make test.cuda_parallel does not complete. I am attaching the logfile here.
On Sat, Jan 25, 2020 at 10:18 AM Sruthi Sudhakar <
sruthisudhakarraji.gmail.com> wrote:
> Yes sir. Even when that was done, we could not complete the installation.
> So I had reinstalled everything once again. Now I could get all the
> executables. Sander.MPI and pmemd.cuda.MPI executables are both present
> now. I have not done the test yet.
>
> On Fri, 24 Jan 2020 at 5:21 PM, Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
>> Did you apply all update patches before compiling serial amber??
>>
>> On Friday, January 24, 2020, Sruthi Sudhakar <
>> sruthisudhakarraji.gmail.com>
>> wrote:
>>
>> > I have defined cuda home and continued with the installation. The
>> > ./configure -cuda -mpi gnu command gets completed. When we do make
>> install
>> > the following error occurred:
>> > kRMSFit.h(106): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (PMEDouble *, PMEDouble)
>> >
>> > kRMSFit.h(192): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, PMEDouble)
>> >
>> > kRMSFit.h(163): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(164): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(165): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(168): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(169): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(170): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(173): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(174): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(175): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(181): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(182): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(183): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(185): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(186): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(187): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(106): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (PMEDouble *, PMEDouble)
>> >
>> > kRMSFit.h(192): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, PMEDouble)
>> >
>> > kRMSFit.h(163): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(164): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(165): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(168): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(169): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(170): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(173): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(174): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(175): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(181): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(182): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(183): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(185): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(186): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > kRMSFit.h(187): error: no instance of overloaded function "atomicAdd"
>> > matches the argument list
>> > argument types are: (double *, double)
>> >
>> > 34 errors detected in the compilation of
>> > "/tmp/tmpxft_00007234_00000000-20_kCalculateNEBForces.cpp4.ii".
>> > make[5]: *** [kCalculateNEBForces.o] Error 2
>> > make[5]: Leaving directory `/apps/amber18/src/pmemd/src/cuda'
>> > make[4]: *** [cuda_spfp_libs] Error 2
>> > make[4]: Leaving directory `/apps/amber18/src/pmemd/src'
>> > make[3]: *** [cuda_parallel_SPFP] Error 2
>> > make[3]: Leaving directory `/apps/amber18/src/pmemd/src'
>> > make[2]: *** [cuda_parallel] Error 2
>> > make[2]: Leaving directory `/apps/amber18/src/pmemd'
>> > make[1]: *** [cuda_parallel] Error 2
>> > make[1]: Leaving directory `/apps/amber18/src'
>> > make: *** [install] Error 2
>> >
>> > On Thu, Jan 23, 2020 at 9:08 PM Elvis Martis <elvis_bcp.elvismartis.in>
>> > wrote:
>> >
>> > > The original tar files for AMBER and AMBERTools contain all files you
>> > need
>> > > for installation.
>> > > For CUDA installation files, visit the NVIDIA website for the same.
>> > >
>> > > On Thursday, January 23, 2020, Sruthi Sudhakar <
>> > > sruthisudhakarraji.gmail.com>
>> > > wrote:
>> > >
>> > > > Thank you sir. I will do the same and check once again. I hope we
>> don't
>> > > > need any other files for installation.
>> > > >
>> > > > On Thu, Jan 23, 2020 at 8:09 PM David Case <david.case.rutgers.edu>
>> > > wrote:
>> > > >
>> > > > > On Thu, Jan 23, 2020, Sruthi Sudhakar wrote:
>> > > > > >
>> > > > > >./configure -cuda -mpi -gnu
>> > > > > >When I continued with this step , I got the following error
>> message:
>> > > > > >Error: CUDA_HOME is not set. This must point to your NVIDIA tools
>> > > > > >installation
>> > > > >
>> > > > > I agree with Elvis that this is odd, since CUDA_HOME would have
>> had
>> > > > > to have been defined when you configured the serial version.
>> > > > >
>> > > > > If you didn't install CUDA yourself, you may need to search your
>> > > > > computer to find out where it is installed (or ask whoever carried
>> > > > > out the installation). The default location is in
>> /usr/local/cuda.
>> > > > > See if that folder exists--it is probably a link to something like
>> > > > > /usr/local/cuda-10.0 (or some other version number). Set
>> CUDA_HOME
>> > to
>> > > > > point to this folder.
>> > > > >
>> > > > > ....dac
>> > > > >
>> > > > >
>> > > > > _______________________________________________
>> > > > > AMBER mailing list
>> > > > > AMBER.ambermd.org
>> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > >
>> > > > _______________________________________________
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>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > >
>> > >
>> > > --
>> > > Best Regards
>> > > Elvis Martis
>> > > Mumbai.
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> --
>> Best Regards
>> Elvis Martis
>> Mumbai.
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Fri Jan 24 2020 - 22:00:02 PST
