Miguel Quiliano Meza wrote:
Hi everyone.
I followed the steps in
http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites
for my problem, but I obtained problems at the moment to perform "make".
So, as mention the web page of gromacs...
If you get errors during GROMACS compilation (the "make" step) that
suggest that you "recompile with -fPIC," then you should return to this
FFTW stage and configure with |--enable-shared| or |--with-pic|.
By the way, previously I performed "make" with FFTW version 3.2.2
(default version in rocks cluster 5.4)
I did:
root@bioinfocluster fftw-3.2.2]# ./configure --enable-threads
--prefix=/share/apps/opt/fftw
Without errors, and then:
[root@bioinfocluster fftw-3.2.2]# make
make[3]: Leaving directory `/share/apps/src/fftw-3.2.2/tools'
make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/tools'
Making all in m4
make[2]: Entering directory `/share/apps/src/fftw-3.2.2/m4'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/m4'
make[1]: Leaving directory `/share/apps/src/fftw-3.2.2'
What could be the problem? please advices.
There is no problem, per se, with what you did. FFTW appears to have been
installed fine. However, as noted in the above quote from the Installation
Instructions, you will need to re-install FFTW using one of the options listed.
-Justin
Miguel Quiliano.
Miguel Quiliano Meza 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
This issue and its resolution are specifically described in the
installation
instructions:
http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites
(Under the "a few tips" heading)
-Justin
> /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>
<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 <http://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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