Hi Jason,
I get the same error with 4.2 but didn't mentioned it because I thought
that 4.2 CUDA version was deprecated. I exported manually on my home
directory CUDA-4.2 and CUDA-5.0 because the supercomputer infrastructure
provides just CUDA-4.1 in the module list, which is not compatible with
Amber12 ("CUDA support requires the use of a 4.2 or later CUDA toolkit.
Aborting compilation."). Therefore my only option is CUDA-4.2 which yields
the following stack trace:
export AMBERHOME=/gpfs/home/lspre124u1/Opt/amber12
export PATH=$AMBERHOME/exe:/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda/bin:$PATH
export
LD_LIBRARY_PATH=$AMBERHOME/lib:/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda/lib64:/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda/lib:$LD_LIBRARY_PATH
module load intel openmpi/1.4.5-intel
export MKL_HOME=/gpfs/apps/compilers/intel/mkl
export MPI_HOME=/gpfs/apps/mpi/openmpi/1.4.5/intel/
export CUDA_HOME=/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda
./configure -cuda intel
make install
ifort -ip -O3 -no-prec-div -xHost -DCUDA -Duse_SPFP -o pmemd.cuda
gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o
mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o
img.o nbips.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o
pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o
pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o
nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o
extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o
constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o
pmemd_lib.o runfiles.o file_io.o bintraj.o binrestart.o pmemd_clib.o
pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o
master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o
gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o
charmm.o charmm_gold.o findmask.o remd.o multipmemd.o remd_exchg.o amd.o \
./cuda/cuda.a -L/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda/lib64
-L/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda/lib -lcurand -lcufft -lcudart
-L/gpfs/home/lspre124u1/Opt/amber12/lib
-L/gpfs/home/lspre124u1/Opt/amber12/lib -lnetcdf -shared-intel
-Wl,--start-group
/gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_intel_lp64.a
/gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_sequential.a
/gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_core.a -Wl,--end-group
-lpthread
/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda/lib64/libcufft.so: undefined
reference to `__isoc99_sscanf.GLIBC_2.7'
make[4]: *** [pmemd.cuda] Error 1
make[4]: Leaving directory `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src'
make[3]: *** [cuda] Error 2
make[3]: Leaving directory `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/gpfs/home/lspre124u1/Opt/amber12/src'
make[1]: [cuda] Error 2 (ignored)
make[1]: Leaving directory
`/gpfs/home/lspre124u1/Opt/amber12/AmberTools/src'
make[1]: Entering directory `/gpfs/home/lspre124u1/Opt/amber12/src'
Starting installation of Amber12 (cuda) at Tue Nov 20 17:22:40 EET 2012.
cd pmemd && make cuda
make[2]: Entering directory `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd'
make -C src/ cuda
make[3]: Entering directory
`/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src'
make -C ./cuda
make[4]: Entering directory
`/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory
`/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory
`/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory
`/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory
`/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory
`/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory
`/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory
`/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory
`/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory
`/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
ifort -ip -O3 -no-prec-div -xHost -DCUDA -Duse_SPFP -o pmemd.cuda
gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o
mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o
img.o nbips.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o
pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o
pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o
nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o
extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o
constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o
pmemd_lib.o runfiles.o file_io.o bintraj.o binrestart.o pmemd_clib.o
pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o
master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o
gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o
charmm.o charmm_gold.o findmask.o remd.o multipmemd.o remd_exchg.o amd.o \
./cuda/cuda.a -L/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda/lib64
-L/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda/lib -lcurand -lcufft -lcudart
-L/gpfs/home/lspre124u1/Opt/amber12/lib
-L/gpfs/home/lspre124u1/Opt/amber12/lib -lnetcdf -shared-intel
-Wl,--start-group
/gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_intel_lp64.a
/gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_sequential.a
/gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_core.a -Wl,--end-group
-lpthread
/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda/lib64/libcufft.so: undefined
reference to `__isoc99_sscanf.GLIBC_2.7'
make[3]: *** [pmemd.cuda] Error 1
make[3]: Leaving directory `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd'
make[1]: *** [cuda] Error 2
make[1]: Leaving directory `/gpfs/home/lspre124u1/Opt/amber12/src'
make: *** [install] Error 2
Can you help me interpret it? Please let me know if there is any other
information you need.
thanks,
Thomas
On 20 November 2012 16:38, Jason Swails <jason.swails.gmail.com> wrote:
> By all reports, CUDA 5 does not yet work with Amber (there will be a patch
> coming out to support this).
>
> For the time being, stick with CUDA 4.2.
>
> Good luck,
> Jason
>
> On Tue, Nov 20, 2012 at 4:50 AM, Thomas Evangelidis <tevang3.gmail.com
> >wrote:
>
> > Greetings,
> >
> > I am trying to compile Amber12 on an Intel Xeon cluster with Infiniband,
> > using the Intel 12.1.0 compilers, OpenMPI 1.4.5 (compiled with Intel) and
> > CUDA 5. The serial and mpi version compile successfully but cuda fails.
> > Bellow are the commands I issue and the stack trace I get:
> >
> > export AMBERHOME=/gpfs/home/lspre124u1/Opt/amber12
> > export
> > PATH=$AMBERHOME/exe:/gpfs/home/lspre124u1/Opt/cuda-5.0/cuda/bin:$PATH
> > export
> >
> >
> LD_LIBRARY_PATH=$AMBERHOME/lib:/gpfs/home/lspre124u1/Opt/cuda-5.0/lib64:/gpfs/home/lspre124u1/Opt/cuda-5.0/lib:$LD_LIBRARY_PATH
> > module load intel openmpi/1.4.5-intel
> > export MKL_HOME=/gpfs/apps/compilers/intel/mkl
> > export MPI_HOME=/gpfs/apps/mpi/openmpi/1.4.5/intel/
> > export CUDA_HOME=/gpfs/home/lspre124u1/Opt/cuda-5.0
> >
> > ./configure -cuda intel
> >
> > ifort -ip -O3 -no-prec-div -xHost -DCUDA -Duse_SPFP -o pmemd.cuda
> > gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o
> mdin_ctrl_dat.o
> > mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o
> dynamics_dat.o
> > img.o nbips.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o
> > pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o
> > pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o
> > nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o
> dihedrals.o
> > extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o
> > constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o
> > pmemd_lib.o runfiles.o file_io.o bintraj.o binrestart.o pmemd_clib.o
> > pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o
> > master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o
> > gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o
> cmap.o
> > charmm.o charmm_gold.o findmask.o remd.o multipmemd.o remd_exchg.o amd.o
> \
> > ./cuda/cuda.a -L/gpfs/home/lspre124u1/Opt/cuda-5.0/lib64
> > -L/gpfs/home/lspre124u1/Opt/cuda-5.0/lib -lcurand -lcufft -lcudart
> > -L/gpfs/home/lspre124u1/Opt/amber12/lib
> > -L/gpfs/home/lspre124u1/Opt/amber12/lib -lnetcdf -shared-intel
> > -Wl,--start-group
> > /gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_intel_lp64.a
> > /gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_sequential.a
> > /gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_core.a -Wl,--end-group
> > -lpthread
> > /gpfs/home/lspre124u1/Opt/cuda-5.0/lib64/libcufft.so: undefined reference
> > to `__isoc99_sscanf.GLIBC_2.7'
> > make[4]: *** [pmemd.cuda] Error 1
> > make[4]: Leaving directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src'
> > make[3]: *** [cuda] Error 2
> > make[3]: Leaving directory `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd'
> > make[2]: *** [cuda] Error 2
> > make[2]: Leaving directory `/gpfs/home/lspre124u1/Opt/amber12/src'
> > make[1]: [cuda] Error 2 (ignored)
> > make[1]: Leaving directory
> > `/gpfs/home/lspre124u1/Opt/amber12/AmberTools/src'
> > make[1]: Entering directory `/gpfs/home/lspre124u1/Opt/amber12/src'
> > Starting installation of Amber12 (cuda) at Tue Nov 20 11:40:18 EET 2012.
> > cd pmemd && make cuda
> > make[2]: Entering directory `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd'
> > make -C src/ cuda
> > make[3]: Entering directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src'
> > make -C ./cuda
> > make[4]: Entering directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
> > make[4]: `cuda.a' is up to date.
> > make[4]: Leaving directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
> > make -C ./cuda
> > make[4]: Entering directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
> > make[4]: `cuda.a' is up to date.
> > make[4]: Leaving directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
> > make -C ./cuda
> > make[4]: Entering directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
> > make[4]: `cuda.a' is up to date.
> > make[4]: Leaving directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
> > make -C ./cuda
> > make[4]: Entering directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
> > make[4]: `cuda.a' is up to date.
> > make[4]: Leaving directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
> > make -C ./cuda
> > make[4]: Entering directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
> > make[4]: `cuda.a' is up to date.
> > make[4]: Leaving directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src/cuda'
> > ifort -ip -O3 -no-prec-div -xHost -DCUDA -Duse_SPFP -o pmemd.cuda
> > gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o
> mdin_ctrl_dat.o
> > mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o
> dynamics_dat.o
> > img.o nbips.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o
> > pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o
> > pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o
> > nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o
> dihedrals.o
> > extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o
> > constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o
> > pmemd_lib.o runfiles.o file_io.o bintraj.o binrestart.o pmemd_clib.o
> > pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o
> > master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o
> > gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o
> cmap.o
> > charmm.o charmm_gold.o findmask.o remd.o multipmemd.o remd_exchg.o amd.o
> \
> > ./cuda/cuda.a -L/gpfs/home/lspre124u1/Opt/cuda-5.0/lib64
> > -L/gpfs/home/lspre124u1/Opt/cuda-5.0/lib -lcurand -lcufft -lcudart
> > -L/gpfs/home/lspre124u1/Opt/amber12/lib
> > -L/gpfs/home/lspre124u1/Opt/amber12/lib -lnetcdf -shared-intel
> > -Wl,--start-group
> > /gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_intel_lp64.a
> > /gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_sequential.a
> > /gpfs/apps/compilers/intel/mkl/lib/intel64/libmkl_core.a -Wl,--end-group
> > -lpthread
> > /gpfs/home/lspre124u1/Opt/cuda-5.0/lib64/libcufft.so: undefined reference
> > to `__isoc99_sscanf.GLIBC_2.7'
> > make[3]: *** [pmemd.cuda] Error 1
> > make[3]: Leaving directory
> > `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd/src'
> > make[2]: *** [cuda] Error 2
> > make[2]: Leaving directory `/gpfs/home/lspre124u1/Opt/amber12/src/pmemd'
> > make[1]: *** [cuda] Error 2
> > make[1]: Leaving directory `/gpfs/home/lspre124u1/Opt/amber12/src'
> > make: *** [install] Error 2
> >
> >
> > Could some please help me interpret it? Below are the hardware details
> of a
> > single node:
> >
> > processor : 0
> > vendor_id : GenuineIntel
> > cpu family : 6
> > model : 44
> > model name : Intel(R) Xeon(R) CPU X5650 . 2.67GHz
> > stepping : 2
> > cpu MHz : 1596.000
> > cache size : 12288 KB
> > physical id : 0
> > siblings : 6
> > core id : 0
> > cpu cores : 6
> > apicid : 0
> > fpu : yes
> > fpu_exception : yes
> > cpuid level : 11
> > wp : yes
> > flags : fpu vme de pse tsc msr pae mce cx8 apic sep
> > mtrr pge mca cmov pat
> > pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall nx pdpe1gb
> > rdtscp lm constant_tsc nonstop_tsc arat pni monitor ds_cpl vmx smx est
> tm2
> > ssse3 cx16 xtpr sse4_1 sse4_2 popcnt lahf_lm
> > bogomips : 5333.67
> > clflush size : 64
> > cache_alignment : 64
> > address sizes : 40 bits physical, 48 bits virtual
> > power management: [8]
> >
> >
> > thanks,
> > Thomas
> >
> >
> > --
> >
> > ======================================================================
> >
> > Thomas Evangelidis
> >
> > PhD student
> > University of Athens
> > Faculty of Pharmacy
> > Department of Pharmaceutical Chemistry
> > Panepistimioupoli-Zografou
> > 157 71 Athens
> > GREECE
> >
> > email: tevang.pharm.uoa.gr
> >
> > tevang3.gmail.com
> >
> >
> > website: https://sites.google.com/site/thomasevangelidishomepage/
> > _______________________________________________
> > 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
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
_______________________________________________
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Received on Tue Nov 20 2012 - 08:00:02 PST
