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
_______________________________________________
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Received on Fri Jan 20 2012 - 10:30:02 PST
