So what happens if you remove ipo from the compilation?
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Thursday, February 10, 2011 08:11
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] problems with latest updates to CUDA code
The default install rule does a clean (including a netcdf_clean) first, so I
don't think this is an issue. In any case, the errors I'm getting are
ipo: warning #11020: unresolved gpu_get_nb_energy_
Referenced in /tmp/ipo_ifortLpW9vm.o
ipo: warning #11020: unresolved gpu_vdw_correction_
Referenced in /tmp/ipo_ifortLpW9vm.o
ipo: warning #11020: unresolved gpu_self_
Referenced in /tmp/ipo_ifortLpW9vm.o
... etc.
which doesn't appear to be netcdf-related.
Thanks!
Jason
On Thu, Feb 10, 2011 at 11:04 AM, Scott Le Grand <SLeGrand.nvidia.com>wrote:
> You've done a make clean right?
>
> If you google this issue, this has been seen before:
>
> https://www.myroms.org/forum/viewtopic.php?f=31&t=269
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Thursday, February 10, 2011 07:59
> To: AMBER Developers Mailing List
> Subject: Re: [AMBER-Developers] problems with latest updates to CUDA code
>
> I'm getting the same errors on my box
>
> ifort 11.1.069, nvcc release 3.2, V0.2.1221
>
> GNU compilers (4.4.1) work just fine. Stupid intel...
>
> --Jason
>
> On Thu, Feb 10, 2011 at 9:29 AM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > Ross is on travel. I will try it next week.
> >
> > > -----Original Message-----
> > > From: Scott Le Grand [mailto:SLeGrand.nvidia.com]
> > > Sent: Thursday, February 10, 2011 6:26 AM
> > > To: amber-developers.ambermd.org
> > > Subject: Re: [AMBER-Developers] problems with latest updates to CUDA
> > > code
> > >
> > > Works at this end with either GNU or Intel, Ross?
> > >
> > >
> > > -----Original Message-----
> > > From: case [mailto:case.biomaps.rutgers.edu]
> > > Sent: Thursday, February 10, 2011 06:15
> > > To: amber-developers.ambermd.org
> > > Subject: [AMBER-Developers] problems with latest updates to CUDA code
> > >
> > > I'm having trouble with the latest git updates to the cuda code:
> > >
> > > make[3]: Leaving directory `/home/case/amber11/src/pmemd/src/cuda'
> > > ifort -ipo -O3 -no-prec-div -xHost -DCUDA -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
> > > 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/lib64
> > > -L/usr/local/cuda/lib -lcufft -lcudart ./cuda/cuda.a
> > > /home/case/amber11/lib/libnetcdf.a -shared-intel -Wl,--start-group
> > > /cottus/opt/intel/Compiler/11.1/069/mkl/lib/em64t/libmkl_intel_lp64.a
> > > /cottus/opt/intel/Compiler/11.1/069/mkl/lib/em64t/libmkl_sequential.a
> > > /cottus/opt/intel/Compiler/11.1/069/mkl/lib/em64t/libmkl_core.a
> > > -Wl,--end-group -lpthread
> > > ipo: warning #11020: unresolved gpu_get_nb_energy_
> > > Referenced in /tmp/ipo_ifort1hg2Wz.o
> > > ipo: warning #11020: unresolved gpu_vdw_correction_
> > > Referenced in /tmp/ipo_ifort1hg2Wz.o
> > >
> > > ....etc
> > >
> > > The problem appears to be with gpu.cpp. When compiled with either icc
> > > (which is what the Makefile uses) or icpc, the resulting gpu.o does not
> > have
> > > any symbols in it(!?!). I can't see the problem. Intel compiler
> version
> > > is 11.1.069.
> > >
> > > Using gnu compilers seems fine, so I can go that way. But intel
> > compilers
> > > *had* been working, up until this last update.
> > >
> > > ....dac
> > >
> > >
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> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >
> >
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> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Feb 10 2011 - 08:30:04 PST
