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
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.
--------------------------------------------------------------------------
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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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 02 2010 - 10:30:03 PDT
