Dear Amber users:
I have a problem during amber 11 + ambertools 1.4 compilation (with gnu
- gcc-4.4.5) with cuda3.2 on a Tesla c2070 (Fedora 13) . Problem comes
after "make cuda" in /opt/amber11/src
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/usr/local/cuda/lib64
-L/usr/local/cuda/lib -lcufft -lcudart ./cuda/cuda.a
../../netcdf/lib/libnetcdf.a
/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[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
I understand that maybe the problem is in the symbolic link to
/usr/lib64/libstdc++.so.6
Can you help me with this problem, please?
Thank you in advance
Fernando
--
==============================================
FERNANDO MARTIN GARCIA
GRUPO DE MODELADO MOLECULAR - LAB 312.1
CENTRO DE BIOLOGíA MOLECULAR SEVERO OCHOA
C/ NICOLáS CABRERA, 1.
CAMPUS UAM. CANTOBLANCO, 28049 MADRID. SPAIN.
TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
=============================================
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Received on Tue Jul 19 2011 - 02:30:02 PDT
