This is not very helpful when it comes to debugging. At this point, I would
suggest removing your entire amber10 directory and unpacking a fresh copy,
and starting from scratch. Don't forget to apply bug fixes (AmberTools 1.2
and Amber10).
Then document the *exact* shell commands you issued, and try redirecting all
stderr/stdout streams for all configure/building steps into files that you
can attach if stuff goes wrong. Also, make sure that
echo $MKL_HOME
returns a null string.
To direct stdout and stderr streams for a process (for instance, when making
amber), do the following
make serial > serial.log 2>&1
(if you're using bash). This will dump all output and error messages into
serial.log. Do the same for configure. If you want to look at the output
at the same time as it's dumping into a file, you can do the following:
(make serial 2>&1) | tee serial.log
Also, like I said previously, install protocols change, and our configure
script is usually updated as necessary to reflect that. When Amber10 was
released, these issues didn't exist. These have since been addressed with
the release of Amber11, which has many more features in addition to being
easier to install. It may be advantageous to upgrade.
All the best,
Jason
On Tue, Mar 15, 2011 at 10:45 AM, Dmitry Osolodkin <divanych.rambler.ru>wrote:
> No effect.
>
> On 03/15/2011 08:41 PM, Jason Swails wrote:
> > Hello,
> >
> > It looks to me like things are all messed up. You have undefined
> references
> > to _gfortran_ stuff, which should almost certainly not be there. It
> looks
> > like you have some object files left over from a previous installation
> with
> > the GNU compilers.
> >
> > You should do a make clean in the amber directory and rerun the
> configures.
> >
> > make clean
> > make -f Makefile_at clean
> > unset MKL_HOME
> > ./configure_amber ifort
> > make serial
> >
> > Hope this helps,
> > Jason
> >
> > On Tue, Mar 15, 2011 at 10:29 AM, Dmitry Osolodkin<divanych.rambler.ru
> >wrote:
> >
> >> On 03/15/2011 08:24 PM, David A Case wrote:
> >>>> You can choose
> >>>> to skip using the MKL by unsetting MKL_HOME, and this error should go
> >> away.
> >>>
> >>> Note that this is likely to be a very good choice: performance
> difference
> >> for
> >>> Amber with/without MKL are very minor. If you are having trouble with
> >> MKL,
> >>> you might want to make sure you really need it.
> >>
> >> Without MKL:
> >>
> >> ifort -o addles lesmain.o addspace.o readprm.o writprm.o readcrd.o
> >> writcrd.o pick.o rline.o nxt.o intgr.o find.o of.o
> >> geti.o unit.o getc.o alert.o echo.o get4c.o getd.o
> >> wlesprm.o lesprm.o les2prm.o checksz.o addspace_atm1st.o ../lib/random.o
> >> ../lib/mexit.o ../lib/nxtsec.o -lsvml
> >> ../lib/random.o: In function `amrand_gen_':
> >> _random.f:(.text+0x3cb): undefined reference to `_gfortran_st_write'
> >> _random.f:(.text+0x3e9): undefined reference to
> >> `_gfortran_transfer_character'
> >> _random.f:(.text+0x3f7): undefined reference to
> `_gfortran_st_write_done'
> >> ../lib/random.o: In function `gauss_gen_':
> >>
> >> # bunch of similar lines
> >>
> >> _nxtsec.f:(.text+0x2c80): undefined reference to
> `_gfortran_st_write_done'
> >> _nxtsec.f:(.text+0x2c8c): undefined reference to
> `_gfortran_stop_numeric'
> >> ld: addles: hidden symbol `__intel_cpu_indicator_init' in
> >> /opt/intel/composerxe-2011.2.137/compiler/lib/ia32/libirc.a(cpu_disp.o)
> >> is referenced by DSO
> >> ld: final link failed: Nonrepresentable section on output
> >> make[1]: *** [addles] Error 1
> >>
> >>
> >>
> >>
> >> --
> >> Dmitry Osolodkin
> >> Researcher
> >> Group of Computational Molecular Design
> >> Department of Chemistry
> >> Moscow State University
> >> Moscow 119991 Russia
> >> e-mail: dmitry_o.qsar.chem.msu.ru
> >> Phone: +7-495-9393557
> >> Fax: +7-495-9390290
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
>
> --
> Dmitry Osolodkin
> Researcher
> Group of Computational Molecular Design
> Department of Chemistry
> Moscow State University
> Moscow 119991 Russia
> e-mail: dmitry_o.qsar.chem.msu.ru
> Phone: +7-495-9393557
> Fax: +7-495-9390290
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Mar 15 2011 - 11:30:04 PDT
