Just updating on the situation. I've extracted again both
ambertools1.5 and amber11 files. Patched them again using bugfix.all
for ambertools and then for amber11. Got some errors while applying
bugfix for amber11. Things like "patching file
src/pmemd/src/cuda/gpu.cpp Hunk #1 FAILED at 277." appeared all the
time. While trying to compile amber11 with cuda, I got a whole new set
of error lines. Now I really don't know what to do.
make -C ./cuda
make[3]: Entering directory `/home/zotac/Downloads/amber11/src/pmemd/src/cuda'
cpp -traditional -P -DBINTRAJ -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
-DBINTRAJ -DCUDA -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon
-c gpu.cpp
In file included from gpu.cpp:23:
gputypes.h:1145: error: declaration of ‘GpuBuffer<int>*
_gpuContext::pbConstraintSoluteID’
gputypes.h:1136: error: conflicts with previous declaration
‘GpuBuffer<int>* _gpuContext::pbConstraintSoluteID’
gputypes.h:1146: error: declaration of ‘GpuBuffer<double>*
_gpuContext::pbConstraintSoluteAtom’
gputypes.h:1137: error: conflicts with previous declaration
‘GpuBuffer<double>* _gpuContext::pbConstraintSoluteAtom’
gputypes.h:1147: error: declaration of ‘GpuBuffer<double>*
_gpuContext::pbConstraintSolute’
gputypes.h:1138: error: conflicts with previous declaration
‘GpuBuffer<double>* _gpuContext::pbConstraintSolute’
gputypes.h:1148: error: declaration of ‘GpuBuffer<long long unsigned
int>* _gpuContext::pbConstraintUllSolute’
gputypes.h:1139: error: conflicts with previous declaration
‘GpuBuffer<long long unsigned int>*
_gpuContext::pbConstraintUllSolute’
gputypes.h:1149: error: declaration of ‘GpuBuffer<int>*
_gpuContext::pbConstraintSolventAtoms’
gputypes.h:1140: error: conflicts with previous declaration
‘GpuBuffer<int>* _gpuContext::pbConstraintSolventAtoms’
gputypes.h:1150: error: declaration of ‘GpuBuffer<double>*
_gpuContext::pbConstraintSolventAtom’
gputypes.h:1141: error: conflicts with previous declaration
‘GpuBuffer<double>* _gpuContext::pbConstraintSolventAtom’
gputypes.h:1151: error: declaration of ‘GpuBuffer<int4>*
_gpuContext::pbConstraintSolventConstraint’
gputypes.h:1142: error: conflicts with previous declaration
‘GpuBuffer<int4>* _gpuContext::pbConstraintSolventConstraint’
gputypes.h:1154: error: declaration of ‘GpuBuffer<int>*
_gpuContext::pbConstraintSoluteID’
gputypes.h:1136: error: conflicts with previous declaration
‘GpuBuffer<int>* _gpuContext::pbConstraintSoluteID’
gputypes.h:1155: error: declaration of ‘GpuBuffer<double>*
_gpuContext::pbConstraintSoluteAtom’
gputypes.h:1137: error: conflicts with previous declaration
‘GpuBuffer<double>* _gpuContext::pbConstraintSoluteAtom’
gputypes.h:1156: error: declaration of ‘GpuBuffer<double>*
_gpuContext::pbConstraintSolute’
gputypes.h:1138: error: conflicts with previous declaration
‘GpuBuffer<double>* _gpuContext::pbConstraintSolute’
gputypes.h:1157: error: declaration of ‘GpuBuffer<long long unsigned
int>* _gpuContext::pbConstraintUllSolute’
gputypes.h:1139: error: conflicts with previous declaration
‘GpuBuffer<long long unsigned int>*
_gpuContext::pbConstraintUllSolute’
gputypes.h:1158: error: declaration of ‘GpuBuffer<int>*
_gpuContext::pbConstraintSolventAtoms’
gputypes.h:1140: error: conflicts with previous declaration
‘GpuBuffer<int>* _gpuContext::pbConstraintSolventAtoms’
gputypes.h:1159: error: declaration of ‘GpuBuffer<double>*
_gpuContext::pbConstraintSolventAtom’
gputypes.h:1141: error: conflicts with previous declaration
‘GpuBuffer<double>* _gpuContext::pbConstraintSolventAtom’
gputypes.h:1160: error: declaration of ‘GpuBuffer<int4>*
_gpuContext::pbConstraintSolventConstraint’
gputypes.h:1142: error: conflicts with previous declaration
‘GpuBuffer<int4>* _gpuContext::pbConstraintSolventConstraint’
gputypes.h:1163: error: declaration of ‘GpuBuffer<int>*
_gpuContext::pbConstraintSoluteID’
gputypes.h:1136: error: conflicts with previous declaration
‘GpuBuffer<int>* _gpuContext::pbConstraintSoluteID’
gputypes.h:1164: error: declaration of ‘GpuBuffer<double>*
_gpuContext::pbConstraintSoluteAtom’
gputypes.h:1137: error: conflicts with previous declaration
‘GpuBuffer<double>* _gpuContext::pbConstraintSoluteAtom’
gputypes.h:1165: error: declaration of ‘GpuBuffer<double>*
_gpuContext::pbConstraintSolute’
gputypes.h:1138: error: conflicts with previous declaration
‘GpuBuffer<double>* _gpuContext::pbConstraintSolute’
gputypes.h:1166: error: declaration of ‘GpuBuffer<long long unsigned
int>* _gpuContext::pbConstraintUllSolute’
gputypes.h:1139: error: conflicts with previous declaration
‘GpuBuffer<long long unsigned int>*
_gpuContext::pbConstraintUllSolute’
gputypes.h:1167: error: declaration of ‘GpuBuffer<int>*
_gpuContext::pbConstraintSolventAtoms’
gputypes.h:1140: error: conflicts with previous declaration
‘GpuBuffer<int>* _gpuContext::pbConstraintSolventAtoms’
gputypes.h:1168: error: declaration of ‘GpuBuffer<double>*
_gpuContext::pbConstraintSolventAtom’
gputypes.h:1141: error: conflicts with previous declaration
‘GpuBuffer<double>* _gpuContext::pbConstraintSolventAtom’
gputypes.h:1169: error: declaration of ‘GpuBuffer<int4>*
_gpuContext::pbConstraintSolventConstraint’
gputypes.h:1142: error: conflicts with previous declaration
‘GpuBuffer<int4>* _gpuContext::pbConstraintSolventConstraint’
make[3]: *** [gpu.o] Error 1
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
Em 22 de julho de 2011 18:30, Fabrício Bracht <bracht.iq.ufrj.br> escreveu:
> 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
Received on Fri Jul 22 2011 - 15:00:04 PDT
