Hello,
On Wed, Jun 2, 2010 at 1:14 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody and apologies for coming back on this one.
>
> I thought that the problem may had been caused by previous installations of
> openmpi.
>
> So I erased by hard disc (!!!) and started from scratch
>
> The serial installation results in:
>
> Finished serial test suite for Amber 11 at Wed Jun 2 18:12:03 CEST 2010.
>
> 407 file comparisons passed
> 0 file comparisons failed
> 0 tests experienced errors
> Test log file saved as logs/test_amber_serial/2010-06-02_17-42-09.log
> No test diffs to save!
>
>
> I installed MPICH2 in /opt as per David Watson's suggestion
>
> george1$ ls /opt/mpich2/
> bin etc include lib sbin share
>
> For the installation, I used Jason Swails' instructions
>
> ./configure FC=gfortran F77=gfortran F90=gfortran CC=gcc CXX=g++
> --prefix=/usr
>
The --prefix=/usr creates a makefile that will automatically put the
binaries/libraries/includes in /usr (/usr/bin, /usr/lib, and /usr/include)
when you run make install. If you want to install it in /opt/mpich2, you
should change this to --prefix=/opt/mpich2.
> make
> sudo make install
>
> In /amber11/src, I used make clean
>
> make parallel give now the following error
>
> cp ../../AmberTools/src/netcdf/include/*.mod .
> cp ../../AmberTools/src/netcdf/bin/ncdump
> /Users/george1/Programs/amber11/bin
> cpp -traditional -P -DBINTRAJ -DMPI constants.f > _constants.f
> mpif90 -c -O3 -mtune=generic -ffree-form -o constants.o _constants.f
> --------------------------------------------------------------------------
> Unfortunately, this installation of Open MPI was not compiled with
> Fortran 90 support. As such, the mpif90 compiler is non-functional.
>
This is the message that you get when you try to use /usr/bin/mpif90 that
comes included with Xcode tools. The mpif90 that you want to use is
/opt/mpich2/bin/mpif90, so make sure that /opt/mpich2/bin comes in your path
before /usr/bin. You should probably also put /opt/mpich2/lib in your
LD_LIBRARY_PATH, especially since building static executables is not
recommended for macs (since mpif90 will properly link the required libraries
at compile time). Do this by putting the following in your .bashrc (or
.bash_profile)
export PATH=/opt/mpich2/bin\:$PATH
export LD_LIBRARY_PATH=/opt/mpich2/lib\:$LD_LIBRARY_PATH
This is why I suggested building in /usr (that has always worked for me). I
started building mpich2 in /mpi/mpich2/ since I decided to install multiple
MPIs to test (mpich2 and openmpi for now), and with multiple MPIs, each one
will need its own directory so they don't trod on each others' feet.
Another option is to replace mpif90 in your config.h file everywhere with
/opt/mpich2/bin/mpif90, to force the correct mpif90 be used regardless of
what comes in the path first. Note that you'll have to do this for both
config.h files in amber11/AmberTools/src and amber11/src, since I believe
they are copies of one another, not hard (or soft) links.
Hope this helps.
Good luck!
Jason
> --------------------------------------------------------------------------
> make[1]: *** [constants.o] Error 1
> make: *** [parallel] Error 2
>
> Your help in this will be greatly appreciated
>
> George
>
>
> On May 31, 2010, at 8:19 PM, Jason Swails wrote:
>
> > Did you make clean in the amber11/src directory before trying to build in
> parallel?
> >
> > It looks like you may have some left-over pieces from a previous
> compilation (in serial).
> >
> > Good luck!
> > Jason
> >
> > --
> > Jason Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> >
> > On May 31, 2010, at 10:52 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> Hi Jason
> >>
> >> Thanks for the latest instructions to compile MPICH2.
> >>
> >> However, I encountered yet another problem. Hopefully it's the last one.
> >>
> >> ./configure -mpi gnu in $AMBERHOME/AmberTools/src works fine
> >>
> >> The configuration file, config.h, was successfully created.
> >>
> >> If you have amber11, the most common next step is to
> >> 'cd ../../src; make clean; make parallel'. See the Users' Manual
> >> for information on building a parallel version of AmberTools
> >>
> >>
> >> Trying to do a "make parallel" in amber11/src gives the error below
> >>
> >> _schlegel_dg_ in schlegel_dg.o
> >> _schlegel_dg_ in schlegel_dg.o
> >> _evb_ntrfc_ in evb_ntrfc.o
> >> _evb_ntrfc_ in evb_ntrfc.o
> >> _evb_ntrfc_ in evb_ntrfc.o
> >> _evb_ntrfc_ in evb_ntrfc.o
> >> _evb_ntrfc_ in evb_ntrfc.o
> >> ___ncsu_abmd_hooks_MOD_on_force in ncsu-abmd-hooks.o
> >> ___ncsu_abmd_hooks_MOD_on_sander_init in ncsu-abmd-hooks.o
> >> ___ncsu_abmd_hooks_MOD_on_sander_init in ncsu-abmd-hooks.o
> >> ___ncsu_abmd_hooks_MOD_on_sander_init in ncsu-abmd-hooks.o
> >> ___ncsu_sander_hooks_MOD_rem_preinit in ncsu-sander-hooks.o
> >> ___ncsu_sander_hooks_MOD_rem_preinit in ncsu-sander-hooks.o
> >> _qm2_load_params_and_allocate_ in
> libsqm.a(qm2_load_params_and_allocate.o)
> >> ld: symbol(s) not found
> >> collect2: ld returned 1 exit status
> >> make[1]: *** [sander.MPI] Error 1
> >> make: *** [parallel] Error 2
> >>
> >> Any ideas?
> >>
> >> Thanks in advance
> >>
> >> George
> >>
> >>
> >>
> >> On May 31, 2010, at 4:01 PM, Jason Swails wrote:
> >>
> >>> Ah, it appears as though you have g77 installed on your machine? I
> think
> >>> that the configure script is trying to use g77 as the Fortran 77
> compiler,
> >>> when it should be using gfortran. Change the configure line to this:
> >>>
> >>> ./configure FC=gfortran F77=gfortran F90=gfortran CC=gcc CXX=g++
> >>> --prefix=/usr
> >>> make
> >>> sudo make install
> >>>
> >>> This should make sure that gfortran and gcc are used as the compilers
> for
> >>> all fortran and c code (and g++ for c++ code).
> >>>
> >>> Good luck!
> >>> Jason
> >>>
> >>> On Mon, May 31, 2010 at 9:47 AM, George Tzotzos <gtzotzos.me.com>
> wrote:
> >>>
> >>>> Hi Jason,
> >>>>
> >>>> Many thanks for the prompt reply.
> >>>>
> >>>> I downloaded MPICH2 as you suggested and tried to install. However,
> I'm
> >>>> unable to proceed with the installation.
> >>>>
> >>>> See the error message below
> >>>>
> >>>> Any suggestions?
> >>>>
> >>>> Many thanks in advance
> >>>>
> >>>> George
> >>>>
> >>>> checking whether g77 accepts the FLIBS found by autoconf... yes
> >>>> checking whether C can link with
> >>>> -L/usr/local/lib/gcc/i686-apple-darwin8.8.1/3.4.0
> >>>> -L/usr/local/lib/gcc/i686-apple-darwin8.8.1/3.4.0/../../.. -lfrtbegin
> >>>> -lg2c... yes
> >>>> checking for linker for Fortran main programs... Use Fortran to link
> >>>> programs
> >>>> checking whether Fortran 77 and C objects are compatible... no
> >>>> checking for file... file
> >>>> configure: error: **** Incompatible Fortran and C Object File Types!
> ****
> >>>> F77 Object File Type produced by "g77 -O2" is : : Mach-O object i386.
> >>>> C Object File Type produced by "gcc -O2" is : : Mach-O 64-bit object
> >>>> x86_64.
> >>>> make: *** No targets specified and no makefile found. Stop.
> >>>> make: *** No rule to make target `install'. Stop.
> >>>>
> >>>> On May 31, 2010, at 3:18 PM, Jason Swails wrote:
> >>>>
> >>>>> Hi George,
> >>>>>
> >>>>> Once you have the compilers built for Mac OS X 10.6, installing Amber
> >>>> itself
> >>>>> is quite simple (all you need is a simple ./configure gnu, make
> serial,
> >>>> and
> >>>>> make serial in the amber11/AmberTools/src and amber11/src
> directories).
> >>>>> Luckily, building the compilers from macports or fink is a one-time
> >>>>> necessity, so from now on Amber11 should be quite easy to build.
> >>>>>
> >>>>> Amber11 in parallel requires, once your system is properly set up,
> only
> >>>> for
> >>>>> you to type "./configure -mpi gnu" in the amber11/AmberTools/src
> >>>> directory
> >>>>> and then make parallel instead of make serial as described above.
> The
> >>>> only
> >>>>> additional thing you need is an MPI installation. You can either use
> >>>>> macports or fink to build the MPI, or you can build your own from
> source.
> >>>> I
> >>>>> would suggest building your own, since it's quite easy.
> >>>>>
> >>>>> First thing to do is pick an MPI and download the source code. As
> has
> >>>> been
> >>>>> suggested many times before, I would suggest MPICH2 (you can download
> the
> >>>>> source code from
> >>>>>
> >>>>
> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.2.1p1/mpich2-1.2.1p1.tar.gz
> >>>>> Untar the archive in a directory, then cd into that directory and
> type
> >>>>> "./configure --prefix=/usr; make; make install".
> >>>>>
> >>>>> This will configure it to be put in /usr/bin and /usr/lib and
> >>>> /usr/include
> >>>>> for the binaries, libraries, and include files, respectively. This
> >>>> should
> >>>>> successfully overwrite the fortran-deficient MPI installation that
> comes
> >>>>> with xcode tools.
> >>>>>
> >>>>> After you've done this, the 3 simple commands described above (and in
> the
> >>>>> Amber11 manual) should be sufficient to build a parallel version.
> >>>> However,
> >>>>> you have to make clean before you do this, since you don't want to
> use
> >>>> the
> >>>>> serial installation as a starting point.
> >>>>>
> >>>>> Mengjuei has also set up a very helpful "amber on mac" weblog that
> you
> >>>> can
> >>>>> find here http://amberonmac.blogspot.com/.
> >>>>>
> >>>>> Good luck!
> >>>>> Jason
> >>>>>
> >>>>> On Mon, May 31, 2010 at 5:09 AM, George Tzotzos <gtzotzos.me.com>
> wrote:
> >>>>>
> >>>>>> Hi folks,
> >>>>>>
> >>>>>> I've made a successful serial installation of AMBER11 on a quad core
> MAC
> >>>>>> (Intel Core i7). My installation was done pretty much on the lines
> >>>> suggested
> >>>>>> in the message of Erik Zuiderweg dated May 24.
> >>>>>>
> >>>>>> My question is whether there's a way to take this as a starting
> point
> >>>> for a
> >>>>>> parallel installation or does one need to recompile the program from
> >>>>>> scratch? If the former option is possible any suggestions on how to
> >>>> proceed
> >>>>>> from there would be most useful. I went through the mail archive but
> >>>> somehow
> >>>>>> I'm getting lost in the detail.
> >>>>>>
> >>>>>> Your help would be greatly appreciated
> >>>>>>
> >>>>>> George
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> 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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> >
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>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jun 02 2010 - 10:30:06 PDT
