[gmx-users] Error during PUMED installation for GROMACS-4.5.3

[andrea spitaleri]

Hi Bipin,
please refer to the plumed mailing list. The error below means that you have already patched the 
gromacs source. are you trying to recompile? have you followed the guidelines in the plumed manual?

hope it helps

and

On 03/03/2011 08:38 AM, bipin singh wrote:
> Hello,
> I am getting following error while installing PLUMED for gromacs
> Please suggest if someone has succesfully installed PLUMED on GROMACS-4.5.3.
> The error is as below:
> -----------------------------------------------------------------------------------------------
> root at bipin-OptiPlex-330:/usr/local/gromacs# ./plumedpatch_gromacs_4.5.1.sh
> <http://plumedpatch_gromacs_4.5.1.sh> -patch
> * I will try to patch PLUMED version 1.2.2 ...
> -- Executing pre script
> -- Setting up symlinks
> ln: creating symbolic link `./src/kernel//metadyn.h': File exists
> ln: creating symbolic link `./src/kernel//biasexchange.c': File exists
> ln: creating symbolic link `./src/kernel//hills.c': File exists
> ln: creating symbolic link `./src/kernel//metadyn.c': File exists
> ln: creating symbolic link `./src/kernel//ptmetad.c': File exists
> ln: creating symbolic link `./src/kernel//read_restraint.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_alfabeta.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_alpharmsd.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_angle.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_antibetarmsd.c': File exists
> ln: creating symbolic link `./src/kernel//restraint.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_coord.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_dihcor.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_dipole.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_dist.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_elstpot.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_energy.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_hbonds.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_helix.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_mindist.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_parabetarmsd.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_position.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_puckering.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_rgyr.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_rmsdtor.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_spath.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_torsion.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_waterbridge.c': File exists
> ln: creating symbolic link `./src/kernel//restraint_zpath.c': File exists
> ln: creating symbolic link `./src/kernel//testderivatives.c': File exists
> -- Applying patches
> patching file ./src/kernel/md.c
> Hunk #1 succeeded at 86 with fuzz 3 (offset -1 lines).
> Hunk #2 succeeded at 1514 with fuzz 3 (offset -2 lines).
> Hunk #3 FAILED at 1928.
> 1 out of 3 hunks FAILED -- saving rejects to file ./src/kernel/md.c.rej
> patching file ./src/kernel/mdrun.c
> Hunk #1 succeeded at 55 with fuzz 3 (offset -1 lines).
> Hunk #2 FAILED at 373.
> Hunk #3 succeeded at 632 with fuzz 3 (offset -2 lines).
> 1 out of 3 hunks FAILED -- saving rejects to file ./src/kernel/mdrun.c.rej
> patching file ./src/kernel/repl_ex.c
> Hunk #1 succeeded at 51 with fuzz 3.
> Hunk #2 FAILED at 84.
> Hunk #3 FAILED at 154.
> Hunk #4 succeeded at 214 with fuzz 3 (offset -1 lines).
> Hunk #5 succeeded at 229 with fuzz 3 (offset -2 lines).
> Hunk #6 succeeded at 523 with fuzz 3 (offset -3 lines).
> Hunk #7 succeeded at 551 with fuzz 3 (offset -4 lines).
> Hunk #8 FAILED at 585.
> Hunk #9 FAILED at 638.
> Hunk #10 FAILED at 679.
> Hunk #11 succeeded at 771 with fuzz 3 (offset -5 lines).
> 5 out of 11 hunks FAILED -- saving rejects to file ./src/kernel/repl_ex.c.rej
> patching file ./src/kernel/Makefile
> Hunk #1 succeeded at 9 with fuzz 3 (offset -10 lines).
> Hunk #2 FAILED at 138.
> Hunk #3 FAILED at 160.
> Hunk #4 FAILED at 362.
> Hunk #5 FAILED at 379.
> Hunk #6 succeeded at 522 with fuzz 3 (offset -11 lines).
> Hunk #7 succeeded at 582 with fuzz 3 (offset -12 lines).
> Hunk #8 succeeded at 605 with fuzz 3 (offset -13 lines).
> 4 out of 8 hunks FAILED -- saving rejects to file ./src/kernel/Makefile.rej
> patching file ./src/kernel/repl_ex.h
> Hunk #1 succeeded at 68 with fuzz 3 (offset -1 lines).
> -- Executing post script
> touch: cannot touch `./src/kernel//.deps/biasexchange.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/hills.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/metadyn.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/ptmetad.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/read_restraint.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_alfabeta.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_alpharmsd.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_angle.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_antibetarmsd.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_coord.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_dihcor.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_dipole.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_dist.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_elstpot.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_energy.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_hbonds.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_helix.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_mindist.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_parabetarmsd.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_position.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_puckering.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_rgyr.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_rmsdtor.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_spath.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_torsion.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_waterbridge.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/restraint_zpath.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/testderivatives.Po': No such file or directory
> touch: cannot touch `./src/kernel//.deps/*.Po': No such file or directory
> - DONE!
>
>
> --
> /
> ---------------------------------
> Thanks and regards
> /Bipin Singh/
> /
> /
> /
>

-- 
-------------------------------------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute c/o Raffaele Scientific Institute
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olgettina 58
20132 Milano
Italy
Tel: 0039-0226434348
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
http://www.linkedin.com/in/andreaspitaleri
-------------------------------------------------------------

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