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
>
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Received on Sat Jul 23 2011 - 08:00:03 PDT
