I was able to do it following these instructions:
http://jswails.wikidot.com/installing-amber11-and-ambertools-1-5
Can you try those?
HTH,
Jason
On Tue, Sep 24, 2013 at 3:19 PM, harry mangalam <harry.mangalam.uci.edu>wrote:
> Hi All,
>
> I'm trying to compile amber11 for a faculty member.
>
> The environment is 64b CentOS 6.4 with the following environment modules
> loaded:
>
> Currently Loaded Modulefiles:
> 1) gmp/5.0.5 3) mpfr/3.1.1 5) gcc/4.7.2
> 2) mpc/1.0.1 4) binutils/2.23.1 6) netcdf/4.2.1.1-share-gcc
>
> My AMBERHOME is set to /data/apps/amber/amber11
>
> I've been given the amber11 and AmberTools tarballs and have patched them
> according to this page: <http://ambermd.org/bugfixes11.html>
>
> This patching succeeds on most patches; but some fail:
>
> Tue Sep 24 12:08:46 [0.24 0.27 0.59] root.hpc-s:/data/apps/amber/amber11
> 1263 $ find . -name \*.rej
> ./src/pmemd/src/cuda/kCCF.h.rej
> ./src/pmemd/src/cuda/gpu.cpp.rej
> ./src/pmemd/src/cuda/gputypes.h.rej
> ./src/pmemd/src/cuda/kBNL.h.rej
> ./src/pmemd/src/cuda/cuda_info.fpp.rej
> ./src/pmemd/src/cuda/gputypes.cpp.rej
> ./src/pmemd/src/cuda/kShake.cu.rej
> ./src/pmemd/src/cuda/kNeighborList.cu.rej
> ./src/pmemd/src/pairs_calc_vec.i.rej
> ./src/pmemd/src/master_setup.fpp.rej
> ./src/pmemd/src/runfiles.fpp.rej
> ./src/pmemd/src/extra_pnts_nb14.fpp.rej
> ./src/pmemd/src/gb_ene.fpp.rej
> ./src/pmemd/src/pairs_calc_novec.i.rej
> ./src/sander/egb.f.rej
> ./src/sander/extra_pts.f.rej
> ./src/sander/nonbond_list.f.rej
> ./src/sander/short_ene.f.rej
> ./AmberTools/src/configure.rej
>
> None of these is in the $AMBERHOME/AmberTools/src/pbsa dir
>
> I've tried to compile the AmberTools as described and with a little
> munging of
> paths, replacing of archaic libtools, and interjecting of other libs (ie.
> our
> local netcdf module) have managed to compile it to ~ the same point
> described
> here: <http://archive.ambermd.org/201111/0442.html>
>
> My compilation ends like:
> Tue Sep 24 12:07:19 [0.18 0.27 0.62] root.hpc-
> s:/data/apps/amber/amber11/AmberTools/src/pbsa
> 1261 $ make
> cpp -traditional -P -DBINTRAJ amg1r5.f > _amg1r5.f
> gfortran -c -O3 -mtune=generic -ffree-form -o amg1r5.o _amg1r5.f
> _amg1r5.f:1203.16:
>
> ifg,a(jtrst),time,ndjtr,ium,mdjtr)
> 1
> Warning: Type mismatch in argument 'jtr' at (1); passed REAL(8) to
> INTEGER(4)
> _amg1r5.f:1216.58:
>
> call pcol(k-1,ierr,ia,ja,iw,imin,imax,imaxw,icg,ifg,u(irst), &
> 1
> Warning: Type mismatch in argument 'ir' at (1); passed REAL(8) to
> INTEGER(4)
> _amg1r5.f:1223.26:
>
> imaxw,ifg,icg,u(irst),time,ierr,irow0,ncolx, &
> 1
> Warning: Type mismatch in argument 'ncolor' at (1); passed REAL(8) to
> INTEGER(4)
> _amg1r5.f:1231.16:
>
> ifg,u(irst),nstcol,ncolx,time,nda,ndja,ium, &
> 1
> Warning: Type mismatch in argument 'ncolor' at (1); passed REAL(8) to
> INTEGER(4)
> _amg1r5.f:3460.23:
>
> external idec,random
> 1
> Error: Return type mismatch of function 'random' at (1) (REAL(8)/REAL(4))
> _amg1r5.f:3028.45:
>
> ja(jlo),a(jlo),f(ilo),u(ilo),nsp,a(jhi+1),a(jhi+1), &
> 1
> Warning: Type mismatch in argument 'isp' at (1); passed REAL(8) to
> INTEGER(4)
> _amg1r5.f:3094.45:
>
> ja(jlo),a(jlo),f(ilo),u(ilo),nsp,a(jhi+1),a(jhi+1), &
> 1
> Warning: Type mismatch in argument 'isp' at (1); passed REAL(8) to
> INTEGER(4)
> _amg1r5.f:3618.17:
>
> external cgalf,cgeps,ctime
> 1
> Error: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4))
> _amg1r5.f:3618.23:
>
> external cgalf,cgeps,ctime
> 1
> Error: Return type mismatch of function 'cgeps' at (1) (REAL(8)/REAL(4))
> make: *** [amg1r5.o] Error 1
>
> The followup AMBER list posting suggests applying the patches to the source
> tree, but I've already done this tho without perfect success.
>
> So, is there an easy fix that I can apply via edit, or is there a
> completely
> patched source code tree that I can D/L to try compile. Also, we have
> most of
> the AmberTools libs already installed; is there an easy way to ignore the
> AmberTools tree and use our own libs?
>
> Also, I see that amber12 is also available. The faculty is licensed for
> amber11, but does amber12 require another fee?
>
> Thanks in advance
> Harry
>
> ---
> Harry Mangalam - Research Computing, OIT, Rm 225 MSTB, UC Irvine
> [m/c 2225] / 92697 Google Voice Multiplexer: (949) 478-4487
> 415 South Circle View Dr, Irvine, CA, 92697 [shipping]
> MSTB Lat/Long: (33.642025,-117.844414) (paste into Google Maps)
> ---
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 24 2013 - 17:00:03 PDT
