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/>] 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
========================================
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