Re: [AMBER] problems installing pmedm.cuda

From: Peter Fojan <fp.nano.aau.dk>
Date: Thu, 26 Apr 2012 14:19:37 +0000

Hi Jason,
I just added the CUDA_HOME to the library path as you suggested and it stopped with exactly the same error message at the same point of the installation.
Best,
    Peter
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: 26. april 2012 15:52
To: AMBER Mailing List
Subject: Re: [AMBER] problems installing pmedm.cuda

On Thu, Apr 26, 2012 at 8:58 AM, Jason Swails <jason.swails.gmail.com>wrote:

> Is CUDA_HOME in your LD_LIBRARY_PATH? If not, try adding it.
>

That's CUDA_HOME/lib, sorry

so something like this:

export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH


>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Apr 26, 2012, at 3:39 AM, Peter Fojan <fp.nano.aau.dk> wrote:
>
> > Hi all,
> > I am trying to install pmemd.cuda on my system. I have the latest
> devdriver and cudatoolkit 4.0 installed on my system and the gnu
> compiler
> 4.4.5
> > configure -cuda gnu
> > runs without error
> > make install stops everytime at the same point.
> > Starting installation of Amber12 (cuda) at Thu Apr 26 10:27:05 CEST 2012.
> > cd pmemd && make cuda
> > make[2]: Entering directory `/usr/local/amber12/src/pmemd'
> > make -C src/ cuda
> > make[3]: Entering directory `/usr/local/amber12/src/pmemd/src'
> > make -C ./cuda
> > make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda'
> > make[4]: `cuda.a' is up to date.
> > make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda'
> > make -C ./cuda
> > make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda'
> > make[4]: `cuda.a' is up to date.
> > make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda'
> > make -C ./cuda
> > make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda'
> > make[4]: `cuda.a' is up to date.
> > make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda'
> > make -C ./cuda
> > make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda'
> > make[4]: `cuda.a' is up to date.
> > make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda'
> > make -C ./cuda
> > make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda'
> > make[4]: `cuda.a' is up to date.
> > make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda'
> > gfortran -O3 -mtune=native -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 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 \
> > -L/usr/local/cuda/lib64 -L/usr/local/cuda/lib -lcurand -lcufft
> -lcudart ./cuda/cuda.a -L/usr/local/amber12/lib
> -L/usr/local/amber12/lib -lnetcdf
> > /usr/bin/ld: ./cuda/cuda.a(gpu.o): undefined reference to symbol
> > 'vtable
> for __cxxabiv1::__class_type_info..CXXABI_1.3'
> > /usr/bin/ld: note: 'vtable for __cxxabiv1::__class_type_info..CXXABI_1.3'
> is defined in DSO /usr/lib64/libstdc++.so.6 so try adding it to the
> linker command line
> > /usr/lib64/libstdc++.so.6: could not read symbols: Invalid operation
> > collect2: ld returned 1 exit status
> > make[3]: *** [pmemd.cuda] Error 1
> > make[3]: Leaving directory `/usr/local/amber12/src/pmemd/src'
> > make[2]: *** [cuda] Error 2
> > make[2]: Leaving directory `/usr/local/amber12/src/pmemd'
> > make[1]: *** [cuda] Error 2
> > make[1]: Leaving directory `/usr/local/amber12/src'
> > make: *** [install] Error 2
> >
> > Can anybody give me an advice how to solve this ?
> > best regards,
> > Peter
> >
> >
> > ''~''
> > ( o o )
> > +-------------------------oooO--(_)--Oooo---------------------------
> > +-+
> > Peter Fojan, PhD Tel. 0045/9940 7491
> > Associate Professor email: fp.nano.aau.dk
> <mailto:fp.nano.aau.dk>
> > Molecular Engineering Group web: www.nano.aau.dk<
> http://www.nano.aau.dk>
> > <SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New';
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> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
>



--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 26 2012 - 07:30:06 PDT
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