Hi Fabricio,
What does nvcc -V return? - Just to check you are definitely using CUDA 3.2
Also what are the other compilers you are using, versions, operating system
version etc?
Also does the rest of AMBER compile and function correctly?
All the best
Ross
> -----Original Message-----
> From: Fabrício Bracht [mailto:bracht.iq.ufrj.br]
> Sent: Saturday, July 23, 2011 7:30 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Error compiling amber cuda
>
> Tried the fresh extraction. Applied the bugfix through
> ./apply_bugfix.x bugfix.all. Same error during compilation occurred.
> Any suggestions?
> Best regards
> Fabrício
>
> 2011/7/22 Jason Swails <jason.swails.gmail.com>:
> > Try a fresh extraction and recompile completely. Compilation should
> not
> > crash after the bug fixes are successfully applied. Don't forget to
> apply
> > the amber11 bugfixes via the script provided on the bugfix website.
> >
> > HTH,
> > Jason
> >
> > 2011/7/22 Fabrício Bracht <bracht.iq.ufrj.br>
> >
> >> Thank you. Here is what happens if I use cuda toolkit 3.2.
> Compilation
> >> finishes successfully but once I try to run pmemd.cuda with my
> system
> >> (75000 atoms aprox.), I get the following error.
> >> Error: unspecified launch failure launching kernel kReduceSoluteCOM
> >>
> >> I probably should expect this error, since I am running on a GTX460.
> >> This has been without applying bugfixes for amber 11.
> >> The problem is that after the bugfixes have been applied,
> compilation
> >> crashes with:
> >> make -C ./cuda
> >> make[3]: Entering directory
> >> `/home/zotac/Downloads/amber11/src/pmemd/src/cuda'
> >> cpp -traditional -P -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> >> -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA cuda_info.fpp cuda_info.f90
> >> gfortran -O3 -mtune=generic -DCUDA -I/usr/local/cuda/include -IB40C
> >> -IB40C/KernelCommon -c cuda_info.f90
> >> gcc -O3 -mtune=generic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> >> -DCUDA -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
> gpu.cpp
> >> gcc -O3 -mtune=generic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> >> -DCUDA -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
> >> gputypes.cpp
> >> /usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode
> >> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -
> DCUDA
> >> -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
> >> kForcesUpdate.cu
> >> kU.h(149): error: expected a declaration
> >>
> >> kU.h(189): error: identifier "pos" is undefined
> >>
> >> kU.h(201): error: identifier "invMass" is undefined
> >>
> >> kU.h(201): error: identifier "dtx" is undefined
> >>
> >> kU.h(209): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(209): error: variable "cSim" has already been defined
> >>
> >> kU.h(209): error: expected a ";"
> >>
> >> kU.h(210): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(210): error: variable "cSim" has already been defined
> >>
> >> kU.h(210): error: expected a ";"
> >>
> >> kU.h(211): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(211): error: variable "cSim" has already been defined
> >>
> >> kU.h(211): error: expected a ";"
> >>
> >> kU.h(220): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(220): error: variable "velX" has already been defined
> >>
> >> kU.h(220): error: expected a ";"
> >>
> >> kU.h(221): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(221): error: variable "velY" has already been defined
> >>
> >> kU.h(221): error: expected a ";"
> >>
> >> kU.h(222): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(222): error: variable "velZ" has already been defined
> >>
> >> kU.h(222): error: expected a ";"
> >>
> >> kU.h(233): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(233): error: variable "cSim" has already been defined
> >>
> >> kU.h(233): error: expected a ";"
> >>
> >> kU.h(234): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(234): error: variable "cSim" has already been defined
> >>
> >> kU.h(234): error: expected a ";"
> >>
> >> kU.h(235): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(235): error: variable "cSim" has already been defined
> >>
> >> kU.h(235): error: expected a ";"
> >>
> >> kU.h(244): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(244): error: variable "cSim" has already been defined
> >>
> >> kU.h(244): error: expected a ";"
> >>
> >> kU.h(245): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(245): error: variable "cSim" has already been defined
> >>
> >> kU.h(245): error: expected a ";"
> >>
> >> kU.h(246): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(246): error: variable "cSim" has already been defined
> >>
> >> kU.h(246): error: expected a ";"
> >>
> >> kU.h(248): error: identifier "atomX" is undefined
> >>
> >> kU.h(249): error: identifier "atomY" is undefined
> >>
> >> kU.h(250): error: identifier "atomZ" is undefined
> >>
> >> kU.h(252): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(252): error: variable "xy" has already been defined
> >>
> >> kU.h(252): error: expected a ";"
> >>
> >> kU.h(253): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(253): error: variable "xy" has already been defined
> >>
> >> kU.h(253): error: expected a ";"
> >>
> >> kU.h(259): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(259): error: variable "cSim" has already been defined
> >>
> >> kU.h(259): error: expected a ";"
> >>
> >> kU.h(260): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(260): error: variable "cSim" has already been defined
> >>
> >> kU.h(260): error: expected a ";"
> >>
> >> kU.h(261): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(261): error: variable "cSim" has already been defined
> >>
> >> kU.h(261): error: expected a ";"
> >>
> >> kU.h(263): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(263): error: variable "cSim" has already been defined
> >>
> >> kU.h(263): error: expected a ";"
> >>
> >> kU.h(264): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(264): error: variable "cSim" has already been defined
> >>
> >> kU.h(264): error: expected a ";"
> >>
> >> kU.h(265): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(265): error: expected a ";"
> >>
> >> kU.h(266): error: expected a declaration
> >>
> >> kU.h(326): warning: parsing restarts here after previous syntax
> error
> >>
> >> kU.h(327): error: variable "forceZ" has already been defined
> >>
> >> kU.h(328): error: variable "velX" has already been defined
> >>
> >> kU.h(329): error: variable "velY" has already been defined
> >>
> >> kU.h(330): error: variable "velZ" has already been defined
> >>
> >> kU.h(338): error: variable "wfac" has already been defined
> >>
> >> kU.h(346): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(346): error: variable "cSim" has already been defined
> >>
> >> kU.h(346): error: expected a ";"
> >>
> >> kU.h(347): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(347): error: variable "cSim" has already been defined
> >>
> >> kU.h(347): error: expected a ";"
> >>
> >> kU.h(348): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(348): error: variable "cSim" has already been defined
> >>
> >> kU.h(348): error: expected a ";"
> >>
> >> kU.h(357): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(357): error: variable "velX" has already been defined
> >>
> >> kU.h(357): error: expected a ";"
> >>
> >> kU.h(358): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(358): error: variable "velY" has already been defined
> >>
> >> kU.h(358): error: expected a ";"
> >>
> >> kU.h(359): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(359): error: variable "velZ" has already been defined
> >>
> >> kU.h(359): error: expected a ";"
> >>
> >> kU.h(370): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(370): error: variable "cSim" has already been defined
> >>
> >> kU.h(370): error: expected a ";"
> >>
> >> kU.h(371): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(371): error: variable "cSim" has already been defined
> >>
> >> kU.h(371): error: expected a ";"
> >>
> >> kU.h(372): error: this declaration has no storage class or type
> specifier
> >>
> >> kU.h(372): error: variable "cSim" has already been defined
> >>
> >> kU.h(372): error: expected a ";"
> >>
> >> kU.h(381): error: this declaration has no storage class or type
> specifier
> >>
> >> Error limit reached.
> >> 100 errors detected in the compilation of
> >> "/tmp/tmpxft_00004a34_00000000-6_kForcesUpdate.compute_20.cpp1.ii".
> >> Compilation terminated.
> >> make[3]: *** [kForcesUpdate.o] Error 4
> >> make[3]: Leaving directory
> >> `/home/zotac/Downloads/amber11/src/pmemd/src/cuda'
> >> make[2]: *** [-L/usr/local/cuda/lib64] Error 2
> >> make[2]: Leaving directory
> `/home/zotac/Downloads/amber11/src/pmemd/src'
> >> make[1]: *** [cuda] Error 2
> >> make[1]: Leaving directory `/home/zotac/Downloads/amber11/src/pmemd'
> >> make: *** [cuda] Error 2
> >>
> >> 2011/7/22 Ross Walker <rosscwalker.gmail.com>:
> >> > This has been discussed many times on the list already. For now
> please
> >> use CUDA 3.2.
> >> >
> >> > All the best
> >> > Ross
> >> >
> >> >
> >> >
> >> > On Jul 22, 2011, at 16:30, Fabrício Bracht <bracht.iq.ufrj.br>
> wrote:
> >> >
> >> >> I am trying to compile amber11 on ubuntu 10.04. Compilation of
> serial
> >> >> amber has gone without any errors but, when I try to compile with
> cuda
> >> >> support I get the following error lines. Any idea of what might
> be
> >> >> happening. The version of cudatoolkit I am using is 4.0. The
> nvidia
> >> >> driver is the latest 275 provided by nvidia.
> >> >> In case you need any extra information, please let me know.
> >> >>
> >> >> make -C ./cuda
> >> >> make[3]: Entering directory
> >> `/home/zotac/Downloads/amber11/src/pmemd/src/cuda'
> >> >> cpp -traditional -P -DDIRFRC_EFS -DDIRFRC_COMTRANS -
> DDIRFRC_NOVEC
> >> >> -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA cuda_info.fpp cuda_info.f90
> >> >> gfortran -O3 -mtune=generic -DCUDA -I/usr/local/cuda/include -
> IB40C
> >> >> -IB40C/KernelCommon -c cuda_info.f90
> >> >> gcc -O3 -mtune=generic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> >> >> -DCUDA -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
> gpu.cpp
> >> >> gcc -O3 -mtune=generic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> >> >> -DCUDA -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
> >> >> gputypes.cpp
> >> >> /usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode
> >> >> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -
> DCUDA
> >> >> -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
> >> >> kForcesUpdate.cu
> >> >> kU.h(149): error: expected a declaration
> >> >>
> >> >> kU.h(189): error: identifier "pos" is undefined
> >> >>
> >> >> kU.h(201): error: identifier "invMass" is undefined
> >> >>
> >> >> kU.h(201): error: identifier "dtx" is undefined
> >> >>
> >> >> kU.h(209): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(209): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(209): error: expected a ";"
> >> >>
> >> >> kU.h(210): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(210): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(210): error: expected a ";"
> >> >>
> >> >> kU.h(211): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(211): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(211): error: expected a ";"
> >> >>
> >> >> kU.h(220): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(220): error: variable "velX" has already been defined
> >> >>
> >> >> kU.h(220): error: expected a ";"
> >> >>
> >> >> kU.h(221): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(221): error: variable "velY" has already been defined
> >> >>
> >> >> kU.h(221): error: expected a ";"
> >> >>
> >> >> kU.h(222): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(222): error: variable "velZ" has already been defined
> >> >>
> >> >> kU.h(222): error: expected a ";"
> >> >>
> >> >> kU.h(233): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(233): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(233): error: expected a ";"
> >> >>
> >> >> kU.h(234): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(234): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(234): error: expected a ";"
> >> >>
> >> >> kU.h(235): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(235): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(235): error: expected a ";"
> >> >>
> >> >> kU.h(244): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(244): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(244): error: expected a ";"
> >> >>
> >> >> kU.h(245): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(245): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(245): error: expected a ";"
> >> >>
> >> >> kU.h(246): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(246): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(246): error: expected a ";"
> >> >>
> >> >> kU.h(248): error: identifier "atomX" is undefined
> >> >>
> >> >> kU.h(249): error: identifier "atomY" is undefined
> >> >>
> >> >> kU.h(250): error: identifier "atomZ" is undefined
> >> >>
> >> >> kU.h(252): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(252): error: variable "xy" has already been defined
> >> >>
> >> >> kU.h(252): error: expected a ";"
> >> >>
> >> >> kU.h(253): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(253): error: variable "xy" has already been defined
> >> >>
> >> >> kU.h(253): error: expected a ";"
> >> >>
> >> >> kU.h(259): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(259): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(259): error: expected a ";"
> >> >>
> >> >> kU.h(260): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(260): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(260): error: expected a ";"
> >> >>
> >> >> kU.h(261): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(261): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(261): error: expected a ";"
> >> >>
> >> >> kU.h(263): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(263): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(263): error: expected a ";"
> >> >>
> >> >> kU.h(264): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(264): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(264): error: expected a ";"
> >> >>
> >> >> kU.h(265): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(265): error: expected a ";"
> >> >>
> >> >> kU.h(266): error: expected a declaration
> >> >>
> >> >> kU.h(326): warning: parsing restarts here after previous syntax
> error
> >> >>
> >> >> kU.h(327): error: variable "forceZ" has already been defined
> >> >>
> >> >> kU.h(328): error: variable "velX" has already been defined
> >> >>
> >> >> kU.h(329): error: variable "velY" has already been defined
> >> >>
> >> >> kU.h(330): error: variable "velZ" has already been defined
> >> >>
> >> >> kU.h(338): error: variable "wfac" has already been defined
> >> >>
> >> >> kU.h(346): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(346): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(346): error: expected a ";"
> >> >>
> >> >> kU.h(347): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(347): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(347): error: expected a ";"
> >> >>
> >> >> kU.h(348): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(348): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(348): error: expected a ";"
> >> >>
> >> >> kU.h(357): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(357): error: variable "velX" has already been defined
> >> >>
> >> >> kU.h(357): error: expected a ";"
> >> >>
> >> >> kU.h(358): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(358): error: variable "velY" has already been defined
> >> >>
> >> >> kU.h(358): error: expected a ";"
> >> >>
> >> >> kU.h(359): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(359): error: variable "velZ" has already been defined
> >> >>
> >> >> kU.h(359): error: expected a ";"
> >> >>
> >> >> kU.h(370): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(370): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(370): error: expected a ";"
> >> >>
> >> >> kU.h(371): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(371): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(371): error: expected a ";"
> >> >>
> >> >> kU.h(372): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> kU.h(372): error: variable "cSim" has already been defined
> >> >>
> >> >> kU.h(372): error: expected a ";"
> >> >>
> >> >> kU.h(381): error: this declaration has no storage class or type
> >> specifier
> >> >>
> >> >> Error limit reached.
> >> >> 100 errors detected in the compilation of
> >> >> "/tmp/tmpxft_00003b14_00000000-
> 6_kForcesUpdate.compute_13.cpp1.ii".
> >> >> Compilation terminated.
> >> >> make[3]: *** [kForcesUpdate.o] Error 4
> >> >> make[3]: Leaving directory
> >> `/home/zotac/Downloads/amber11/src/pmemd/src/cuda'
> >> >> make[2]: *** [-L/usr/local/cuda/lib64] Error 2
> >> >> make[2]: Leaving directory
> `/home/zotac/Downloads/amber11/src/pmemd/src'
> >> >> make[1]: *** [cuda] Error 2
> >> >> make[1]: Leaving directory
> `/home/zotac/Downloads/amber11/src/pmemd'
> >> >> make: *** [cuda] Error 2
> >> >>
> >> >> _______________________________________________
> >> >> 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
> >> >
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > 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
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Received on Sat Jul 23 2011 - 09:30:03 PDT
