Thank yo...
After adding PMEMD_FLIBSF variable, the compilation was completed.
On Wed, Jul 30, 2014 at 5:56 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, 2014-07-30 at 16:48 +0530, Saikat Dutta chowdhury wrote:
>
> >
> > *make[4]: Leaving directory
> > `/home/saikat/amber12/src/pmemd/src/cuda'gfortran -O3 -mtune=native
> > -DCUDA -Duse_SPFP -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 gbsa.o \ ./cuda/cuda.a
> > -L/usr/local/cuda-5.5/lib64 -L/usr/local/cuda-5.5/lib -lcurand -lcufft
> > -lcudart -L/home/saikat/amber12/lib /home/saikat/amber12/lib/libnetcdf.a
> > /usr/bin/ld: ./cuda/cuda.a(gpu.o): undefined reference to symbol
> 'operator
> > new[](unsigned long)..GLIBCXX_3.4'/usr/bin/ld: note: 'operator
> > new[](unsigned long)..GLIBCXX_3.4' is defined in DSO
> > /usr/lib/x86_64-linux-gnu/libstdc++.so.6 so try adding it to the linker
> > command line
>
> This right here gives you the key hint to solving the problem. The
> Fortran compiler is used to link pmemd.cuda (the command that fails
> starts with 'gfortran'), and in this case the C++ standard library is
> not added to the list of 'default' libraries that are linked (as it
> would be if the C++ compiler was used as the linker instead).
>
> The solution is to explicitly link libstdc++ on the link line. So edit
> $AMBERHOME/config.h and add -lstdc++ to the PMEMD_FLIBSF variable
> (toward the bottom). Then run "make install" again (no need to make
> clean -- it should finish very quickly).
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
9681144106
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Received on Thu Jul 31 2014 - 23:30:02 PDT
