PM, Ruxi Qi <ruxiq.uci.edu> wrote:
> >>>>> 1. I once encountered the same error. Indeed, this error is not
> because
> >>>>> of linking CUSP library. It's nvcc that complains the outdated ICC
> >>>>> version. Per the Nvidia official documents, CUDA 7.5 only supports
> ICC
> >>>>> 15.0.0, as shown bellow:
> >>>> This is not really the case, at least for Intel compilers version 14.
> >>>> I was just able to compile pmemd.cuda from Amber 16 and
> >>>> cpptraj/pmemd.cuda from amber17-with-patches with Intel V 14 compilers
> >>>> and CUDA 7.5. I think this issue is really CUSP-related since as Brent
> >>>> stated he was previously able to compile pmemd.cuda from Amber 16 with
> >>>> Intel V12 compilers and CUDA 7.5.
> >>>>
> >>>>> 3. Adding a --no-pbsa.cuda option is good for safety's sake in this
> >>>>> release. I agree with Hai that we may put it built as default, since
> it
> >>>>> generally follows the Nvidia CUDA installation rule.
> >>>> Probably the best solution would be to add logic to 'configure' that
> >>>> will disable pbsa.cuda if the Intel compiler version is not high
> >>>> enough. May need to do the same thing for GNU compilers if there is a
> >>>> similar issue.
> >>>>
> >>>> -Dan
> >>>>
> >>
> >> _______________________________________________
> >> AMBER-Developers mailing list
> >> AMBER-Developers.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
> >
> >
>
>
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>
--
_______________________________________________
Brent P. Krueger.....................phone: 616 395 7629
Professor.................................fax: 616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI 49423
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Received on Fri Apr 07 2017 - 11:00:02 PDT
