Make sure all bug fixes are applied. If this is the recent patch
bugfix.1to17.tar.bz2, then you also need to fully patch AmberTools 1.5 (the
Amber 11 patch should print out a message to that extent). There were
changes to configure necessary to the new pmemd.cuda patch.
HTH,
Jason
On Tue, Aug 23, 2011 at 3:15 PM, Dmitry Mukha <dvmukha.gmail.com> wrote:
> Another error during compilation, now on Fedora 14 (and, perhaps, later).
> It
> concerns pmemd.cuda. gcc 4.5.1, GNU ld version 2.20.51.0.7-8.fc14 20100318
>
> make[3]: Entering directory `/opt/amber11/src/pmemd/src/cuda'
> make[3]: `cuda.a' is up to date.
> make[3]: Leaving directory `/opt/amber11/src/pmemd/src/cuda'
> gfortran -O3 -mtune=generic -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/opt/cuda/lib64
> -L/opt/cuda/lib -L/usr/lib64 -lcurand -lcufft -lcudart ./cuda/cuda.a
> /opt/amber11/lib/libnetcdf.a
> /usr/bin/ld: ./cuda/cuda.a(kNLRadixSort.o): undefined reference to symbol
> '__cxa_pure_virtual..CXXABI_1.3'
> /usr/bin/ld: note: '__cxa_pure_virtual..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[2]: *** [pmemd.cuda] Error 1
> make[2]: Leaving directory `/opt/amber11/src/pmemd/src'
> make[1]: *** [cuda] Error 2
> make[1]: Leaving directory `/opt/amber11/src/pmemd'
> make: *** [cuda] Error 2
>
> The solution was (applying after the configuration with -cuda flag)
> uname -a | grep 'fc14.x86_64' >/dev/null 2>&1
> if [ $? -eq 0 ]; then
> echo
> echo DM PATCH2 on a11
> echo -n "Patching $AMBERHOME/src/config.h "
> sed -i 's[PMEMD_CU_LIBS=-L$(CUDA_HOME)/lib64
> -L$(CUDA_HOME)/lib[PMEMD_CU_LIBS=-L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib
> -L/usr/lib64 -lstdc++[' $AMBERHOME/src/config.h
> echo
> fi
>
> --
> Sincerely,
> Dmitry Mukha
> Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
> _______________________________________________
> 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
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Received on Tue Aug 23 2011 - 15:00:03 PDT
