I haven't installed OpenMPI myself, but I'm using the one that comes with
Rocks 5.3. However, changing ifort to mpif90 results in
gfortran: unrecognized option '-tpp7'
gfortran: language W not recognized
gfortran: language W not recognized
gfortran: runmd.f90: linker input file unused because linking not done
again, dozens of these..
On Sat, Oct 30, 2010 at 11:28 PM, Jason Swails <jason.swails.gmail.com>wrote:
> If you've properly installed OpenMPI, you should be able to use mpif90 to
> link the proper MPI libraries and such.
>
> Remove everything after MPI_LIBRARY (or MPI_LIB, or something), and change
> FC and LOAD to mpif90. This should work if OpenMPI is working.
>
> Good luck!
> Jason
>
> On Sat, Oct 30, 2010 at 4:23 PM, Seren Soner <seren.soner.gmail.com>
> wrote:
>
> > That clearly is the reason, but now I decided to go all the way with
> > OpenMPI, and I can't.
> >
> > I compiled everything with make serial, then compiled sander with ifort
> and
> > openMPI, by modifying the following row;
> >
> > FC= ifort -I/opt/openmpi/include
> >
> > The only thing remaining is pmemd, but I can't compile it. I'm trying to
> > build the config.h using ./configure linux_em64t ifort openmpi
> > Trying "make" results in;
> >
> > parallel_dat.f90(92): error #5102: Cannot open include file
> 'mpif-common.h'
> > include 'mpif-common.h'
> > --------------^
> > parallel_dat.f90(223): error #6404: This name does not have a type, and
> > must
> > have an explicit type. [MPI_COMM_WORLD]
> > call mpi_abort(mpi_comm_world, i, err_ret_code)
> > -------------------^
> > compilation aborted for parallel_dat.f90 (code 1)
> > make[1]: *** [parallel_dat.o] Error 1
> >
> > So then I again modify the F90 row to include openmpi headers, which
> > results
> > in the following error:
> >
> > ifort -o pmemd gbl_constants.o gbl_datatypes.o state_info.o
> file_io_dat.o
> > parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o
> > dynamics_dat.o img.o parallel.o pme_direct.o pme_recip.o pme_fft.o
> fft1d.o
> > bspline.o pme_force.o pbc.o nb_pairlist.o cit.o dynamics.o bonds.o
> angles.o
> > dihedrals.o runmd.o loadbal.o shake.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 alltasks_setup.o pme_setup.o
> > ene_frc_splines.o nextprmtop_section.o -L/opt/openmpi//lib -pthread
> > -L/opt/openmpi/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic
> > -lnsl -lutil -lm -ldl -limf -lsvml
> > -Wl,-rpath=/export/apps/intel/lib/intel64:/opt/gridengine/lib/lx26-amd64
> > /export/apps/intel/lib/intel64/libimf.so: warning: warning: feupdateenv
> is
> > not implemented and will always fail
> > parallel_dat.o: In function `parallel_dat_mod_mp_mexit_':
> > parallel_dat.f90:(.text+0x50): undefined reference to `mpi_group_free_'
> >
> > And then undefined reference to mpi_* follows with some huge amount of
> > lines..
> >
> > Any idea to solve this problem ?
> >
> > Thanks,
> > Seren
> >
> > On Fri, Oct 29, 2010 at 8:25 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > On Fri, Oct 29, 2010 at 11:33 AM, Seren Soner <seren.soner.gmail.com>
> > > wrote:
> > >
> > > > Thanks for the quick replies :)
> > > >
> > > > But in fact, I have that row in the config.h for pmemd;
> > > > MPI_DEFINES = -DMPI
> > > >
> > > > I had used
> > > > ./configure -mpich2 ifort_x86_64;
> > > > make parallel
> > > >
> > > > in order to compile Amber.
> > > >
> > > > And i have never compiled amber serial, and besides the compilation
> > time
> > > > for
> > > > pmemd and pmemd.MPI are exactly equal.
> > > >
> > > > Any other ideas ?
> > > >
> > >
> > > The last idea I have: the mpirun/mpiexec you're using is from a
> different
> > > MPI implementation than the one that you used to build pmemd. Paste
> the
> > > following two things here: the entire config.h you used to build pmemd
> > (if
> > > you had to make modifications, send the modified version), and the
> > results
> > > of running the command "which mp****", where mpi**** is the
> > mpirun/mpiexec
> > > program you used to actually run pmemd in parallel. If you specified a
> > > specific mpirun using a path, then provide the path of that mpirun.
> > >
> > > What I'm guessing here is that your computer has a "system" MPI build
> > (i.e.
> > > Mac OS X comes pre-installed with a fortran-disabled OpenMPI version),
> > and
> > > you used your custom MPI build to compile Amber 9, but when you run
> > > "mpirun"
> > > without specifying a path, it's using the system-MPI version of mpirun,
> > > which isn't playing nice with your custom MPI implementation. I've
> seen
> > > this kind of behaviour when I've done this exact thing.
> > >
> > > Good luck!
> > > Jason
> > >
> > >
> > > >
> > > > On Fri, Oct 29, 2010 at 7:28 PM, Jason Swails <
> jason.swails.gmail.com
> > > > >wrote:
> > > >
> > > > > Ross's observation is exactly what I would guess, as well.
> However,
> > > your
> > > > > email suggests that you're trying to use pmemd, not sander. In
> that
> > > > case,
> > > > > it would appear as though pmemd was compiled without parallel
> > support.
> > > > > What
> > > > > does the config.h file in $AMBERHOME/src/pmemd/ look like? Do you
> > see
> > > a
> > > > > "-DMPI" in the MPI_DEFINES variable?
> > > > >
> > > > > Better yet, do you know the configure command used to configure
> > pmemd?
> > > > > Also, remember that if you first build pmemd in parallel followed
> by
> > a
> > > > > serial build, both executables are named pmemd, so the serial
> version
> > > > will
> > > > > overwrite the parallel version. This has been changed in amber11,
> > > where
> > > > > the
> > > > > default build installs both pmemd and pmemd.MPI, similar to what is
> > > done
> > > > > with sander.
> > > > >
> > > > > All the best,
> > > > > Jason
> > > > >
> > > > > On Fri, Oct 29, 2010 at 12:21 PM, Ross Walker <
> ross.rosswalker.co.uk
> > >
> > > > > wrote:
> > > > >
> > > > > > Hi Seren,
> > > > > >
> > > > > > It definitely looks to me like you are running the serial version
> > of
> > > > > sander
> > > > > > but with mpirun. Make sure you are using a parallel version of
> the
> > > > code.
> > > > > > Make sure the executable given to mpirun is sander.MPI and NOT
> just
> > > > > sander.
> > > > > >
> > > > > > All the best
> > > > > > Ross
> > > > > >
> > > > > > > -----Original Message-----
> > > > > > > From: Seren Soner [mailto:seren.soner.gmail.com]
> > > > > > > Sent: Friday, October 29, 2010 9:10 AM
> > > > > > > To: AMBER Mailing List
> > > > > > > Subject: Re: [AMBER] Output problem on Amber 9
> > > > > > >
> > > > > > > Thanks for the reply Adrian.
> > > > > > >
> > > > > > > But I'm afraid that isnt the case. In fact, I just reinstalled
> > > AMBER
> > > > on
> > > > > a
> > > > > > > clean and fresh server using MPICH2.
> > > > > > >
> > > > > > > The tests all seem just fine, and the run keeps going, but the
> > > > > coordinate
> > > > > > > file is corrupt (according to ptraj), and the .out file from
> the
> > > > pmemd
> > > > > is
> > > > > > as
> > > > > > > following:
> > > > > > >
> > > > > > > NSTEP = 5005 TIME(PS) = 10.010 TEMP(K) = 293
> > > > > > > NSTEP = 5020 TIME(PS) = 10.040 TEMP(K) = 292.63
> > > PRESS
> > > > =
> > > > > > > 274.9
> > > > > > > Etot = -206080.1422 EKtot = 50018.8412 EPtot
> =
> > > > > > > -256098.9834
> > > > > > > BOND = 1158.7574 ANGLE = 3226.4692 DIHED
> =
> > > > > > > 4959.5549
> > > > > > > 1-4 NB = 1696.6991 1-4 EEL = 21230.7542 VDWAALS
> =
> > > > > > > 32958.6284
> > > > > > > EELEC = -321329.8466 EHBOND = 0.0000 RESTRAINT
> =
> > > > > > > 0.0000
> > > > > > > EKCMT = 22722.9567 VIRIAL = 17729.8009 VOLUME
> =
> > > > > > > 841143.0522
> > > > > > > Density
> =
> > > > > > > 1.0138
> > > > > > > Ewald error estimate: 0.5244E-04
> > > > > > > --------------------
> > > > > > > NSTEP = 5010 TIME(PS) = 10.020 TEMP(K) = 293
> > > > > > > NSTEP = 5025 TIME(PS) = 10.050 TEMP(K) = 293.83
> > > PRESS
> > > > =
> > > > > > > 220.5
> > > > > > > Etot = -206067.1820 EKtot = 50223.4622 EPtot
> =
> > > > > > > -256290.6442
> > > > > > > BOND = 1143.5592 ANGLE = 3270.5782 DIHED
> =
> > > > > > > 4942.4778
> > > > > > > 1-4 NB = 1674.3206 1-4 EEL = 21252.6748 VDWAALS
> =
> > > > > > > 32893.7176
> > > > > > > EELEC = -321467.9724 EHBOND = 0.0000 RESTRAINT
> =
> > > > > > > 0.0000
> > > > > > > EKCMT = 22820.5212 VIRIAL = 18815.7936 VOLUME
> =
> > > > > > > 841238.7879
> > > > > > > Density
> =
> > > > > > > 1.0137
> > > > > > > Ewald error estimate: 0.4236E-04
> > > > > > > --------------------
> > > > > > > NSTEP = 5015 TIME(PS) = 10.030 TEMP(K) = 292
> > > > > > > NSTEP = 5030 TIME(PS) = 10.060 TEMP(K) = 293.63
> > > PRESS
> > > > =
> > > > > > > 162.4
> > > > > > > Etot = -206054.1128 EKtot = 50189.3052 EPtot
> =
> > > > > > > -256243.4180
> > > > > > > BOND = 1095.1010 ANGLE = 3234.5279 DIHED
> =
> > > > > > > 4948.3120
> > > > > > > 1-4 NB = 1664.1808 1-4 EEL = 21271.6600 VDWAALS
> =
> > > > > > > 32890.3861
> > > > > > > EELEC = -321347.5860 EHBOND = 0.0000 RESTRAINT
> =
> > > > > > > 0.0000
> > > > > > > EKCMT = 22884.4044 VIRIAL = 19934.3426 VOLUME
> =
> > > > > > > 841311.4130
> > > > > > > Density
> =
> > > > > > > 1.0136
> > > > > > > Ewald error estimate: 0.6402E-04
> > > > > > > --------------------
> > > > > > > NSTEP = 5020 TIME(PS) = 10.040 TEMP(K) = 292
> > > > > > > NSTEP = 5035 TIME(PS) = 10.070 TEMP(K) = 292.97
> > > PRESS
> > > > =
> > > > > > > 108.3
> > > > > > > Etot = -206041.0229 EKtot = 50075.8387 EPtot
> =
> > > > > > > -256116.8616
> > > > > > > BOND = 1188.6496 ANGLE = 3253.7780 DIHED
> =
> > > > > > > 4958.3474
> > > > > > > 1-4 NB = 1657.4676 1-4 EEL = 21231.7085 VDWAALS
> =
> > > > > > > 32913.2619
> > > > > > > EELEC = -321320.0746 EHBOND = 0.0000 RESTRAINT
> =
> > > > > > > 0.0000
> > > > > > > EKCMT = 22908.5928 VIRIAL = 20940.4972 VOLUME
> =
> > > > > > > 841363.6741
> > > > > > > Density
> =
> > > > > > > 1.0136
> > > > > > > Ewald error estimate: 0.9973E-04
> > > > > > > --------------------
> > > > > > >
> > > > > > >
> > > > > > > There seems to be a problem of synchronization, but I don't
> have
> > > any
> > > > > idea
> > > > > > > what causes it, or what can solve it.
> > > > > > >
> > > > > > > Thanks,
> > > > > > > Seren Soner
> > > > > > >
> > > > > > > On Mon, Oct 18, 2010 at 1:40 PM, Adrian Roitberg
> > > > > > > <roitberg.qtp.ufl.edu>wrote:
> > > > > > >
> > > > > > > > I have seen this before, and it is usually due to more than
> one
> > > > > > instance
> > > > > > > > of amber trying to write to the same files. Check that there
> is
> > > > only
> > > > > > one
> > > > > > > > set of amber runs active in that directory.
> > > > > > > >
> > > > > > > > Adrian
> > > > > > > >
> > > > > > > >
> > > > > > > > On 10/18/10 11:16 AM, Seren Soner wrote:
> > > > > > > > > Hello there,
> > > > > > > > >
> > > > > > > > > I've been using AMBER in our server for some time, and
> after
> > > the
> > > > > > > > > server crash a few weeks back, my output files have been
> > acting
> > > > > > weird.
> > > > > > > > > My computer administrator tells me nothing has been changed
> > > after
> > > > > the
> > > > > > > > > server crash, and the output file becomes as follows:
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > NSTEP = 219965 TIME(PS) = 12939.930 TEMP(K) = 299
> > > > > > > > > NSTEP = 220080 TIME(PS) = 12940.160 TEMP(K) = 299.63 PRESS
> =
> > > 79.6
> > > > > > > > > Etot = -203606.8511 EKtot = 51214.7469 EPtot = -254821.5980
> > > > > > > > > BOND = 1362.7033 ANGLE = 3547.3148 DIHED = 4862.2996
> > > > > > > > > 1-4 NB = 1683.6634 1-4 EEL = 21484.6416 VDWAALS =
> 32232.8437
> > > > > > > > > EELEC = -319995.0644 EHBOND = 0.0000 RESTRAINT = 0.0000
> > > > > > > > > EKCMT = 23099.5614 VIRIAL = 21648.8530 VOLUME = 844163.5532
> > > > > > > > >
> > > > > > > > > Or, sometimes I may see NSTEP = 219000 information at one
> > line,
> > > > and
> > > > > > > > > then NSTEP = 218990, NSTEP = 218995, and NSTEP = 219000
> > again.
> > > > > > > > >
> > > > > > > > > Does anyone have any idea what may cause this problem ?
> > > > > > > > >
> > > > > > > > > _______________________________________________
> > > > > > > > > AMBER mailing list
> > > > > > > > > AMBER.ambermd.org
> > > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > Dr. Adrian E. Roitberg
> > > > > > > > Associate Professor
> > > > > > > > Quantum Theory Project, Department of
> Chemistry
> > > > > > > > University of Florida
> > > > > > > >
> > > > > > > > Senior Editor. Journal of Physical Chemistry.
> > > > > > > >
> > > > > > > > on Sabbatical in Barcelona until August 2011.
> > > > > > > > Email roitberg.ufl.edu
> > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > 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
> > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Jason M. Swails
> > > > > Quantum Theory Project,
> > > > > University of Florida
> > > > > Ph.D. Graduate Student
> > > > > 352-392-4032
> > > > > _______________________________________________
> > > > > 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
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Oct 30 2010 - 14:00:03 PDT
