Jason,
Thanks for the clarification on setting CUDA_HOME (I did list it in my
email, but it was a big sloppy mess, you I can see how you missed it).
So here's my new environment settings:
root.NEI-GPU:/usr/local/src/amber12# echo $CUDA_HOME
/usr/local/cuda
root.NEI-GPU:/usr/local/src/amber12# echo $LD_LIBRARY_PATH
/usr/local/src/amber12/lib:/usr/local/src/amber12/lib64:/usr/local/cuda/lib:/usr/local/cuda/lib64
My default gcc was v4.7, so I had to re-route the gcc softlink to
v4.6, which I guess makes sense, since I had CUDA_HOME pointed towards
nvidia-cuda-toolkit before. This time I can't compile PMEMD
successfully, ironically with the same error as the 'make test' I
reported on in my original email:
Starting installation of Amber12 (cuda parallel) at Wed May 8
21:35:42 EDT 2013
.
cd pmemd && make cuda_parallel
make[2]: Entering directory `/usr/local/src/amber12/src/pmemd'
make -C src/ cuda_parallel
make[3]: Entering directory `/usr/local/src/amber12/src/pmemd/src'
make -C ./cuda
make[4]: Entering directory `/usr/local/src/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/src/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/usr/local/src/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/src/amber12/src/pmemd/src/cuda'
mpif90 -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
-Duse_SPFP -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
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 gbsa.o \
./cuda/cuda.a -L/usr/local/cuda/lib64 -L/usr/local/cuda/lib
-lcurand -lcufft -lcudart -L/usr/local/src/amber12/lib
-L/usr/local/src/amber12/lib -lnetcdf
./cuda/cuda.a(kCalculateGBBornRadii.o): In function `cudaError
cudaFuncSetShared
MemConfig<void ()>(void (*)(), cudaSharedMemConfig)':
tmpxft_00001f62_00000000-6_kCalculateGBBornRadii.compute_30.cudafe1.cpp:(.text._
Z26cudaFuncSetSharedMemConfigIFvvEE9cudaErrorPT_19cudaSharedMemConfig[cudaError
cudaFuncSetSharedMemConfig<void ()>(void (*)(),
cudaSharedMemConfig)]+0x1c): undefined reference to
`cudaFuncSetSharedMemConfig'
collect2: ld returned 1 exit status
make[3]: *** [pmemd.cuda.MPI] Error 1
make[3]: Leaving directory `/usr/local/src/amber12/src/pmemd/src'
make[2]: *** [cuda_parallel] Error 2
make[2]: Leaving directory `/usr/local/src/amber12/src/pmemd'
make[1]: *** [cuda_parallel] Error 2
make[1]: Leaving directory `/usr/local/src/amber12/src'
make: *** [install] Error 2
I would consider starting over from scratch (serial --> parallel -->
parallel-cuda), but I don't see how that is the issue right now.
Again, thanks for the initial quick reply, if you have more ideas,
that's great.
Blake
On Wed, May 8, 2013 at 3:19 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Do you have CUDA_HOME set? You need to have this set to build Amber, so if
> it's not set anymore, re-set it to the value it had when you compiled.
>
> Then try adding CUDA_HOME/lib and $CUDA_HOME/lib64 to your LD_LIBRARY_PATH:
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib:$CUDA_HOME/lib64
>
> This should hopefully allow the shared library with the
> cudaFuncSetSharedMemConfig
> symbol to be located at runtime.
>
> Good luck,
> Jason
>
>
> On Wed, May 8, 2013 at 2:32 PM, Blake Mertz <mertzjb.gmail.com> wrote:
>
>> Hello,
>>
>> I've been following Jason Swails' blog post on compiling Amber12 and
>> AmberTools12 (thanks, by the way), and can get serial, parallel, and
>> parallel with cuda versions of PMEMD compiled on my workstation
>> equipped with two GPUs, using both openmpi (v1.4) and mpich2. "make
>> test" runs successfully for both the serial and parallel versions of
>> PMEMD, but when I run make test for the cuda-based version of PMEMD, I
>> get the following error message for each test:
>>
>> cd nmropt/pme/distance/ && ./Run.dist_pbc SPFP
>> /usr/local/src/amber12/include/netcdf.mod
>> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
>> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
>> cudaFuncSetSharedMemConfig
>> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
>> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
>> cudaFuncSetSharedMemConfig
>> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
>> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
>> cudaFuncSetSharedMemConfig
>> ./Run.dist_pbc: Program error
>> make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
>> cd nmropt/pme/nmropt_1_torsion/ && ./Run.nmropt_1_torsion SPFP
>> /usr/local/src/amber12/include/netcdf.mod
>> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
>> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
>> cudaFuncSetSharedMemConfig
>> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
>> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
>> cudaFuncSetSharedMemConfig
>> ./Run.nmropt_1_torsion: Program error
>> make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
>>
>> I've searched for the symbol 'cudaFuncSetSharedMemConfig' without much
>> luck -- no occurrences on the amber mailing list, and very few from a
>> google search. The only reference I could find was for someone using
>> openmpi v1.6, which I don't think applies to this particular
>> situation, since I got the same error with openmpi and mpich-based
>> PMEMD codes. Here is the relevant information with the steps and
>> environment variables I used:
>>
>> - Debian v7
>> - CUDA libraries and toolkit installed from Debian repositories,
>> version 4.2.9-2, nvidia driver 304.88
>> - openmpi v.1.4.5-1 and mpich2 v1.4.1-4.2
>>
>> root.NEI-GPU:/usr/local/src/amber12# echo $CUDA_HOME
>> /usr/lib/nvidia-cuda-toolkit
>>
>> root.NEI-GPU:/usr/local/src/amber12# echo $LD_LIBRARY_PATH
>>
>> /usr/lib:/usr/lib/mpich2/lib:/usr/local/src/amber12/lib:/usr/local/cuda/lib:/usr/local/cuda/lib64
>>
>> root.NEI-GPU:/usr/local/src/amber12# echo $AMBERHOME
>> /usr/local/src/amber12
>>
>> root.NEI-GPU:/usr/local/src/amber12# mpif90 -show
>> gfortran -Wl,-z,relro -I/usr/include/mpich2 -I/usr/include/mpich2
>> -L/usr/lib -lmpichf90 -lmpichf90 -lmpich -lopa -lmpl -lrt -lcr
>> -lpthread
>>
>> root.NEI-GPU:/usr/local/src/amber12# mpicc -show
>> gcc -D_FORTIFY_SOURCE=2 -Wl,-z,relro -I/usr/include/mpich2 -L/usr/lib
>> -lmpich -lopa -lmpl -lrt -lcr -lpthread
>>
>> To get the openmpi-based version of cuda PMEMD to compile, I had to
>> add the -lmpi_cxx flag to PMEMD_CU_LIBS line in config.h, as per Tru
>> Huynh's suggestion on the amber mailing list:
>>
>> http://archive.ambermd.org/201210/0097.html
>>
>> I've been banging on this for a few days now, and thought I had it
>> licked after successfully compiling the cuda-based PMEMD, but I'm
>> definitely stuck on getting these tests to pass. Any help would be
>> awesome. Thanks!
>>
>> Blake
>>
>> _______________________________________________
>> 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
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Received on Wed May 08 2013 - 19:00:02 PDT
