[gmx-users] Gromacs installed , but no directory /bin under it

[Justin A. Lemkul]

On 5/23/12 10:06 PM, aiqunhuang at knights.ucf.edu wrote:
> Hi Justin,
>
> I am gonna reinstall Gromacs 4.5.5, and this time I am not gonna use LAM or MPI.
> But can you explicitly tell me what inconsistencies are in my commands?

Please ignore that earlier remark.  I misread your directory structure when I 
mentioned that.

-Justin

> because after I run 'make distclean' in all directories
> (/home/Program/lam-7.1.4, /home/Program/fftw-3.3.1, /home/Program/gromacs-4.5)I
> probably use these commands again except disabling MPI.
>
> commands:
> 1) tar -zxvf fftw-3.3.1.tar.gz
> tar –zxvf gromacs-4.5.tar.gz
> tar -zxvf lam-7.1.4.tar.gz
>
> (2) cd lam-7.1.3 ./configure --prefix=/home/Program/lam-7.1.4 --with-rsh="ssh-x"
> make
> sudo make install
> (3)
> export PATH=$PATH:/home/Program/lam-7.1.4/bin
>
> (4)
> cd fftw-3.3.1
> &n! bsp; ./configure --enable-float --enable-mpi --prefix=/home/Program/fftw-3.3.1
> make
> make install
> ! (3)
> export CPPFLAGS=-I/home/Program/fftw-3.3.1/include
> export LDFLAGS=-L/home/Program/fftw-3.3.1/lib
>
> (4) cd gromacs-4.5 ./configure --prefix=/home/Program/gromacs-4.5 --enable-mpi
> --program-suffix=_mpi
> make
> sudo make install
>
>
>
>  > Date: Wed, 23 May 2012 21:44:28 +0200
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] Gromacs installed , but no directory /bin under it
>  >
>  >
>  >
>  > On 5/23/12 9:37 PM, aiqunhuang at knights.ucf.edu wrote:
>  > > Hi Justin, thanks a lot for replying.
>  > > Regarding your question, in the beginning there were errors like this in
> config.log:
>  > >
>  > > " cc: error: unrecognized option '-V'
>  > > cc: fatal error: no in! put files
>  > > compilation terminated.
>  > > configure:4343: $? = 4
>  > > configure:4332: cc -qversion >&5
>  > > cc: error: unrecognized option '-qversion'
>  > > cc: fatal error: no input files
>  > > .......
>  > > configure:6186: checking how to run the C preprocessor
>  > > configure:6217: mpicc -E -I/home/Program/fftw-3.3.1/include conftest.c
>  > > configure:6217: $? = 0
>  > > configure:6231: mpicc -E -I/home/Program/fftw-3.3.1/include conftest.c
>  > > conftest.c:21:28: fatal error: ac_nonexistent.h: No such file or directory
>  > > compilation terminated.
>  > > mpicc: No such file o! r directory
>  > > configure:6231: $? = 1
>  > > configure: failed program was:
>  > > .......
>  > >
>  > > Thread model: posix
>  > > gcc version 4.6.1 (Ubuntu/Linaro 4.6.1-9ubuntu3)
>  > > configure:9684: $? = 0
>  > > configure:9673: mpicc -V >! ;&5
>  > > gcc: error: unrecognized option '-V'
>  > > gcc: fatal error: no input files
>  > > compilation terminated.
>  > > configure:9684: $? = 4
>  > > configure:9673: mpicc -qversion >&5
>  > > gcc: error: unrecognized option '-qversion'
>  > > gcc: fatal error: no input files
>  > > compilation terminated
>  > > .....
>  > >
>  > > fatal error: libxml/parser.h: No such file or directory "
>  > >
>  > > I searched a little and found this page
>  > > http://verahill.blogspot.com/2012/01/debian-testing-64-whee!
>  > > zy-compiling_20.html
>  > >
> <http://verahill.blogspot.com/2012/01/debian-testing-64-wheezy-compiling_20.html> to
>  > > run this command
>  > > /sudo apt-get install libxml2-dev /
>  > > /and fixed the last fatal error: /libxml/parser.h: No such file or directory
>  > > but I did't do anything about the other errors
>  >! >
>  >
>  > libxml is an optional package.
>  >
>  > > In the first beginning I tried to install 4.5.5, but I didn't succeed. I got
>  > > something like this"*** No rule to make target `../gmxlib/libgmx_mpi.la',
> needed
>  > > by `libmd_mpi.la'"
>  > > I tried both enable shared and disable shared for cofiguring Gromacs4.5.5. It
>  > > didn't succeed.
>  > >
>  >
>  > This comes from the above error regarding mpicc not being found. I see you
>  > installed lam previously. Don't use it. There are newer and better packages,
>  > and likely you can easily install an Ubuntu package for a modern version of
>  > OpenMPI that will be automatically configured for your environment.
>  >
>  > > Ok, since there are more threads, I won't use mpi. can I ask you that what do
>  > > you mean by " not
>  > > > install Gromacs within the source tree "? Can I create a new folder like
>  > >! ; /home/program and install FFTW and Gromacs and everything needed in the
>  > > /home/program?
>  > >
>  >
>  > You can install programs wherever you like. What I was saying was to choose an
>  > installation such that binaries are not installed as a subdirectory of the
>  > source code. If you're not planning on doing any development, the source just
>  > gunks up disk space, since all you're after is the executables.
>  >
>  > For instance, you may find it useful to install all your programs in some
>  > subdirectory within $HOME. Just be careful to specify the locations correctly.
>  > After sending my last message, I noticed a number of inconsistencies in your
>  > commands that likely refer to nonexistent directories.
>  >
>  > -Justin
>  >
>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul, Ph.D.
>  > Research Scientist
>  > Department of Biochemistry> Virginia Tech
>  > Blacksburg, VA
>  > jalemkul[at]vt.edu | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================