You must never run such tests as root. Re-run the tests as normal user.
On Saturday, January 25, 2020, Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
wrote:
> 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
> >> > > > >
> >> > > > _______________________________________________
> >> > > > 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
> >> > >
> >> > _______________________________________________
> >> > 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
> >>
> >
>
--
Best Regards
Elvis Martis
Mumbai.
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Received on Sat Jan 25 2020 - 19:00:02 PST
