Hi all,
So this is the error message I get after running configure with the
following parameters:
./configure -cuda_DPDP -mpi
There's an unreferenced fortran function called mexit(). I know it's under
pmemd_lib.f90 and its object file is actually getting linked to the
master_setup.o. So why does this error persist?
However, compiling just -cuda_DPDP and the tests pass with flying colors:
54 file comparisons passed
0 file comparisons failed
0 tests experienced errors
Test log file saved as logs/test_amber_cuda/2011-05-25_19-11-35.log
No test diffs to save!
Thanks,
Paul
==Tail of build log with -cuda_DPDP -mpi==
make[3]: Entering directory
`/extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/src/pmemd/src/cuda'
make[3]: `cuda.a' is up to date.
make[3]: Leaving directory
`/extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/src/pmemd/src/cuda'
mpif90 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -Duse_DPDP -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
/extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/lib/libnetcdf.a
master_setup.o: In function `__master_setup_mod__printdefines':
master_setup.f90:(.text+0xaa2): undefined reference to `mexit_'
collect2: ld returned 1 exit status
make[2]: *** [pmemd.cuda] Error 1
make[2]: Leaving directory
`/extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/src/pmemd/src'
make[1]: *** [cuda] Error 2
make[1]: Leaving directory
`/extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/src/pmemd'
make: *** [cuda] Error 2
07:01 PM 28580 prigor.nimbus/extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/src
Thanks,
Paul
--
Paul Rigor
http://www.ics.uci.edu/~prigor
On Wed, May 25, 2011 at 6:51 PM, Paul Rigor <paul.rigor.uci.edu> wrote:
> Here's the log after recompiling, applying the patches, etc (but still no
> cuda_parallel target) and without having to mess with the netCDF library.
>
> 42 file comparisons passed
> 12 file comparisons failed
> 0 tests experienced errors
> Test log file saved as logs/test_amber_cuda/2011-05-25_18-22-30.log
> Test diffs file saved as logs/test_amber_cuda/2011-05-25_18-22-30.diff
>
> Thanks,
> Paul
>
>
> --
> Paul Rigor
> http://www.ics.uci.edu/~prigor
>
>
>
> On Wed, May 25, 2011 at 5:53 PM, Paul Rigor <paul.rigor.uci.edu> wrote:
>
>> Hi gang,
>>
>> So I'm still checking with our system admin, I still do not see the
>> cuda_parallel target, just serial, parallel and cuda. So we probably don't
>> have the latest sources? In any case, here are the logs for the serial and
>> mpi versions of amber. I've made sure to patch and also clean up before
>> running their respective make target.
>>
>> I'll keep you posted on the cuda and cuda_parallel builds for SDK 4.0 (and
>> 3.2).
>>
>> Thanks,
>> Paul
>>
>>
>>
>> --
>> Paul Rigor
>> http://www.ics.uci.edu/~prigor
>>
>>
>>
>> On Wed, May 25, 2011 at 4:18 PM, Ross Walker <ross.rosswalker.co.uk>wrote:
>>
>>> > > Yes it does. Line 45 of $AMBERHOME/src/Makefile
>>> > >
>>> > > cuda_parallel: configured_cuda configured_parallel clean $(NETCDFLIB)
>>> > > .echo "Starting installation of ${AMBER} (cuda parallel) at
>>> > `date`".
>>> > > cd pmemd && $(MAKE) cuda_parallel
>>> > >
>>> > > Something smells fishy with your copy of AMBER 11 to me if it is
>>> > missing
>>> > > this.
>>> > >
>>> >
>>> > Could be unpatched. I don't think we had cuda_parallel at Amber11
>>> > release, right?
>>>
>>> But how would he get any parallel version compiled??? - Or maybe it is
>>> just
>>> the serial version linked with MPI. Ugh...
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
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Received on Wed May 25 2011 - 19:30:03 PDT
