[Users] Using gmake - Re: ETK in NERSC machines (Hopper/Carver) does not work properly

Jose Fiestas Iquira jafiestas at lbl.gov
Wed Mar 14 16:27:03 CDT 2012


Hello,

I wrote the mail too fast (or my google account tried to correct my text :(.

I sent binary.th but will try THORNLIST. Thanks.

By using hopper_intel.cfg I realized I need to give it the whole path, so:

gmake grbinary-config
CACTUS_CONFIG_FILES='/global/homes/f/fiestas/Cactus/hopper-intel.cfg'
thornlist='grbinary.th'

otherwise it will not find it.

This:

gmake grbinary-config CACTUS_CONFIG_FILES='hopper-intel.cfg' thornlist='
grbinary.th'

does not work.

Is it normal?

Thanks,
Jose

On Wed, Mar 14, 2012 at 3:25 AM, Ian Hinder <ian.hinder at aei.mpg.de> wrote:

>
> On 14 Mar 2012, at 10:48, Jose Fiestas Iquira wrote:
>
> > As mentioned, using the configuration files located in
> simfactory/mdb/optionslists/ helped. And compiling with gmake worked.
> >
> > The only thing it confuses me is that after
> >
> > gmake binary-config thornlist='binary,th'
>
> It should be THORNLIST not thornlist, and it should be binary.th not
> binary,th.  You don't need the single quotes around the thornlist name, as
> it does not contain any shell-special characters.
>
> In an ideal world, Cactus would complain that you had specified an
> unrecognised argument (thornlist).  Unfortunately, the current "make"-based
> system makes that impossible.  There is an open ticket which would solve
> this problem if it was addressed:
> https://trac.einsteintoolkit.org/ticket/332.
>
> > I always need to copy the binary,th in configs/binary/
> >
> > and then
> >
> > gmake binary
> >
> > otherwise, the compiler uses all thorns in the arrangements directory,
> and not only the listed in binary.th. It should not, right?
>
> Since cactus thinks you have not given it any thornlist, it defaults to a
> thornlist containing all available thorns.
>
> May I ask, why you are not using simfactory?
>
>
> >
> > Best,
> > Jose
> >
> >
> > On Tue, Mar 13, 2012 at 1:25 AM, Ian Hinder <ian.hinder at aei.mpg.de>
> wrote:
> >
> > On 13 Mar 2012, at 07:57, Jose Fiestas Iquira wrote:
> >
> > > Hello Ian, all,
> > >
> > > I am trying now to use gmake to create an executable using McLachlan
> for a
> > > simulation of binary coalescence.
> > >
> > > When I do:
> > > gmake grbinary
> > >
> > > I obtain:
> > > .....
> > > CST finished.
> > >
> /global/u1/f/fiestas/CACTUS/Cactus/arrangements/Carpet/CarpetLib/src/make.configuration.defn:5:
> > > *** Configuration error: The Carpet thorns require MPI.  Please
> configure
> > > with MPI, or remove the Carpet thorns from the ThornList..  Stop.
> > > gmake: *** [grbinary] Error 2
> > > ..........
> > >
> > > I checked the configuration and I found following line while
> > > doing: gmake grbinary-config thornlist='thornlists/grbinary.th'
> > >
> > > ............
> > > Configuring without MPI
> > > ............
> > >
> > > So, I tried:
> > >
> > > export mpi=native
> > > gmake grbinary-config
> > >
> > > and
> > >
> > > - setting mpi=native in a config. file and using it
> > > gmake grbinary-config options='grbinary-config.txt'
> > >
> > > Initially looks OK:
> > >
> > > fiestas at hopper09:~/CACTUS/Cactus> gmake grbinarypgi-config
> > > options='grbinary-config-pgi'
> > > Cactus - version: 4.0.0
> > > Reconfiguring grbinarypgi.
> > > Adding configuration options from 'grbinary-config-pgi'...
> > >  Setting mpi to 'native'
> > >  Setting CC to 'mpicc'
> > >  Setting CXX to 'mpicxx'
> > > End of options from 'grbinary-config-pgi'.
> > > ....
> > >
> > > but later I get again the message:
> > >
> > > ...........
> > > Configuring without MPI
> > > ........
> > >
> > > Am I doing something wrong?
> > >
> > > Btw, if I configure with my own thronlist and add it as above, it keeps
> > > reading all thorns in the arrangements directory while compiling. So, I
> > > copied my thornlist in configs/grbinary/ to force the compilation
> using my
> > > thornlist. Is it normal?
> >
> > Hi Jose,
> >
> > You have not specified an optionlist.  There are a large number of
> variables which usually need to be set on HPC machines (compiler locations,
> flags, library paths, MPI paths etc).  I strongly recommend that you use
> simfactory for this, as I believe that most of the work has already been
> done for the NERSC machines.  If there is a problem with the configuration
> of simfactory on these machines, then we can help to find the problem and
> fix it.  Building up an optionlist and submit script etc from scratch will
> take a lot of time if you aren't very familiar with the machine and Cactus.
> >
> >
> >
> > >
> > > Thanks,
> > > Jose
> > >
> > >
> > > On Mon, Mar 12, 2012 at 4:24 AM, Ian Hinder <ian.hinder at aei.mpg.de>
> wrote:
> > >
> > >>
> > >> On 10 Mar 2012, at 01:41, Jose Fiestas Iquira wrote:
> > >>
> > >>> Dear colleagues,
> > >>>
> > >>> I was trying the last days to install an own application based on
> ETK in
> > >>> NERSC machines (Hopper/Carver), having some problems during the
> > >> compilation.
> > >>> Before trying to find the real problem, I started from scratch and
> > >> realize
> > >>> I can not even checkout ETK properly.
> > >>> Does somebody tried it in machines different as LONI machines since
> the
> > >>> last release? Would appreciate any experience about it.
> > >>> Below my steps:
> > >>>
> > >>>
> > >>> 1. GetComponents <Einstein Toolkit>  (release version)
> > >>> curl -O https://raw.github.com/gridaphobe/CRL/master/GetComponents
> > >>> ..............................
> > >>> *183 components checked out.*
> > >>> *  0 components updated.*
> > >>> *
> > >>> *
> > >>> *  Unable to process simfactory2*
> > >>> *  Unable to process LSUThorns/QuasiLocalMeasures*
> > >>> *  Unable to process LSUThorns/SummationByParts*
> > >>> *  Unable to process LSUThorns/Vectors*
> > >>
> > >> These are all hosted on svn.cct.lsu.edu, which we have found to be
> very
> > >> unreliable.  It might be that the machine (or connection) was down
> when you
> > >> tried it.  Can you try it again?
> > >>
> > >> We might want to think about moving these repositories to a more
> reliable
> > >> server, for example svn.einsteintoolkit.org.
> > >>
> > >> Alternatively, it might be that there is a routing problem between
> NERSC
> > >> and CCT.  Can you try
> > >>
> > >>       ping svn.cct.lsu.edu
> > >>
> > >> from one of the affected machines?
> > >>
> > >> PS: your WaveDemo build fails because the wavedemo thornlist is not
> up to
> > >> date.  It needs to be modified to include the Vectors thorn (see the
> ET
> > >> thornlist for an example).
> > >>
> > >> The Cactus thornlists are out of date - see
> > >>
> > >>       https://trac.einsteintoolkit.org/ticket/663
> > >>
> > >> and
> > >>
> > >>       https://trac.einsteintoolkit.org/ticket/641
> > >>
> > >>> *
> > >>> *
> > >>> *Summary of Warnings:*
> > >>> *
> > >>> *
> > >>> *Could not checkout module simfactory2*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *Could not checkout module LSUThorns/QuasiLocalMeasures*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *Could not checkout module LSUThorns/SummationByParts*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *Could not checkout module LSUThorns/Vectors*
> > >>> *
> > >>> *
> > >>>
> > >>> *  Time Elapsed: 26 minutes, 19 seconds*
> > >>> ..............................................
> > >>>
> > >>> 2. GetComponent  <WaveDemo>
> > >>> ./GetComponents
> > >>>
> http://cactuscode.org/documentation/tutorials/wavetoydemo/WaveDemo.th
> > >>>
> > >>> * Went OK*
> > >>> *
> > >>> *
> > >>> 3.  cd Cactus
> > >>> gmake WaveDemo-config
> > >>> gmake WaveDemo
> > >>>
> > >>>
> > >>> *------------------------------------------------------*
> > >>> *Warnings were generated during execution of the CST*
> > >>> *------------------------------------------------------*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *CST error 1:*
> > >>> *  -> Duplicate thornname LocalReduce in CactusBase and
> CactusNumerical*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *CST error 2:*
> > >>> *  -> Thorn 'CarpetLib' requires the capability 'Vectors'.*
> > >>> *     Please add a thorn that provides 'Vectors' to your ThornList or
> > >>> remove 'CarpetLib' from it !*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *CST error 3:*
> > >>> *  -> Thorn 'ML_BSSN' requires the capability 'Vectors'.*
> > >>> *     Please add a thorn that provides 'Vectors' to your ThornList or
> > >>> remove 'ML_BSSN' from it !*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *CST error 4:*
> > >>> *  -> Thorn 'ML_BSSN_O2' requires the capability 'Vectors'.*
> > >>> *     Please add a thorn that provides 'Vectors' to your ThornList or
> > >>> remove 'ML_BSSN_O2' from it !*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *CST error 5:*
> > >>> *  -> ID_BIN_BH (thorn Meudon_Bin_BH) inherits from SummationByParts*
> > >>> *     No thorn in your current ThornList implements SummationByParts*
> > >>> *     Either remove Meudon_Bin_BH, or add a thorn to your*
> > >>> *      ThornList implementing SummationByParts*
> > >>> *     Available thorns in arrangements directory implementing
> > >>> SummationByParts:*
> > >>> *        LSUThorns/SummationByParts*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *CST error 6:*
> > >>> *  -> MEUDON_BIN_NS (thorn Meudon_Bin_NS) inherits from
> SummationByParts*
> > >>> *     No thorn in your current ThornList implements SummationByParts*
> > >>> *     Either remove Meudon_Bin_NS, or add a thorn to your*
> > >>> *      ThornList implementing SummationByParts*
> > >>> *     Available thorns in arrangements directory implementing
> > >>> SummationByParts:*
> > >>> *        LSUThorns/SummationByParts*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *CST error 7:*
> > >>> *  -> Configuration script for thorn BLAS returned exit code 1*
> > >>> *     Error message: 'Error while building BLAS. Aborting.'*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *CST error 8:*
> > >>> *  -> Configuration script for thorn LAPACK returned exit code 1*
> > >>> *     Error message: 'Error while building LAPACK. Aborting.'*
> > >>> *
> > >>> *
> > >>> *------------------------------------------------------*
> > >>> *
> > >>> *
> > >>> *gmake[1]: ***
> > >>>
> > >>
> [/project/projectdirs/snfactry/hshukla/CACTUS/Cactus/configs/WaveDemo/config-data/make.thornlist]
> > >>> Error 1*
> > >>> *gmake: *** [WaveDemo] Error 2*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> 4.  Copied LSUThorns by hand and repeated step 3 and got the same
> errors.
> > >>> *
> > >>>
> > >>> *183 components checked out.*
> > >>> *  0 components updated.*
> > >>> *
> > >>> *
> > >>> *  Unable to process simfactory2*
> > >>> *  Unable to process LSUThorns/QuasiLocalMeasures*
> > >>> *  Unable to process LSUThorns/SummationByParts*
> > >>> *  Unable to process LSUThorns/Vectors*
> > >>> *
> > >>> *
> > >>> *Summary of Warnings:*
> > >>> *
> > >>> *
> > >>> *Could not checkout module simfactory2*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *Could not checkout module LSUThorns/QuasiLocalMeasures*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *Could not checkout module LSUThorns/SummationByParts*
> > >>> *
> > >>> *
> > >>> *
> > >>> *
> > >>> *Could not checkout module LSUThorns/Vectors*
> > >>> *
> > >>> *
> > >>>
> > >>> *  Time Elapsed: 26 minutes, 19 seconds*
> > >>>
> > >>> Best,
> > >>> Jose
> > >>> _______________________________________________
> > >>> Users mailing list
> > >>> Users at einsteintoolkit.org
> > >>> http://lists.einsteintoolkit.org/mailman/listinfo/users
> > >>
> > >> --
> > >> Ian Hinder
> > >> http://numrel.aei.mpg.de/people/hinder
> > >>
> > >>
> >
> > --
> > Ian Hinder
> > http://numrel.aei.mpg.de/people/hinder
> >
> >
>
> --
> Ian Hinder
> http://numrel.aei.mpg.de/people/hinder
>
>
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