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/
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Received on Tue Nov 20 2012 - 02:00:02 PST
