AMBER Archive (2007)

Subject: Re: AMBER: Troubles installing amber

From: Wei Zhang (zweig_at_scripps.edu)
Date: Fri Dec 07 2007 - 13:54:47 CST

Hi,

    You need install yacc by yourself, it is required to compile xleap.

    I have no experience with centos so I can not give you advise about
installing yacc. usually you can find the package from the original CD

    Sincerely,

    Wei

Margaret Doll wrote:
> I have an SGI cluster running Centos 2.6.9-42 and Rocks 4.2.1. I am
> not interested in installing the software to run in parallel on the
> cluster.
>
>
> I untarred the amber9 files into /state/partition1/apps/amber9
> I copied the bugfix.all files off the web pages to
> /state/partition1/apps/amber9/amberpatches
>
> patch -p0 -N -r patch_rejects < amberpatches
>
> I was required to provide a name of the file to be modified for
> line 18066 in amberpatches.
>
> I provided /state/partition1/apps/amber9/src/sander/runmd.f
>
> The results of the patch replacements were
> more patch_rejects
> ***************
> *** 814,820 ****
> iprint = 0
> if( nstep == 0 .or. nstep+1 == nstlim ) iprint = 1
> ! TIME_force is started and stopped inside force
> !
> call force(xx,ix,ih,ipairs,x,f,ener(23),vir, &
> xx(l96),xx(l97),xx(l98),xx(l99), qsetup,qpsander, &
> do_list_update)
> --- 814,825 ----
> iprint = 0
> if( nstep == 0 .or. nstep+1 == nstlim ) iprint = 1
> ! TIME_force is started and stopped inside force
> ! #ifdef MPI
> ! if( initremd ) then
> ! irespa = 0
> ! end if
> ! #endif
> !
> call force(xx,ix,ih,ipairs,x,f,ener(23),vir, &
> xx(l96),xx(l97),xx(l98),xx(l99), qsetup,qpsander, &
> do_list_update)
>
>
> export AMBERHOME=/state/partition1/apps/amber9
> cd src
> ./configure pgf90
> make serial
>
> pdbFile.c: In function `writeTER':
> pdbFile.c:1761: warning: initialization from incompatible pointer type
> gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -O2 -m32 -o tools.o tools.c
> tools.c: In function `iToolDistanceSearch':
> tools.c:1643: warning: passing arg 1 of `SortByDouble' from
> incompatible pointer type
> tools.c:1643: warning: passing arg 4 of `SortByDouble' from
> incompatible pointer type
> tools.c: In function `ToolOrientPrincipleAxisAlongCoordinateAxis':
> tools.c:1714: warning: passing arg 2 of `MathOpDiagonalize' from
> incompatible pointer typegcc -c -I/usr/X11R6/include
> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m32 -o variables.o
> variables.c
> yacc parser.y
> make[2]: yacc: Command not found
> make[2]: *** [parser.c] Error 127
> make[2]: Leaving directory
> `/state/partition1/apps/amber9/src/leap/src/leap'
> make[1]: *** [install] Error 2
> make[1]: Leaving directory `/state/partition1/apps/amber9/src/leap'
> make: *** [serial] Error 2
>
>
> make test.serial fails with
> ptraj: test ptraj on averaging les trajectory to normal trajectory
> diffing hef_averaged.crd.save with hef_averaged.crd
> PASSED
> ==============================================================
> cd leap; ./Run.tleap
> Error: ./tleap -> ../../exe/teLeap does not exist
> make: *** [test.leap] Error 1
>
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