Hello
I recently bought a GTX-760 card which I was told will work with AMBER14.
I installed CentOS 7 and also installed CUDA-7,0 (as per the NVIDIA GUIDE)
all tests passed..
The Serial installation of AMBER14 was successful but the installation with
CUDA gave following error messages (highlighted in red at the bottom)
-----------------------------------
cd AmberTools/src && make install
make[1]: Entering directory `/opt/amber14/AmberTools/src'
AmberTools14 has no CUDA-enabled components
(cd ../../src && make cuda )
make[2]: Entering directory `/opt/amber14/src'
Starting installation of Amber14 (cuda) at Fri Nov 20 12:13:30 IST 2015.
cd pmemd && make cuda
make[3]: Entering directory `/opt/amber14/src/pmemd'
make -C src/ cuda
make[4]: Entering directory `/opt/amber14/src/pmemd/src'
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c gbl_constants.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c gbl_datatypes.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c state_info.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c file_io_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pmemd_lib.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c parallel_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c file_io.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c mdin_ctrl_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c mdin_emil_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c axis_optimize.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c fft1d.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c charmm.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c nextprmtop_section.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c prmtop_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c mdin_ewald_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c mdin_debugf_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c -o AmberNetcdf.o
../../../AmberTools/src/lib/AmberNetcdf.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c remd.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c binrestart.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c inpcrd_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c findmask.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c random.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c ti.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c constraints.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c mol_list.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c extra_pnts_nb14.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c prfs.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c dynamics_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c dynamics.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pbc.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c energy_records.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c nmr_lib.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c nmr_calls.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c angles.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c angles_ub.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c bonds.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c constantph_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c cmap.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c dihedrals.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c dihedrals_imp.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c bspline.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c emap.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c timers.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c gbsa.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c gb_ene.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c gb_parallel.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c img.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pme_recip_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pme_fft_dat.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pme_blk_fft.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pme_slab_fft.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c shake.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c cit.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c nb_exclusions.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c parallel.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c bintraj.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c sgld.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c runfiles.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c amd.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c scaledMD.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c gb_force.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c ene_frc_splines.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c nb_pairlist.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c loadbal.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pme_blk_recip.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pme_slab_recip.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c nbips.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pme_direct.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pme_force.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c emil.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c barostats.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c degcnt.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c get_cmdline.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c multipmemd.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c relaxmd.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c constantph.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c remd_exchg.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c runmd.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c runmin.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c veclib.F90
gcc -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-DBINTRAJ -DCUDA -Duse_SPFP -I/opt/amber14/include -c pmemd_clib.c
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c gb_alltasks_setup.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pme_alltasks_setup.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pme_setup.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c master_setup.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c pmemd.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c erfcfun.F90
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/opt/amber14/include -c charmm_gold.F90
make -C ./cuda
make[5]: Entering directory `/opt/amber14/src/pmemd/src/cuda'
gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
-I/usr/local/cuda-7.0/include -IB40C -IB40C/KernelCommon -c cuda_info.F90
Warning: Nonexistent include directory "B40C/KernelCommon"
gcc -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-DBINTRAJ -DCUDA -Duse_SPFP -I/usr/local/cuda-7.0/include -IB40C
-IB40C/KernelCommon -c gpu.cpp
gcc -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-DBINTRAJ -DCUDA -Duse_SPFP -I/usr/local/cuda-7.0/include -IB40C
-IB40C/KernelCommon -c gputypes.cpp
/usr/local/cuda-7.0/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode
arch=compute_30,code=sm_30 -gencode arch=compute_50,code=sm_50
-use_fast_math -O3 -DCUDA -Duse_SPFP -I/usr/local/cuda-7.0/include -IB40C
-IB40C/KernelCommon -c kForcesUpdate.cu
ptxmacros.h(69): error: function "__shfl(unsigned int, int, int)" has
already been defined
ptxmacros.h(100): error: function "__shfl(double, int, int)" has already
been defined
ptxmacros.h(116): error: function "__shfl(long long, int, int)" has already
been defined
ptxmacros.h(148): error: function "__shfl(unsigned long long, int, int)"
has already been defined
4 errors detected in the compilation of
"/tmp/tmpxft_00005e14_00000000-13_kForcesUpdate.compute_50.cpp1.ii".
make[5]: *** [kForcesUpdate.o] Error 2
make[5]: Leaving directory `/opt/amber14/src/pmemd/src/cuda'
make[4]: *** [cuda/cuda.a] Error 2
make[4]: Leaving directory `/opt/amber14/src/pmemd/src'
make[3]: *** [cuda] Error 2
make[3]: Leaving directory `/opt/amber14/src/pmemd'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/opt/amber14/src'
make[1]: [cuda] Error 2 (ignored)
make[1]: Leaving directory `/opt/amber14/AmberTools/src'
make[1]: Entering directory `/opt/amber14/src'
Starting installation of Amber14 (cuda) at Fri Nov 20 12:13:54 IST 2015.
cd pmemd && make cuda
make[2]: Entering directory `/opt/amber14/src/pmemd'
make -C src/ cuda
make[3]: Entering directory `/opt/amber14/src/pmemd/src'
make -C ./cuda
make[4]: Entering directory `/opt/amber14/src/pmemd/src/cuda'
/usr/local/cuda-7.0/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode
arch=compute_30,code=sm_30 -gencode arch=compute_50,code=sm_50
-use_fast_math -O3 -DCUDA -Duse_SPFP -I/usr/local/cuda-7.0/include -IB40C
-IB40C/KernelCommon -c kForcesUpdate.cu
ptxmacros.h(69): error: function "__shfl(unsigned int, int, int)" has
already been defined
ptxmacros.h(100): error: function "__shfl(double, int, int)" has already
been defined
ptxmacros.h(116): error: function "__shfl(long long, int, int)" has already
been defined
ptxmacros.h(148): error: function "__shfl(unsigned long long, int, int)"
has already been defined
4 errors detected in the compilation of
"/tmp/tmpxft_00005e34_00000000-13_kForcesUpdate.compute_50.cpp1.ii".
make[4]: *** [kForcesUpdate.o] Error 2
make[4]: Leaving directory `/opt/amber14/src/pmemd/src/cuda'
make[3]: *** [cuda/cuda.a] Error 2
make[3]: Leaving directory `/opt/amber14/src/pmemd/src'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/opt/amber14/src/pmemd'
make[1]: *** [cuda] Error 2
make[1]: Leaving directory `/opt/amber14/src'
make: *** [install] Error 2
---------------------------------------------------------------------------------
Is CUDA-7.0 not compatible with AMBER14 or CentOS 7?? or any other
incompatibility issue?
Many Thanks in advance for the help and clarification on this issue
Regards
Elvis Martis
Bombay College of Pharmacy
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Received on Fri Nov 20 2015 - 00:00:03 PST
