Hi Paul,
Thank you for the assurance. I tried to compare both mdout.tip5p and
mdout.tip5p.save and they look comparable except the saved version is the
output using a single processor.
Hadrian
On Tue, Oct 5, 2010 at 1:01 PM, Paul S. Nerenberg <psn.berkeley.edu> wrote:
> Hi Hadrian,
>
> The same test also "fails" for me, but take a look at the log file
> generated by the test (/test/tip5p/mdout.tip5p). In my case, the log
> file shows that the test actually ran just fine (so there's no need to
> worry). However, there is a small difference at the end of the output
> file in the averages/rms section -- specifically, the saved test case
> output has rms fluctuations for volume, while my test output doesn't.
> I see the same "error" in a version I compiled with PGI (on another
> machine) though, which makes me suspect that there may be something
> slightly awry with the saved tip5p test case. (The saved tip5p_nve
> test case doesn't have any rms fluctuations for volume, which adds to
> my suspicion re: tip5p.) Maybe someone else on the list knows more?
>
> Best,
>
> Paul
>
>
> On Oct 4, 2010, at 9:52 PM, Hadrian Djohari wrote:
>
> > Hi Paul and Case,
> >
> > Thank you for the responses.
> > The changed flags below did the trick to compile Amber successfully
> > with
> > openmpi and intel.
> >
> > All the AmberTools test.parallel passed, while all but 1 of Amber11
> > passed.
> > This is the failed one:
> > ==============================================================
> > export TESTsander='../../exe/pmemd.MPI'; cd tip5p && ./Run.tip5p
> > diffing mdout.tip5p.save with mdout.tip5p
> > possible FAILURE: check mdout.tip5p.dif
> > ==============================================================
> >
> > Let me know if I should be concerned with this single test failure.
> >
> > Hadrian.
> >
> > On Mon, Oct 4, 2010 at 12:40 PM, Paul S. Nerenberg
> > <psn.berkeley.edu> wrote:
> >
> >> Hi Hadrian,
> >>
> >> The last problem (compiling pmemd) is now a known issue with the
> >> intel
> >> compilers.* It revolves around the -fast optimization flag and the
> >> other flags it is automatically calling (-static) and the type of
> >> libraries you have on your system (looks like dynamic). Try editing
> >> your $AMBERHOME/src/config.h (and $AMBERHOME/AmberTools/src/config.h)
> >> file and replacing '-fast' with '-ipo -O3 -no-prec-div -xHost'. Then
> >> do a "make clean" and recompile the parallel version.
> >>
> >> Best,
> >>
> >> Paul
> >>
> >> *It's not really a bug, you just have to be "heads up" about whether
> >> you've got static or dynamic libraries.
> >>
> >>
> >> On Oct 3, 2010, at 10:30 PM, Hadrian Djohari wrote:
> >>
> >>> Hi everyone,
> >>>
> >>>
> >>>> I have some difficulty installing Amber 11 in our cluster, so I
> >>>> would
> >>>> appreciate everyone's help. I would like the answers to all the
> >>>> questions
> >>>> below, but if someone can help me with the answer for the specific
> >>>> openmpi/intel installation right at the bottom part, I would be
> >>>> really
> >>>> grateful.
> >>>>
> >>>> Amber installation questions:
> >>>>
> >>>> 1. The instruction in the Amber and AmberTools document seem to
> >>>> direct
> >>>> people to have both the source and the compiled binaries in the
> >>>> same
> >>>> directory by using only "make" instead of "make install". Is this
> >>>> the only
> >>>> way? We prefer to have the source and the compiled binaries in
> >>>> different
> >>>> directories (/usr/local/src/amber and /usr/local/amber). If we
> >>>> want separate
> >>>> directories, which one should $AMBERHOME point to?
> >>>>
> >>>> 2. The installer should be "root" or a user? I compiled "make
> >>>> serial"
> >>>> just fine as a user, but found some errors compiling as "root",
> >>>> probably due
> >>>> to some paths not being recognized.
> >>>>
> >>>> 3. Since I'm installing Amber, I should also install AmberTools.
> >>>> And
> >>>> I'd like to install the parallel version. So, is there a step-by-
> >>>> step
> >>>> instructions on how to install Amber (with AmberTools) as
> >>>> parallel code
> >>>> (please see no.1 too)? That would be EXTREMELY HELPFUL. Some of
> >>>> these
> >>>> questions needed answers (why do I have to install the serial
> >>>> versions
> >>>> first? how do I link to an existing libraries (fftw, mpi, mkl)?
> >>>> what paths
> >>>> are needed by the installer to execute?). These small things can
> >>>> lead to an
> >>>> unsuccessful compilation, so I would really like some more detailed
> >>>> information about this.
> >>>>
> >>>> 4. Once the code is compiled, is there a short test job that use
> >>>> PBS
> >>>> submission, not the "make test" that is available in the
> >>>> directories?
> >>>>
> >>>>
> >>>> Also, I have tried this approach to install MD on a RHEL5.5 server:
> >>> export AMBERHOME=/usr/local/amber/amber11
> >>> cd $AMBERHOME/AmberTools/src
> >>> ./configure -mpi intel
> >>> make parallel
> >>> This is successful.
> >>>
> >>> And then:
> >>> cd $AMBERHOME/src
> >>> make parallel
> >>>
> >>> But it produces this error;
> >>> ...
> >>> mpif90 -fast -c charmm_gold.f90
> >>> mpif90 -fast -o pmemd.MPI gbl_constants.o gbl_datatypes.o
> >>> state_info.o
> >>> file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_dat.o
> >>> prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o parallel_dat.o
> >>> parallel.o
> >>> gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o
> >>> pme_blk_recip.o
> >>> pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o
> >>> pme_force.o
> >>> pbc.o nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o
> >>> angles.o
> >>> dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o
> >>> mol_list.o
> >>> runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o
> >>> timers.o
> >>> pmemd_lib.o runfiles.o file_io.o bintraj.o pmemd_clib.o pmemd.o
> >>> random.o
> >>> degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o
> >>> master_setup.o
> >>> pme_alltasks_setup.o pme_setup.o ene_frc_splines.o
> >>> gb_alltasks_setup.o
> >>> nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o
> >>> charmm_gold.o ../../netcdf/lib/libnetcdf.a
> >>> ipo: remark #11000: performing multi-file optimizations
> >>> ipo: remark #11005: generating object file /tmp/ipo_ifortPoYvAz.o
> >>> /usr/bin/ld: cannot find -lmpi_f90
> >>> make[2]: *** [pmemd.MPI] Error 1
> >>> make[2]: Leaving directory `/usr/local/amber/amber11/src/pmemd/src'
> >>> make[1]: *** [parallel] Error 2
> >>> make[1]: Leaving directory `/usr/local/amber/amber11/src/pmemd'
> >>> make: *** [parallel] Error 2
> >>>
> >>> I don't know why it cannot find -lmpi_f90 since libmpi_f90.* are in
> >>> the
> >>> directory that is in the ld_library path
> >>> hxd58.login:/usr/local/amber/amber11/src$ echo $LD_LIBRARY_PATH
> >>> /usr/local/openmpi/openmpi-intel/lib/:/usr/local/lib:/usr/local/
> >>> intel/compilers/11.1.056/lib/intel64:/usr/local/intel/compilers/
> >>> 11.1.056/idb/lib/intel64
> >>> hxd58.login:/usr/local/amber/amber11/src$ ll
> >>> /usr/local/openmpi/openmpi-intel/lib
> >>> ...
> >>> -rwxr-xr-x 1 root root 1129 Mar 26 2010 libmpi_f90.la
> >>> lrwxrwxrwx 1 root root 19 Mar 26 2010 libmpi_f90.so ->
> >>> libmpi_f90.so.0.0.0
> >>> lrwxrwxrwx 1 root root 19 Mar 26 2010 libmpi_f90.so.0 ->
> >>> libmpi_f90.so.0.0.0
> >>> -rwxr-xr-x 1 root root 17140 Mar 26 2010 libmpi_f90.so.0.0.0
> >>> ...
> >>>
> >>> Thank you,
> >>>
> >>> --
> >>> Hadrian Djohari
> >>> HPCC Manager
> >>> Case Western Reserve University
> >>> (W): 216-368-0395
> >>> (M): 216-798-7490
> >>>
> >>>
> >>>
> >>> --
> >>> Hadrian Djohari
> >>> HPCC Manager
> >>> Case Western Reserve University
> >>> (W): 216-368-0395
> >>> (M): 216-798-7490
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Hadrian Djohari
> > HPCC Manager
> > Case Western Reserve University
> > (W): 216-368-0395
> > (M): 216-798-7490
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Hadrian Djohari
HPCC Manager
Case Western Reserve University
(W): 216-368-0395
(M): 216-798-7490
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Received on Tue Oct 05 2010 - 23:00:05 PDT
