[AMBER] HELP Needed: AMBER12 cuda compilation ERROR

From: Saikat Dutta chowdhury <pbr322.dutta.gmail.com>
Date: Wed, 30 Jul 2014 16:48:19 +0530

Hi Amber users,
Recently we have acquired a K20 NVIDIA GPU to use it with Amber12.

We have Ubuntu12.04 istalled in our machine. After installing the hardware
we compiled the CUDA5.5 there. Then we set the CUDA_HOME path in our
.bashrc file.

Then we extracted the Amber12 and AmberTools using following commands:

*tar jxvf Amber12.tar.bz2tar jxvf AmberTools13.tar.bz2*

after changing the directory to amber12 we ran the following command:

*./configure -cuda gnu*

All the patches were accepted and configured.
Then we executed this command:

*make install*

After some time this exited with the following errors:

*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/usr/lib/x86_64-linux-gnu/libstdc++.so.6: could not read
symbols: Invalid operationcollect2: ld returned 1 exit statusmake[3]: ***
[pmemd.cuda] Error 1make[3]: Leaving directory
`/home/saikat/amber12/src/pmemd/src'make[2]: *** [cuda] Error 2make[2]:
Leaving directory `/home/saikat/amber12/src/pmemd'make[1]: *** [cuda] Error
2make[1]: Leaving directory `/home/saikat/amber12/src'make: *** [install]
Error 2*

It would be very help if anyone can point out what is problem and how
should I rectify this issue.

Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
AMBER mailing list
Received on Wed Jul 30 2014 - 04:30:02 PDT
Custom Search