Re: [AMBER-Developers] AmberTools12.lyx now open, more...

From: Scott Brozell <>
Date: Fri, 22 Mar 2013 00:08:21 -0400


On Thu, Mar 21, 2013 at 04:38:57PM -0400, David A Case wrote:
> Aside: something seems to have broken all the Intel builds on the cruise
> control page. Seems to be recently changes to pmemd. I'm using a newer
> version of the Intel compilers, and don't get these errors, but if someone has
> easy access to the 11.1.069 compilers, you might see if the error logs match
> what you get, and make any sense.

intel-compilers-11.1.056 builds and tests fine for me
(except for some known failures - ORCA issue; ./rdc/gcg.dip.o.dif ).

However, I am probably not at the head of master:
%git pull
Updating c147f84..b185632
AmberTools/src/cpptraj/src/Action_Diffusion.cpp: needs update
AmberTools/src/cpptraj/src/Action_MakeStructure.cpp: needs update
AmberTools/src/cpptraj/src/Action_Rmsd.cpp: needs update
AmberTools/src/cpptraj/src/Action_SymmetricRmsd.cpp: needs update
AmberTools/src/cpptraj/src/Analysis_CrdFluct.cpp: needs update
AmberTools/src/cpptraj/src/Analysis_Rms2d.cpp: needs update
AmberTools/src/cpptraj/src/Analysis_RmsAvgCorr.cpp: needs update
AmberTools/src/cpptraj/src/ImageRoutines.cpp: needs update
AmberTools/src/cpptraj/src/ImageRoutines.h: needs update
AmberTools/src/paramfit/Makefile: needs update
AmberTools/src/paramfit/bounds_check.c: needs update
AmberTools/src/paramfit/calc_r_squared.c: needs update
AmberTools/src/paramfit/defaults.c: needs update
AmberTools/src/paramfit/example_config_files/ needs update
AmberTools/src/paramfit/file_io.c: needs update
AmberTools/src/paramfit/fitting_control.c: needs update
AmberTools/src/paramfit/function_def.h: needs update
AmberTools/src/paramfit/genetic_algorithm.c: needs update
AmberTools/src/paramfit/mem_alloc.c: needs update
AmberTools/src/paramfit/options_summary.c: needs update
AmberTools/src/paramfit/param_summary.c: needs update
AmberTools/src/paramfit/parameter_optimiser.c: needs update
AmberTools/src/paramfit/process_command_line.c: needs update
AmberTools/src/paramfit/process_job_control_setting.c: needs update
AmberTools/src/paramfit/process_prmtop.c: needs update
AmberTools/src/paramfit/write_input.c: needs update
error: Entry 'AmberTools/src/cpptraj/src/Action_Diffusion.cpp' not uptodate. Cannot merge.

%git ls-files -m | xargs -t rm
%git ls-files -d | xargs -t git checkout --
%git pull
Updating c147f84..b185632
error: Untracked working tree file 'AmberTools/src/paramfit/dihedral_fitting.c' would be overwritten by merge.
%rm -fr AmberTools/src/paramfit/*
%git ls-files -d | xargs -t git checkout --
Your branch is behind the tracked remote branch 'origin/master' by 120 commits,
and can be fast-forwarded.
%git pull
Updating c147f84..b185632
error: Untracked working tree file 'AmberTools/test/paramfit/dihedral_perfect_fit_NMA/' would be overwritten by merge.

Various variations of above ultimately fail the same way.
Is there a way out of this mess besides blowing away everything ?
Note that I was uptodate a few days ago and had made no modifications.


AMBER-Developers mailing list
Received on Thu Mar 21 2013 - 21:30:02 PDT
Custom Search