Re: [AMBER-Developers] problems in buildling pbsa.cuda

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Sat, 08 Apr 2017 01:43:23 +0000

Hi,

cpptraj.cuda should build. If you are compiling from a recent amber17 tree
you can try 'make build_cpptraj' from AMBERHOME/AmberTools/src to check.

-Dan

On Fri, Apr 7, 2017 at 9:18 PM Brent Krueger <kruegerb.hope.edu> wrote:

> Ruxi and I have been trying a few ways to try to work around my old Intel
> 12.0 compiler and I'm afraid that we are unable to get anything simple to
> work (Ruxi -- latest error messages below). I think that for things to
> work on my system I'm going to need some kind of no-cuda-AT option.
> Preferably this would skip all of the cuda-related things that are in
> AmberTools but still build pmemd.cuda in amber16 the same way it did
> previously.
>
> This may mean that we can no longer support older compilers with cuda?
> Something we can worry about more with amber18.
>
>
> Thanks,
> Brent
>
>
>
> /usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -gencode arch=compute_50,code=sm_50 -gencode
> arch=compute_52,code=sm_52 -gencode arch=compute_53,code=sm_53
> -use_fast_math -O3 -ccbin icpc -I../cusplibrary-0.6.0-rc -o
> cuda_cg_wrapper.o -c cuda_cg_wrapper.cu -DCUSP -DPCG -DJacobi -DDIA
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(235): error:
> allowing all exceptions is incompatible with previous function "__isinff"
> /usr/local/cuda/bin/..//include/math_functions.h(7279): here
>
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(236): error:
> allowing all exceptions is incompatible with previous function "__isinf"
> /usr/local/cuda/bin/..//include/math_functions.h(7294): here
>
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(238): error:
> allowing all exceptions is incompatible with previous function "__isinfl"
> /usr/local/cuda/bin/..//include/math_functions.h(7632): here
>
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(245): error:
> allowing all exceptions is incompatible with previous function "__isnanf"
> /usr/local/cuda/bin/..//include/math_functions.h(7280): here
>
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(246): error:
> allowing all exceptions is incompatible with previous function "__isnan"
> /usr/local/cuda/bin/..//include/math_functions.h(7293): here
>
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(248): error:
> allowing all exceptions is incompatible with previous function "__isnanl"
> /usr/local/cuda/bin/..//include/math_functions.h(7633): here
>
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(275): error:
> allowing all exceptions is incompatible with previous function "__finitef"
> /usr/local/cuda/bin/..//include/math_functions.h(7291): here
>
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(276): error:
> allowing all exceptions is incompatible with previous function "__finite"
> /usr/local/cuda/bin/..//include/math_functions.h(7290): here
>
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(278): error:
> allowing all exceptions is incompatible with previous function "__finitel"
> /usr/local/cuda/bin/..//include/math_functions.h(7631): here
>
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(285): error:
> allowing all exceptions is incompatible with previous function "__signbitf"
> /usr/local/cuda/bin/..//include/math_functions.h(7297): here
>
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(286): error:
> allowing all exceptions is incompatible with previous function "__signbit"
> /usr/local/cuda/bin/..//include/math_functions.h(7292): here
>
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(288): error:
> allowing all exceptions is incompatible with previous function "__signbitl"
> /usr/local/cuda/bin/..//include/math_functions.h(7625): here
>
> /usr/local/cuda/bin/..//include/math_functions.h(8862): warning: exception
> specification is incompatible with that of previous function
> "signbit(double)"
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(281): here
>
> /usr/local/cuda/bin/..//include/math_functions.h(8870): warning: exception
> specification is incompatible with that of previous function
> "isfinite(double)"
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(261): here
>
> /usr/local/cuda/bin/..//include/math_functions.h(8880): warning: exception
> specification is incompatible with that of previous function
> "isnan(double)"
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(241): here
>
> /usr/local/cuda/bin/..//include/math_functions.h(8888): warning: exception
> specification is incompatible with that of previous function
> "isinf(double)"
> /opt/intel/composerxe-2011.0.084/compiler/include/math.h(231): here
>
> 12 errors detected in the compilation of
> "/tmp/tmpxft_00002718_00000000-19_cuda_cg_wrapper.compute_53.cpp1.ii".
> make[2]: *** [cuda_cg_wrapper.o] Error 2
> make[2]: Leaving directory
> `/extra/krieg/source/amber16_AT17_rc2/AmberTools/src/pbsa'
> make[1]: *** [cuda_serial] Error 2
> make[1]: Leaving directory
> `/extra/krieg/source/amber16_AT17_rc2/AmberTools/src'
> make: *** [install] Error 2
>
>
>
> On Fri, Apr 7, 2017 at 3:03 PM, Ruxi Qi <ruxiq.uci.edu> wrote:
>
> > Hi Brent,
> >
> > Commenting out just #error line in "#if defined(__ICC)" block should do
> > the trick. Or you can remove the whole block from "#if defined(__ICC)"
> > to "#endif /*__ICC */".
> >
> > Thanks!
> >
> > Ruxi
> >
> >
> > On 4/7/17 10:41, Brent Krueger wrote:
> > > 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
> > >>>>
> > >>>
> > >>
> > >> _______________________________________________
> > >> AMBER-Developers mailing list
> > >> AMBER-Developers.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >>
> > >
> > >
> >
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
>
>
>
> --
> _______________________________________________
> Brent P. Krueger.....................phone: 616 395 7629
> Professor.................................fax: 616 395 7118
> Hope College..........................Schaap Hall 2120
> Department of Chemistry
> Holland, MI 49423
> _______________________________________________
> AMBER-Developers mailing list
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>
-- 
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Apr 07 2017 - 19:00:03 PDT
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