I have never seen this error before. That said, CUDA 7 is not recommended
for use. I suggest upgrading to CUDA 7.5 instead. However, that probably
will not fix this error.
What version of AmberTools are you using? What is the output of
$AMBERHOME/update_amber --version? Have you made any changes yourself to
any of the source code?
Make sure you have all updates applied. Your output of update_amber
--version should look like this:
Version is reported as <version>.<patches applied>
AmberTools version 15.05
Amber version 14.13
HTH,
Jason
On Fri, Nov 20, 2015 at 2:36 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 20 2015 - 05:00:04 PST
