Hi Thomas,
Can you quickly try GCC instead and see if that works?
>From a completely clean tree - best to untar and start from scratch.
./configure -cuda gnu (say yes to applying the patches)
./configure -cuda gnu (say yes again)
..Repeat until configure doesn't ask you to patch anymore - this is an
unfortunate bug in the patching system that we can't retroactively fix..
./configure -cuda gnu
make install
There is no difference in performance for GPU runs between the GNU or
Intel compilers and the GNU ones (amazingly!) seem to be more stable these
days.
All the best
Ross
On 11/20/12 7:53 AM, "Thomas Evangelidis" <tevang3.gmail.com> wrote:
>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=$AMBERHOME/lib:/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda/lib
>64:/gpfs/home/lspre124u1/Opt/cuda-4.2/cuda/lib:$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/
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 20 2012 - 08:30:02 PST
