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
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Received on Fri Jul 22 2011 - 19:00:03 PDT
