bestenborstel wrote:
Did run sudo make install again, but before I executed configure with
prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before
manually. Content in the gromacs folder: bin include lib share
Gromacs finished again with:
GROMACS is installed under /usr/local/gromacs.
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.
Shall I execute now 'sudo make links' or 'make links', please? Sorry, I also don't really know how to update my PATH variable.
You need sudo. It will write links into /usr/local/bin. It is not strictly
necessary, as you can follow:
http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation
The GMXRC script magically configures your environment for you.
Do I have to execute 'make test' as the Gromacs page says test set is broken?
No, it won't do anything.
Finally, is there something like 'make clean' to allow for a proper, clean
re-installation?
Yes.
-Justin
I thought I better ask again.
Sorry.
Gudrun
Am 16.03.2012 um 20:05 schrieb David van der Spoel:
On 2012-03-16 21:03, bestenborstel wrote:
Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do
whatever I can :-)
What do you ask me please to do?
sudo make install
and check on the screen where the stuff is copied to.
Am 16.03.2012 um 19:54 schrieb David van der Spoel:
On 2012-03-16 20:49, bestenborstel wrote:
Thank you for your quick reply.
'make links' produces:
Saturn:gromacs-4.5.5 gudrun$ make links
cd /usr/local/gromacs/bin&& programs=`ls`&& cd /usr/local/bin&& \
for i in $programs; do \
(test ! -f $i&& ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done
/bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
make: *** [links] Error 1
I have a /usr/local/ but there is no gromacs. Not even after running again
'sudo make -n install'
Sorry, I am not sure where to post this lengthy output.
-n means "not really"
run it without to install.
But do you have permission to write in /usr/local?
Thank you for your help.
Kind regards
Gudrun
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell& Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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