You can compile with the gnu compilers, in which case that OpenMPI should
work. However, the ifort compiler offers significant speedup for pmemd.
To compile with the gfortran compiler, you can use the config.h file you
have right now and simply remove all of the ifort-specific flags.
(basically, just remove every flag that you get a complaint about, like
-tpp7)
Good luck!
Jason
On Sat, Oct 30, 2010 at 4:48 PM, Seren Soner <seren.soner.gmail.com> wrote:
> Here's what mpif90 -show returned:
>
> gfortran -I/opt/openmpi/include -pthread -I/opt/openmpi/lib
> -L/opt/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl
> -Wl,--export-dynamic -lnsl -lutil -lm -ldl
>
> I thought compiling amber w/o compiling openmpi myself would take shorter,
> but apparently I was wrong. That's what I'm going to do if I still fail :)
>
> On Sat, Oct 30, 2010 at 11:46 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > This openMPI was compiled around the gnu compilers -- note the gfortran.
> > What does mpif90 -show return? It may be worthwhile to compile your own
> > MPI
> > with the compilers you want.
> >
> > Good luck!
> > Jason
> >
> > On Sat, Oct 30, 2010 at 4:33 PM, Seren Soner <seren.soner.gmail.com>
> > wrote:
> >
> > > 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
> > > >
> > > _______________________________________________
> > > 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
Received on Sat Oct 30 2010 - 14:00:06 PDT
