OK, AMBER compiles on the cluster with MVAPICH2, CUDA-4.2 and GNU compilers
but it fails on my laptop (Fedora 17 64bit, GeForce GT 650M). MPICH2 fails
to compile AMBER, e.g. for pemd.MPI I get:
/tmp/ifort5nUvG0.i90(742): catastrophic error: Too many errors, exiting
compilation aborted for binrestart.F90 (code 1)
In contrast, it is compiles with OpenMPI.
On the other hand, pmemd.CUDA version yields an error like inlining failed
in call to 'bool b40c::IsKeysOnly()' which is produced from file
amber12/src/pmemd/src/cuda/B40C/kernel/radixsort_kernel_common.cu. Below is
the full stack trace. Is there any change to make it work??
sudo ln -s /usr/bin/gcc34 /usr/local/cuda/bin/gcc # I did this because
gcc-4.7.2 is not supported by CUDA-4.2 (gcc34 = 3.4.6)
configure -cuda gnu
make install
make[5]: Entering directory
`/home/thomas/Programs/amber12/src/pmemd/src/cuda'
/usr/local/cuda/bin/nvcc -use_fast_math -gencode arch=compute_13,code=sm_13
-gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30
-DCUDA -Duse_SPFP -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
kForcesUpdate.cu
./kForcesUpdate.cu(87): Advisory: Loop was not unrolled, cannot deduce loop
trip count
./kForcesUpdate.cu(127): Advisory: Loop was not unrolled, cannot deduce
loop trip count
/usr/local/cuda/bin/nvcc -use_fast_math -gencode arch=compute_13,code=sm_13
-gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30
-DCUDA -Duse_SPFP -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
kCalculateLocalForces.cu
/usr/local/cuda/bin/nvcc -use_fast_math -gencode arch=compute_13,code=sm_13
-gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30
-DCUDA -Duse_SPFP -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
kCalculateGBBornRadii.cu
/usr/local/cuda/bin/nvcc -use_fast_math -gencode arch=compute_13,code=sm_13
-gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30
-DCUDA -Duse_SPFP -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
kCalculatePMENonbondEnergy.cu
/usr/local/cuda/bin/nvcc -use_fast_math -gencode arch=compute_13,code=sm_13
-gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30
-DCUDA -Duse_SPFP -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
kCalculateGBNonbondEnergy1.cu
/usr/local/cuda/bin/nvcc -use_fast_math -gencode arch=compute_13,code=sm_13
-gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30
-DCUDA -Duse_SPFP -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
kNLRadixSort.cu
B40C/kernel/radixsort_kernel_common.cu: In static member function `static
bool b40c::BaseRadixSortingEnactor<K, V, Storage>::KeysOnly() [with K =
unsigned int, V = unsigned int, Storage =
b40c::MultiCtaRadixSortStorage<unsigned int, unsigned int>]':
B40C/kernel/radixsort_kernel_common.cu:134: sorry, unimplemented: inlining
failed in call to 'bool b40c::IsKeysOnly() [with V = unsigned int]':
function not considered for inlining
tmpxft_00004c7f_00000000-6_kNLRadixSort.compute_13.cudafe1.stub.c:106:
sorry, unimplemented: called from here
make[5]: *** [kNLRadixSort.o] Error 1
make[5]: Leaving directory
`/home/thomas/Programs/amber12/src/pmemd/src/cuda'
make[4]: *** [cuda/cuda.a] Error 2
make[4]: Leaving directory `/home/thomas/Programs/amber12/src/pmemd/src'
make[3]: *** [cuda] Error 2
make[3]: Leaving directory `/home/thomas/Programs/amber12/src/pmemd'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/home/thomas/Programs/amber12/src'
make[1]: [cuda] Error 2 (ignored)
make[1]: Leaving directory `/home/thomas/Programs/amber12/AmberTools/src'
make[1]: Entering directory `/home/thomas/Programs/amber12/src'
Starting installation of Amber12 (cuda) at Wed Nov 21 00:52:15 EET 2012.
cd pmemd && make cuda
make[2]: Entering directory `/home/thomas/Programs/amber12/src/pmemd'
make -C src/ cuda
make[3]: Entering directory `/home/thomas/Programs/amber12/src/pmemd/src'
make -C ./cuda
make[4]: Entering directory
`/home/thomas/Programs/amber12/src/pmemd/src/cuda'
/usr/local/cuda/bin/nvcc -use_fast_math -gencode arch=compute_13,code=sm_13
-gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30
-DCUDA -Duse_SPFP -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -c
kNLRadixSort.cu
B40C/kernel/radixsort_kernel_common.cu: In static member function `static
bool b40c::BaseRadixSortingEnactor<K, V, Storage>::KeysOnly() [with K =
unsigned int, V = unsigned int, Storage =
b40c::MultiCtaRadixSortStorage<unsigned int, unsigned int>]':
B40C/kernel/radixsort_kernel_common.cu:134: sorry, unimplemented: inlining
failed in call to 'bool b40c::IsKeysOnly() [with V = unsigned int]':
function not considered for inlining
tmpxft_00004f77_00000000-6_kNLRadixSort.compute_13.cudafe1.stub.c:106:
sorry, unimplemented: called from here
make[4]: *** [kNLRadixSort.o] Error 1
make[4]: Leaving directory
`/home/thomas/Programs/amber12/src/pmemd/src/cuda'
make[3]: *** [cuda/cuda.a] Error 2
make[3]: Leaving directory `/home/thomas/Programs/amber12/src/pmemd/src'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/home/thomas/Programs/amber12/src/pmemd'
make[1]: *** [cuda] Error 2
make[1]: Leaving directory `/home/thomas/Programs/amber12/src'
make: *** [install] Error 2
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Received on Tue Nov 20 2012 - 15:30:03 PST
