[AMBER] Cuda compilation problem

From: Fernando Martín García <fmgarcia.cbm.uam.es>
Date: Mon, 18 Jul 2011 11:14:35 +0200

 Dear Amber users:

 I have a problem during amber 11 + ambertools 1.4 compilation (with
 gnu) 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 Mon Jul 18 2011 - 02:30:04 PDT
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