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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Received on Mon May 31 2010 - 08:00:04 PDT
