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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Received on Thu Mar 04 2010 - 13:00:07 PST
