How about the one in $AMBERHOME/src? That's the one I really need.
On Fri, Jan 20, 2012 at 1:17 PM, Massimiliano Porrini <M.Porrini.ed.ac.uk>wrote:
> Thanks for replying Jason.
>
> Attached you can find the config.h file created with
>
> ./configure -cuda gnu
>
> in $AMBERHOME/AmberTools/src/ .
>
> Cheers,
>
>
> Il 20 gennaio 2012 14:20, Jason Swails <jason.swails.gmail.com> ha
> scritto:
> > The NetCDF library is not being linked in from what I can tell. You
> should
> > see something like "/home/max/amber11/lib/libnetcdf.a" in that last link
> > line. Can you post your config.h here so I can see what's happening?
> >
> > Thanks,
> > Jason
> >
> > On Fri, Jan 20, 2012 at 8:52 AM, Massimiliano Porrini <
> M.Porrini.ed.ac.uk>wrote:
> >
> >> Thank you Jason, now all the Amber11 tests passed (both serial and
> >> parallel).
> >>
> >> But now I have troubles in compiling the cuda version of pmemd.
> >>
> >> After successfully creating the config.h file, I tried to compile
> >> the cuda serial version:
> >>
> >> make cuda
> >>
> >> but I got the following errors (I post only the last
> >> bit of what appeared on the monitor during the compilation):
> >>
> >>
> >>
> >>
> ##############################################################################
> >> make[3]: Entering directory `/home/max/amber11/src/pmemd/src/cuda'
> >> make[3]: `cuda.a' is up to date.
> >> make[3]: Leaving directory `/home/max/amber11/src/pmemd/src/cuda'
> >> 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
> >> bintraj.o: In function `__bintraj_mod_MOD_checkerror':
> >> bintraj.f90:(.text+0xc3): undefined reference to
> >> `__netcdf_MOD_nf90_strerror'
> >> bintraj.o: In function `__bintraj_mod_MOD_open_binary_files':
> >> bintraj.f90:(.text+0x1e2): undefined reference to
> >> `__netcdf_MOD_nf90_create'
> >> bintraj.f90:(.text+0x23b): undefined reference to
> >> `__netcdf_MOD_nf90_def_dim'
> >> bintraj.f90:(.text+0x275): undefined reference to
> >> `__netcdf_MOD_nf90_def_dim'
> >> bintraj.f90:(.text+0x2af): undefined reference to
> >> `__netcdf_MOD_nf90_def_dim'
> >> bintraj.f90:(.text+0x2e9): undefined reference to
> >> `__netcdf_MOD_nf90_def_dim'
> >> bintraj.f90:(.text+0x326): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x369): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x3ac): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x3ef): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x432): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.o:bintraj.f90:(.text+0x475): more undefined references to
> >> `__netcdf_MOD_nf90_put_att_text' follow
> >> bintraj.o: In function `__bintraj_mod_MOD_open_binary_files':
> >> bintraj.f90:(.text+0x512): undefined reference to
> >> `__netcdf_MOD_nf90_def_var_manydims'
> >> bintraj.f90:(.text+0x5ac): undefined reference to
> >> `__netcdf_MOD_nf90_def_var_manydims'
> >> bintraj.f90:(.text+0x5e9): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x6a5): undefined reference to
> >> `__netcdf_MOD_nf90_def_var_manydims'
> >> bintraj.f90:(.text+0x6e8): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x738): undefined reference to
> >> `__netcdf_MOD_nf90_def_dim'
> >> bintraj.f90:(.text+0x778): undefined reference to
> >> `__netcdf_MOD_nf90_def_dim'
> >> bintraj.f90:(.text+0x81a): undefined reference to
> >> `__netcdf_MOD_nf90_def_var_manydims'
> >> bintraj.f90:(.text+0x8ca): undefined reference to
> >> `__netcdf_MOD_nf90_def_var_manydims'
> >> bintraj.f90:(.text+0x978): undefined reference to
> >> `__netcdf_MOD_nf90_def_var_manydims'
> >> bintraj.f90:(.text+0x9bb): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0xa69): undefined reference to
> >> `__netcdf_MOD_nf90_def_var_manydims'
> >> bintraj.f90:(.text+0xaac): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0xaef): undefined reference to
> >> `__netcdf_MOD_nf90_set_fill'
> >> bintraj.f90:(.text+0xb20): undefined reference to
> >> `__netcdf_MOD_nf90_enddef'
> >> bintraj.f90:(.text+0xc6a): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_1d_text'
> >> bintraj.f90:(.text+0xdc7): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_1d_text'
> >> bintraj.f90:(.text+0xf2b): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_1d_text'
> >> bintraj.f90:(.text+0xf83): undefined reference to
> >> `__netcdf_MOD_nf90_create'
> >> bintraj.f90:(.text+0xfda): undefined reference to
> >> `__netcdf_MOD_nf90_def_dim'
> >> bintraj.f90:(.text+0x1014): undefined reference to
> >> `__netcdf_MOD_nf90_def_dim'
> >> bintraj.f90:(.text+0x104e): undefined reference to
> >> `__netcdf_MOD_nf90_def_dim'
> >> bintraj.f90:(.text+0x1088): undefined reference to
> >> `__netcdf_MOD_nf90_def_dim'
> >> bintraj.f90:(.text+0x10c5): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x1108): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x114b): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x118e): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x11d1): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.o:bintraj.f90:(.text+0x1214): more undefined references to
> >> `__netcdf_MOD_nf90_put_att_text' follow
> >> bintraj.o: In function `__bintraj_mod_MOD_open_binary_files':
> >> bintraj.f90:(.text+0x12b1): undefined reference to
> >> `__netcdf_MOD_nf90_def_var_manydims'
> >> bintraj.f90:(.text+0x134b): undefined reference to
> >> `__netcdf_MOD_nf90_def_var_manydims'
> >> bintraj.f90:(.text+0x1388): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x1444): undefined reference to
> >> `__netcdf_MOD_nf90_def_var_manydims'
> >> bintraj.f90:(.text+0x1487): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x14c4): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_one_fourbytereal'
> >> bintraj.f90:(.text+0x14f9): undefined reference to
> >> `__netcdf_MOD_nf90_set_fill'
> >> bintraj.f90:(.text+0x152a): undefined reference to
> >> `__netcdf_MOD_nf90_enddef'
> >> bintraj.f90:(.text+0x1674): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_1d_text'
> >> bintraj.f90:(.text+0x186a): undefined reference to
> >> `__netcdf_MOD_nf90_def_var_manydims'
> >> bintraj.f90:(.text+0x18ad): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_text'
> >> bintraj.f90:(.text+0x18ea): undefined reference to
> >> `__netcdf_MOD_nf90_put_att_one_fourbytereal'
> >> bintraj.o: In function `__bintraj_mod_MOD_close_binary_files':
> >> bintraj.f90:(.text+0x1934): undefined reference to
> >> `__netcdf_MOD_nf90_close'
> >> bintraj.f90:(.text+0x195c): undefined reference to
> >> `__netcdf_MOD_nf90_close'
> >> bintraj.o: In function
> `__bintraj_mod_MOD_write_binary_crds_axis_flipped':
> >> bintraj.f90:(.text+0x1b8c): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_2d_fourbytereal'
> >> bintraj.o: In function `__bintraj_mod_MOD_write_binary_crds':
> >> bintraj.f90:(.text+0x1d66): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_2d_eightbytereal'
> >> bintraj.o: In function
> `__bintraj_mod_MOD_write_binary_vels_axis_flipped':
> >> bintraj.f90:(.text+0x2019): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_2d_fourbytereal'
> >> bintraj.o: In function `__bintraj_mod_MOD_write_binary_vels':
> >> bintraj.f90:(.text+0x21a8): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_2d_eightbytereal'
> >> bintraj.o: In function `__bintraj_mod_MOD_write_binary_cell_dat':
> >> bintraj.f90:(.text+0x23c2): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
> >> bintraj.f90:(.text+0x2504): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
> >> bintraj.o: In function `__bintraj_mod_MOD_end_binary_frame':
> >> bintraj.f90:(.text+0x26ea): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
> >> bintraj.f90:(.text+0x2712): undefined reference to
> `__netcdf_MOD_nf90_sync'
> >> bintraj.f90:(.text+0x286a): undefined reference to
> >> `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
> >> bintraj.f90:(.text+0x2892): undefined reference to
> `__netcdf_MOD_nf90_sync'
> >> ./cuda/cuda.a(gpu.o): In function `gpu_amrset_':
> >> gpu.cpp:(.text+0xae8): undefined reference to `curandCreateGenerator'
> >> gpu.cpp:(.text+0xafe): undefined reference to
> >> `curandSetPseudoRandomGeneratorSeed'
> >> ./cuda/cuda.a(kForcesUpdate.o): In function `kRandom':
> >>
> >>
> tmpxft_000073e2_00000000-4_kForcesUpdate.compute_20.cudafe1.cpp:(.text+0x3d2d):
> >> undefined reference to `curandGenerateNormalDouble'
> >> collect2: ld returned 1 exit status
> >> make[2]: *** [pmemd.cuda] Error 1
> >> make[2]: Leaving directory `/home/max/amber11/src/pmemd/src'
> >> make[1]: *** [cuda] Error 2
> >> make[1]: Leaving directory `/home/max/amber11/src/pmemd'
> >> make: *** [cuda] Error 2
> >>
> >>
> ##############################################################################
> >>
> >>
> >> I would appreciate if you have any hint to get this issue sorted out.
> >>
> >> Best,
> >>
> >>
> >>
> >> Il 19 gennaio 2012 19:33, Jason Swails <jason.swails.gmail.com> ha
> >> scritto:
> >> > It sounds like the permissions where not preserved when the archive
> was
> >> > unpacked. Thus, every test script needs to be made executable as
> well.
> >> > Try these commands:
> >> >
> >> > cd $AMBERHOME/AmberTools/test
> >> > chmod +x `find . -name "Run*"` `find . -name "*.sh"`
> >> > cd $AMBERHOME/test
> >> > chmod +x `find . -name "Run*"` `find . -name "*.sh"`
> >> >
> >> > In the future, I would suggest using the "-p" or
> "--preserve-permissions"
> >> > flag when untarring an archive on that machine, since it seems like
> >> they're
> >> > not preserved by default for you.
> >> >
> >> > HTH,
> >> > Jason
> >> >
> >> > On Thu, Jan 19, 2012 at 2:20 PM, Massimiliano Porrini <
> >> M.Porrini.ed.ac.uk>wrote:
> >> >
> >> >> Thanks a lot for replying dac.
> >> >>
> >> >> I have just checked the availability of /bin/sh and I have it.
> >> >>
> >> >> Moreover I had already tried to change the permissions of that bash
> >> script
> >> >> as follows:
> >> >>
> >> >> chmod a+x test_amber_serial.sh
> >> >>
> >> >> and I get the following error(s):
> >> >>
> >> >> ###################################################################
> >> >> make[1]: Entering directory `/home/max/amber11/test'
> >> >> cd dmp && ./Run.dmp
> >> >> /bin/sh: ./Run.dmp: Permission denied
> >> >> make[1]: [test.sander.BASIC.nopar] Error 126 (ignored)
> >> >> cd adenine && ./Run.adenine
> >> >> /bin/sh: ./Run.adenine: Permission denied
> >> >> make[1]: [test.sander.BASIC.nopar] Error 126 (ignored)
> >> >> cd variable_14 && ./Run.variable_14_igb1
> >> >> /bin/sh: ./Run.variable_14_igb1: Permission denied
> >> >> ***
> >> >> ***
> >> >> ***
> >> >> make[1]: [test.serial.pmemd] Error 126 (ignored)
> >> >>
> >> >> Finished serial test suite for Amber 11 at Thu Jan 19 19:12:40 GMT
> 2012.
> >> >>
> >> >> make[1]: Target `test.serial' not remade because of errors.
> >> >> make[1]: Leaving directory `/home/max/amber11/test'
> >> >> 0 file comparisons passed
> >> >> 0 file comparisons failed
> >> >> 354 tests experienced errors
> >> >> ####################################################################
> >> >>
> >> >> which still seems related to a permissions matter.
> >> >>
> >> >> Even though I can not figure out why I have these problems, as I did
> not
> >> >> modify any permission of any file/directory and AT1.5 did not create
> >> >> any trouble.
> >> >>
> >> >> Best,
> >> >>
> >> >>
> >> >>
> >> >> Il 19 gennaio 2012 19:06, David A Case <case.biomaps.rutgers.edu> ha
> >> >> scritto:
> >> >> > On Thu, Jan 19, 2012, Massimiliano Porrini wrote:
> >> >> >
> >> >> >> ./test_amber_serial.sh
> >> >> >> make: execvp: ./test_amber_serial.sh: Permission denied
> >> >> >
> >> >> > Check the permissions on the file
> amber11/test/test_amber_serial.sh:
> >> it
> >> >> needs
> >> >> > to have execute permission. [It is theoretically possible that
> >> /bin/sh
> >> >> is
> >> >> > not available on your system, but that seems rather unlikely....]
> >> >> >
> >> >> > ....dac
> >> >> >
> >> >> >
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Dr Massimiliano Porrini
> >> >> Institute for Condensed Matter and Complex Systems
> >> >> School of Physics & Astronomy
> >> >> The University of Edinburgh
> >> >> James Clerk Maxwell Building
> >> >> The King's Buildings
> >> >> Mayfield Road
> >> >> Edinburgh EH9 3JZ
> >> >>
> >> >> Tel +44-(0)131-650-5229
> >> >>
> >> >> E-mails : M.Porrini.ed.ac.uk
> >> >> mozz76.gmail.com
> >> >> maxp.iesl.forth.gr
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Jason M. Swails
> >> > Quantum Theory Project,
> >> > University of Florida
> >> > Ph.D. Candidate
> >> > 352-392-4032
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> Dr Massimiliano Porrini
> >> Institute for Condensed Matter and Complex Systems
> >> School of Physics & Astronomy
> >> The University of Edinburgh
> >> James Clerk Maxwell Building
> >> The King's Buildings
> >> Mayfield Road
> >> Edinburgh EH9 3JZ
> >>
> >> Tel +44-(0)131-650-5229
> >>
> >> E-mails : M.Porrini.ed.ac.uk
> >> mozz76.gmail.com
> >> maxp.iesl.forth.gr
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini.ed.ac.uk
> mozz76.gmail.com
> maxp.iesl.forth.gr
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 20 2012 - 12:00:02 PST
