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-- 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'; mso-fareast-font-family: 'Times New Roman'; mso-fareast-theme-font: > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Apr 26 2012 - 06:00:04 PDT