Hi
I am giving the details of the installation procedure which I followed
to install Amber12 and Ambertools.
In the first step I created a directory named amber12 under
/Volumes/data/common/
Then I extracted the amber12 and amber12 tools software to the amber12
directory using below commands.
tar xvfj AmberTools12.tar.bz2
tar xvfj Amber12.tar.bz2
Then I set the amber environment variable
export AMBERHOME=/Volumes/data/common/amber12
Then I downloaded and applyed the patches as below
cd $AMBERHOME
./patch_amber.py --update-tree
Then I ran the configure script inside the AMBERHOME directory by
choosing the gnu compiler as below
./configure gnu
make install
All the above steps went fine.
make test
In the make test step one test experienced error was found related
to amber12 installation and also 2 file comparison failures in
amber12tools installation. I think this is because of the rounding
off differences.
In the next step for the parallel installation, first I tried to
install mpich2 using macports by giving the below command.
sudo port install mpich2 +gcc44
But after a overnight of time the installation was not complete.
It was not moving from one step called configure. so i cancelled it.
Then first i downloaded the openmpi version 1.5.4 and extracted inside
the $AMBERHOME/AmberTools/src directory and ran the configure_openmpi
script with compiler option as gnu as below
cd $AMBERHOME/AmberTools/src
./configure_openmpi gnu
Then I went to AMBERHOME directory and ran the configure script as below
cd $AMBERHOME
./configure -mpi gnu
This step went fine without any error. I also added the below line to
the bashrc file.
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\:$AMBERHOME/lib
In the next step (make install), it throw the error.
make install
Then the parallel installation was not successful.
Then I followed the same procedure as openmpi for the mpich2 (V 1.4.1)
installation and configuration. The mpich2 installation went fine
without error. But the ./configure -mpi gnu step ended with error.
The error outputs from the mpich2 configuration step was posted in
the AMBER mailing list.
For your information I have also other mpich installations in the
below directories. which is been used by other applications.
/Volumes/data/common/mpich/ch_p4/bin/mpicc
/Volumes/data/common/mpich2/bin/mpicc
/Volumes/data/common/mpich2-64/bin/mpicc
May be the older version of installation may cause the problem.
As suggested in your previous mail to me i also ran the below commands
and the output also given here.
applecluster:~ admin$ which mpif90
/usr/bin/mpif90
applecluster:~ admin$ which mpicc
/common/mpich/ch_p4/bin/mpicc
applecluster:~ admin$ icc --version
icc (ICC) 11.0 20090318
Copyright (C) 1985-2009 Intel Corporation. All rights reserved.
applecluster:~ admin$ mpicc -show
cc -DUSE_STDARG -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_UNISTD_H=1
-DHAVE_STDARG_H=1 -DUSE_STDARG=1 -DMALLOC_RET_VOID=1
-L/common/mpich/ch_p4/lib -lpmpich -lmpich -lpmpich -lmpich
Thanks
M.Prabu
On Wed, Aug 1, 2012 at 7:38 PM, David A Case <case.biomaps.rutgers.edu> wrote:
>
> On Wed, Aug 01, 2012, Prabu Manoharan wrote:
> >
> > I am successful in installing both openmpi and mpich2 (as per the
> > procedure given in the ambertools manual)
>
> It was not the intent to have people install both MPI versions. I think you
> will get the one that was installed last, but I'm not sure we have tested for
> conflicts.
>
> I would be better to say what you actually did. Just saying "per the
> procedure in the manual" leaves a lot of uncertainty.
>
> >
> > applecluster:amber12 admin$ make install
> > cd AmberTools/src && make install
> > Starting installation of AmberTools12 MPI at Wed Aug 1 17:33:45 IST 2012.
> > (cd etc && make parallel)
> > mpif90 -DBINTRAJ -DMPI -o numprocs numprocs.F90
> > ld: warning: -macosx_version_min not specificed, assuming 10.6
> > ld: warning: could not create compact unwind for _main: register 3
> > saved somewhere other that in frame
> > ld: warning: could not create compact unwind for _MAIN__: register 6
> > saved somewhere other that in frame
> > ld: warning: ignoring file
> > /opt/local/lib/gcc46/gcc/i386-apple-darwin9/4.6.3//libgcc.a, file was
> > built for archive which is not the architecture being linked (x86_64)
>
> We don't know which mpif90 you are running. Could you provide the output from
> "which mpif90"? It looks like your MPI installation cannot be used to compile
> any fortran programs.
>
> > (cd sff && make libsff_mpi )
> > mpicc -c -Dflex -O3 -mtune=native -msse -mfpmath=sse -DBINTRAJ -DHASGZ
> > -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI
> > -I/Volumes/data/common/amber12/include -o binpos.o binpos.c
> > icc: command line error: invalid argument for option '-mtune'
>
> Here you are accessing an mpicc that uses the Intel compilers, but you
> said earlier in your post that you were using the gnu compilers. You have
> to be consistent; this is also the reason I wanted to know exactly how you
> installed your MPI. It would help to know the output of the following
> commands:
>
> which mpicc
> icc --version
> mpicc --show (or mpicc -show)
>
> Jason is correct that you can probably install MPI from macports. But we
> would certainly like to figure out why the scripts we provide are not working.
>
> Finally, since you say you are new to Amber: be sure you really need the
> parallel capability before investing a lot of time in getting it to work.
>
> ...good luck....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
M. Prabu
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Received on Thu Aug 02 2012 - 06:00:04 PDT
