Hi Ross,
Commenting on just the AmberTools compilation, I suspect the problem is
your version of gcc. gfortran has been part of gcc since version 4.0
but your gcc reports as version 3.4.6. I would doubt that this version
would know what to do with -lgfortran. This same problem occurs using
Apple's gcc even though it is > version 4.0. In this latter case gcc
was built without fortran support.
Tyler
Ross Walker wrote:
> Hi All,
>
> 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)
>
> ./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.
>
> 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.
>
> 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?
>
> 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.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
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Received on Thu Mar 04 2010 - 13:00:05 PST
