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>
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Received on Thu Apr 26 2012 - 01:00:04 PDT
