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

[Justin A. Lemkul]

On 5/23/12 7:55 PM, aiqunhuang at knights.ucf.edu wrote:
>
>
> Hi everybody,
>
> I am installing Gromacs, in the shell it is said that Gromacs has been installed :
>
> GROMACS is installed under /home/Program/gromacs-4.5.
>
> but I couldn't find the directory bin under /gromacs-4.5, I don't know I have
> installed su! c cessfully or not, any one could help?
>
> Here is the commands which I used to install Gromacs, my system is Ubuntu 11.10,
> gcc complier.
>
> There are some errors in config.log saying: gcc: fatal error no imput files. !
>

With respect to what?

> I don't know if this matters or not, i tried to fix the fatal errors in log
> file, but I didn't get anywhere.
>

What were the errors and what did you do to fix them?  Anything catastrophic 
should have been printed in a more obvious form to the terminal.

> In the last part of showing up in the shell it says something like this:
>
> /usr/bin/install -c -m 644 'xpm2ps.1'
> '/home/Program/gromacs-4.5/share/man/man1/xpm2ps_mpi.1'
>
> but I couldn't find man/man1 under /gromacs-4.5/share/, anyone could help?
> installation 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/la! m -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
> ./configure --enable-float --enable-mpi --prefix=/home/Program/fftw-3.3.1

You don't need an MPI-enabled version of FFTW.

> 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

You should not compile the complete Gromacs distribution with MPI.  There is no 
need for it; only mdrun is MPI-aware, and in version 4.5 and onward, can make 
use of threads instead, if your architecture supports it.

> sudo make install

You likely don't need superuser privileges to write in the /home directory or 
subdirectories thereof.  Note as well that you're attempting to write to 
/home/Program/gromacs-4.5, but the output below indicates you're looking in 
/home/qunzi/Program/gromacs-4.5; I suspect this is your problem.  You're either 
installing or looking in the wrong place.  I would also recommend you not 
install Gromacs within the source tree - choose a new location for the 
installation and consider installing version 4.5.5 rather than an old version (4.5).

-Justin

> *Here below are the last &n! bs p;part of output in the shell after I run "sudo
> make install"*
> /usr/bin/install -c -m 644 'trjorder.1'
> '/home/Program/gromacs-4.5/share/man/man1/trjorder_mpi.1'
> /usr/bin/install -c -m 644 'xpm2ps.1'
> '/home/Program/gromacs-4.5/share/man/man1/xpm2ps_mpi.1'
> make[3]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man/man1'
> make[2]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man/man1'
> Making install in man7
> make[2]: Entering directory `/home/qunzi/Program/gromacs-4.5/man/man7'
> make[3]: Entering directory `/home/qunzi/Program/gromacs-4.5/man/man7'
> make[3]: Nothing to be done for `install-exec-am'.
> test -z "/home/Program/gromacs-4.5/share/man/man7" || /bin/mkdir -p
> "/home/Program/gromacs-4.5/share/man/man7"
> /usr/bin/install -c -m 644 'gromacs.7'
> '/home/Program/gromacs-4.5/share/man/man7/gromacs_mpi.7'
> make[3]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man/man7'
> make[2]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man/man7'
> make[2]: Entering directory `/home/qunzi/Program/gromacs-4.5/man'
> make[3]: Entering directory `/home/qunzi/Program/gromacs-4.5/man'
> make[3]: Nothing to be done for `install-exec-am'.
> make[3]: Nothing to be done for `install-data-am'.
> make[3]: Leaving directory ! `/h ome/qunzi/Program/gromacs-4.5/man'
> make[2]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man'
> make[1]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man'
> make[1]: Entering directory `/home/qunzi/Program/gromacs-4.5'
> make[2]: Entering directory `/home/qunzi/Program/gromacs-4.5'
> make install-exec-hook
> make[3]: Entering directory `/home/qunzi/Program/gromacs-4.5'
>
> GROMACS is installed under /home/Program/gromacs-4.5.
> Make sure to update your PATH and MANPATH to find the
> programs and unix manual pages, and possibly LD_LIBRARY_PATH
> or /etc/ld.so.conf if you are using dynamic libraries.
>
> Please run "make tests" now to verify your installation.
>
> If you want links to the executables in /usr/local/bin,
> you can issue "make links" now.
> make[3]: Leaving directory `/home/qunzi/Program/gromacs-4.5'
> make[2]: Nothing to be done for `install-data-am'.
> make[2]: Leaving directory `/home/qunzi/Program/gromacs-4.5'
> make[1]: Leaving directory `/home/qunzi/Program/gromacs-4.5'
> qunzi at qunzi-AO722:~/Program/gromacs-4.5$ ls
> acinclude.m4 AUTHORS config configure COPYING-GPU include Makefile man share
> aclocal.m4 cmake config.log configure.ac Doxyfile ! ; INSTALL-GPU Makefile.am
> README src
> admin CMakeLists.txt config.status COPYING Doxyfile.in libtool Makefile.in
> scripts tests
> qunzi at qunzi-AO722:~/Program/gromacs-4.5$ echo $PATH
> /opt/intel/bin:/opt/intel/bin:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/Program/lam-7.1.4/bin
> qunzi at qunzi-AO722:~/Program/gromacs-4.5$ make tests
> make: `tests' is up to date.
> qunzi at qunzi-AO722:~/Program/gromacs-4.5$ make tests
> make: `tests' is up to date.
> qunzi at qunzi-AO722:~/Program/gromacs-4.5$ man mdrun_mpi
> No manual entry for mdrun_mpi
> See 'man 7 undocumented' for help when manual pages are not available.
> qunzi at qunzi-AO722:~/Program/gromacs-4.5$ man mdrun_mpi.1
> No manual entry for mdrun_mpi.1
> qunzi at qunzi-AO722:~/Program/gromacs-4.5$
>
> **
>
>

-- 
========================================

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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