CYGWIN_NT-5.1 mojyt 1.7.1(0.218/5/3) 2009-12-07 11:48 i686 Cygwin
I am of course running the tests :-)
Only a few of the AT tests fail, most of that is precision/output formatting
changes.
I have never had any trouble with the dacdif script.
-Dan
On Thu, Mar 4, 2010 at 3:57 PM, Thorsten M Woelfle <twoelfle.sdsc.edu>wrote:
> Daniel
>
> Can you do a quick comment, which version of cygwin are you using and how
> you solved the problem
> that the dacdif script in the test directory uses an old version of getopt
> (posix 1 ?!) which is not supported on that
> platform any more?
> You are running the test as well, right?
>
>
> Thorsten
>
>
> On Mar 4, 2010, at 12:49 PM, Daniel Roe wrote:
>
> > I am still able to compile AmberTools (serial and parallel) on cygwin
> with
> > gcc/gfortran:
> > gcc (GCC) 4.3.4 20090804 (release) 1
> > GNU Fortran (GCC) 4.3.4 20090804 (release) 1
> >
> > On Thu, Mar 4, 2010 at 3:46 PM, Scott Brozell <sbrozell.rci.rutgers.edu
> >wrote:
> >
> >> Hi,
> >>
> >> quick comments.
> >>
> >> On Thu, Mar 04, 2010 at 12:30:25PM -0800, Ross Walker wrote:
> >>> I thought I would post an overview of the current state of the CVS
> tree,
> >> as
> >>> seen on my RHEL4 machine (which incidentally builds AMBER 10 fine and
> as
> >> of
> >>> a month or so ago built AMBER 11 fine). I am hoping some volunteers
> will
> >> try
> >>> to go through and address some of these issues.
> >>>
> >>> 1) Attempt 1 - Using GNU compilers - Serial
> >>> -------------------------------------------
> >>>
> >>> cvs co amber11
> >>> export AMBERHOME=~/cvs_checkouts/amber11
> >>>
> >>> gcc -v
> >>> gcc version 3.4.6 20060404 (Red Hat 3.4.6-11)
> >>>
> >>> gfortran -v
> >>> gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)
> >>
> >> different gnu versions is asking for trouble.
> >>
> >>
> >>> ./configure gnu
> >>> make -f Makefile_at
> >>>
> >>> ...
> >>> gcc -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o
> io.o
> >>> trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o mask.o
> >> rms.o
> >>> display.o interface.o energy.o experimental.o ptraj.o actions.o
> analyze.o
> >>> thermo.o pubfft.o cluster.o clusterLib.o
> >>> /home/rcw/cvs_checkouts/amber11/lib/libpdb.a
> >>> /home/rcw/cvs_checkouts/amber11/lib/arpack.a
> >>> -L/opt/intel/mkl/10.1.1.019//lib/em64t -Wl,--start-group
> >>> /opt/intel/mkl/10.1.1.019//lib/em64t/libmkl_intel_lp64.a
> >>> /opt/intel/mkl/10.1.1.019//lib/em64t/libmkl_sequential.a
> >>> /opt/intel/mkl/10.1.1.019//lib/em64t/libmkl_core.a -Wl,--end-group
> >> -lpthread
> >>> -lgfortran ../netcdf/lib/libnetcdf.a -lm
> >>> /usr/bin/ld: cannot find -lgfortran
> >>> collect2: ld returned 1 exit status
> >>>
> >>> locate libgfortran
> >>> /usr/lib64/libgfortran.so.1
> >>> ...
> >>> /usr/lib/libgfortran.so.1
> >>> ...
> >>> etc
> >>>
> >>> Removing -lgfortan gives
> >>> thermo.o(.text+0x395): In function `thermo_':
> >>> : undefined reference to `_gfortran_st_write'
> >>> ...
> >>> As well as lots of arpack.a issues:
> >>>
> >>> /home/rcw/cvs_checkouts/amber11/lib/arpack.a(dsgets.o)(.text+0x5d): In
> >>> function `dsgets_':
> >>> : undefined reference to `_gfortran_compare_string'
> >>>
> >>> Which are related I guess.
> >>
> >> does this work if u use the same gnu versions ?
> >>
> >>
> >>> So giving up on AMBERTools and just going on to building AMBER -
> Knowing
> >> of
> >>> course that mm_pbsa won't compile since it now needs nab so requires
> >>> AMBERTools to have been built properly first. One used to be able to
> >> build
> >>> AMBER as a standalone.
> >>>
> >>> make
> >>>
> >>> This works. make -j8 also works.
> >>>
> >>> cd ../test
> >>> make
> >>>
> >>> This gives (non-benign) failures for (TEST failures file is attached):
> >>>
> >>> possible FAILURE: check mdout.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/abmd_ANALYSIS
> >>> possible FAILURE: check monitor.txt.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/abmd_ANALYSIS
> >>> possible FAILURE: check mdout.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/abmd_FLOODING
> >>> possible FAILURE: check monitor.txt.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/abmd_FLOODING
> >>> possible FAILURE: check umbrella.ncdump.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/abmd_FLOODING
> >>> possible FAILURE: check mdout.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/abmd_UMBRELLA
> >>> possible FAILURE: check mdout.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/abmd_UMBRELLA
> >>> possible FAILURE: check monitor.txt.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/abmd_UMBRELLA
> >>> possible FAILURE: check mdout.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/smd
> >>> possible FAILURE: check smd.txt.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/smd
> >>> possible FAILURE: check mdout.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/pmd
> >>> possible FAILURE: check pmd.txt.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/pmd
> >>> possible FAILURE: check mdout.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/smd2
> >>> possible FAILURE: check work.txt.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ncsu/smd2
> >>>
> >>> All of these have the error:
> >>>> ** NCSU-Error ** : expected list value for key 'i', got '<EMPTY>'
> >> instead
> >>>
> >>> The rest are just minor difference. Things not being updated for AMBER
> 11
> >>> being printed in the output, roundoff etc.
> >>
> >> There are test crashes with other compilers:
> >> pgi 9.0.4
> >> cd mtmdtest && ./Run.mtmdtest
> >> SANDER: Multiply-targeted MD, new to AMBER 11
> >> Tested on an RNA duplex.
> >> ./Run.mtmdtest: Program error
> >> make: [test.sander.BASIC] Error 1 (ignored)
> >> NAN's in the energies; i'll probably submit a bug report after a quick
> >> look.
> >>
> >>
> >>> 2) Attempt 1 - Using GNU compilers - Parallel
> >>> ---------------------------------------------
> >>>
> >>> cd $AMBERHOME/src
> >>> ./configure -mpi gnu
> >>>
> >>> Fails because of needing yacc from a successful AMBER tools build. Even
> >>> though this is NOT needed for building AMBER in parallel. Hacking out
> the
> >> if
> >>> statement and proceeding:
> >>>
> >>> which mpif90
> >>> /server-home/netbin/mpi/mpich2-1.0.7-gfortran-4.1.2/bin/mpif90
> >>>
> >>> make -f Makefile_at clean
> >>> make clean
> >>> make parallel (This works, -j8 also works after I updated the depend
> >> file)
> >>> cd ../test
> >>> make clean
> >>> export DO_PARALLEL='mpirun -np 2'
> >>> make test.parallel
> >>>
> >>> This gives the following non-benign errors:
> >>>
> >>> cd dhfr && ./Run.dhfr.noboxinfo
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0[cli_0]:
> >> aborting
> >>> job:
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> rank 0 in job 18 caffeine.sdsc.edu_59236 caused collective abort of
> >> all
> >>> ranks
> >>> exit status of rank 0: return code 1
> >>> diffing mdout.dhfr.noboxinfo.save with mdout.dhfr.noboxinfo
> >>> PASSED
> >>>
> >>> This is the correct error since this just tests that the code prints an
> >>> error about the box info being missing from the inpcrd file and quits
> but
> >> it
> >>> may confuse the user.
> >>>
> >>> possible FAILURE: check trajene.out.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/trajene_box
> >>> < 1 -9.4141E+3 1.7335E+1 7.4542E+1 N 7
> >>>> 1 -9.4141E+3 1.7335E+1 7.4541E+1 N 7
> >>> < VDWAALS = 1371.5986 EEL = -11615.0228 HBOND =
> >> 0.
> >>>> VDWAALS = 1371.7742 EEL = -11615.1955 HBOND =
> >> 0.
> >>> < minimization completed, ENE=-0.94141269E+4 RMS= 0.173345E+2
> >>>> minimization completed, ENE=-0.94141240E+4 RMS= 0.173348E+2
> >>>
> >>> This is benign I think but we have lots of precision in the output
> files
> >>> which will always cause problems.
> >>>
> >>> possible FAILURE: check out.0.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/softcore/min
> >>> 210c210
> >>> < 100 -8.9414E+3 1.6490E+1 4.6223E+1 O 40
> >>>> 100 -8.9463E+3 1.6490E+1 4.6223E+1 O 40
> >>> < VDWAALS = 937.0834 EEL = -9878.4642 HBOND =
> >> 0.
> >>>> VDWAALS = 932.1686 EEL = -9878.4642 HBOND =
> >> 0.
> >>> < DV/DL = -0.6676
> >>> < SC_VDW = -0.3007 SC_EEL = 0. SC_DERIV=
> >> -10.4972
> >>>> SC_VDW = -0.3007 SC_EEL = 0. SC_DERIV= 0.
> >>>
> >>> This is uncomfortably different. Same with
> >>>
> >>> possible FAILURE: check out.1.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/softcore/min
> >>>
> >>> possible FAILURE: check ti_decomp_1.out.dif
> >>> /home/rcw/cvs_checkouts/amber11/test/ti_decomp
> >>> Lots of issues here.
> >>>
> >>> As before NONE of the NCSU test cases work.
> >>>
> >>> export DO_PARALLEL='mpirun -np 4'
> >>> make test.parallel.4proc
> >>>
> >>> Just about EVERY SINGLE test case fails here. See the attached
> >>> TEST_FAILURES.diff.4cpu_gnu
> >>>
> >>> export DO_PARALLEL='mpirun -np 8'
> >>> make test.parallel.8proc
> >>>
> >>> Both NEB tests fail - See attached TEST_FAILURES.diff.8cpu_gnu
> >>>
> >>> export DO_PARALLEL='mpirun -np 32'
> >>> make test.parallel.32proc
> >>>
> >>> This test fails.
> >>>
> >>> So is anybody actually regularly running the parallel tests?
> >>
> >> Not me and the parallel tests have been in a poor state for a long time.
> >>
> >>
> >>> I'll provide an overview of the situation with the Intel compiler
> >> shortly. I
> >>> would encourage people to start looking at what they may have done to
> >> break
> >>> some of the parallel test cases. In particular the softcore stuff and
> >> also
> >>> why none of the NCSU stuff works.
> >>>
> >>> 3) Attempt 1 - Using GNU compilers - Cuda
> >>> -----------------------------------------
> >>>
> >>> make clean
> >>> make -f Makefile_at clean
> >>> ./configure -cuda gnu
> >>> make -j8 cuda (This works)
> >>> cd ../test
> >>> make test.serial.cuda
> >>>
> >>> These all pass with the exception of dhfr_min which is a known problem.
> >>
> >> scott
> >>
> >>
> >> _______________________________________________
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> >> AMBER-Developers.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
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> > http://lists.ambermd.org/mailman/listinfo/amber-developers
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>
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Received on Thu Mar 04 2010 - 13:30:03 PST
