Hello,
I just built PMEMD for GPGPUs according to (
http://ambermd.org/gpus/), I
used the Intel MPI version (intel/impi/4.0.1.007). Then I tested it with
the standard jac benchmark without vlimit
short md, jac, power 2 FFT
&cntrl
ntx=7, irest=1,
ntc=2, ntf=2, tol=0.0000001,
nstlim=1000,
ntpr=5, ntwr=10,
dt=0.001,
cut=9.,
ntt=0, temp0=300.,
/
&ewald
nfft1=64,nfft2=64,nfft3=64,
/
Has anybody seen this problem? The build ends successfully. I am using PBS
with 2 nodes. Did I forget any patches?
[0:node037] rtc_register failed 196608 [0] error(0x30000): unknown error
Assertion failed in file ../../dapl_module_send.c at line 4711: 0
internal ABORT - process 0
rank 0 in job 1 node037_43404 caused collective abort of all ranks
exit status of rank 0: killed by signal 9
----------------------------------------
Final step in the build:
Leaving directory `/home/applications/AMBER/11/amber11/src/pmemd/src/cuda'
mpif90 -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -o pmemd.cuda.MPI
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 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
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 -L/usr/local/cuda-3.2/lib64
-L/usr/local/cuda-3.2/lib -lcufft -lcudart ./cuda/cuda.a
/home/cpsosa/applications/AMBER/11/amber11/lib/libnetcdf.a
make[2]: Leaving directory
`/home/applications/AMBER/11/amber11/src/pmemd/src'
Installation of pmemd.cuda.MPI complete
make[1]: Leaving directory `/home/applications/AMBER/11/amber11/src/pmemd'
Thanks
--
Carlos P Sosa
*Biomedical Informatics and Computational Biology* (BICB) Consultant
Minnesota Supercomputing Institute
for Advanced Computational Research
University of Minnesota
Walter Library 509
117 Pleasant Street
Minneapolis, MN 55455
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Received on Tue Aug 23 2011 - 10:30:03 PDT
