Please make sure to keep all discussion on the list.
Miguel Quiliano Meza wrote:
Hi Justin.
Unfortunately, the problem persist. So... for the moment I had to
Well, unless you can provide exact input (commands) and output (error messages)
for what you're doing, you're going to stay stuck, unfortunately.
install GROMACS 4.0.5 (pre-compiled for Rocks 5.4). This is because We
want to know the performance of our cluster.
Could you tell me please one BIG...BIG.. inconvenient for this version?
I mean, I know that in the web page of GROMACS, one can notice it
(http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.0.x), but
for me the majority of updates are unknown, as a product of my few
experience with the program. Will this version permit us run "common"
calculations (a big range )?
Perhaps you can state exactly what you're trying to do. I don't know what "a
big range" of "common calculations" pertains to. You can run MD with any
Gromacs version you like.
If you're looking for differences between the 4.0.x series and 4.5.x, you're
simply looking in the wrong place. Hundreds of relevant updates are listed here:
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x
-Justin
Thanks in advance.
M.
--- El *mar, 12/4/11, Justin A. Lemkul /<jalem...@vt.edu>/* escribió:
De: Justin A. Lemkul <jalem...@vt.edu>
Asunto: Re: How to install GROMACS in Rocks Cluster 5.4 : ERROR
Para: "Miguel Quiliano Meza" <qil...@yahoo.es>
Fecha: martes, 12 de abril, 2011 10:20
The complete output from configuration and compilation are
unnecessary. The text you posted below is enough to solve this
issue. See my post to the list.
-Justin
Miguel Quiliano Meza wrote:
> Hi Justin.
>
> Sorry if I disturb you for this way. But my message to the
GROMACS FORUM has to wait for moderator approval (it`s little
big...). For the moment, I consult my doubt for these mail:
>
> I wrote...
>
>
----------------------------------------------------------------------------------------------------------------------
>
> Dear community.
>
> Justin was right.
>
> I did not want to make the explanation so long, but you're right
I have to put those details. As you will see I had to redirect the
"outputs" after perform "*./configure*" and "*make*" (these files
are attach to this mail).
>
> I sincerely hope you can give their opinions and help.
>
> Thanks in advance.
>
> Miguel Quiliano.
>
> Here are the general procedure:
>
> root@bioinfocluster src]# tar xf gromacs-4.5.4.tar.gz
[root@bioinfocluster src]# export LDFLAGS="-L/opt/rocks/lib"
> [root@bioinfocluster src]# export CPPFLAGS="-I/opt/rocks/include"
> [root@bioinfocluster gromacs-4.5.4]# ./configure --enable-mpi
--prefix=/share/apps/opt/gromacs > output
> [root@bioinfocluster gromacs-4.5.4]# make >output2 mempool.c: In
function '_gmx_sel_mempool_alloc_group':
> mempool.c:201: warning: dereferencing type-punned pointer will
break strict-aliasing rules
> selelem.c: In function '_gmx_selelem_mempool_reserve':
> selelem.c:203: warning: dereferencing type-punned pointer will
break strict-aliasing rules
> selelem.c:208: warning: dereferencing type-punned pointer will
break strict-aliasing rules
> checkpoint.c: In function 'do_cpt_state':
> checkpoint.c:852: warning: dereferencing type-punned pointer will
break strict-aliasing rules
> /usr/bin/ld: /opt/rocks/lib/libfftw3f.a(plan-guru-dft-c2r.o):
relocation R_X86_64_32 against `a local symbol' can not be used when
making a shared object; recompile with -fPIC
> /opt/rocks/lib/libfftw3f.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[3]: *** [libmd_mpi.la <http://libmd_mpi.la/>] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all] Error 2
> make: *** [all-recursive] Error 1
>
-- ========================================
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
========================================
--
========================================
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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