[Users] Using gmake - Re: ETK in NERSC machines (Hopper/Carver) does not work properly
Jose Fiestas Iquira
jafiestas at lbl.gov
Tue Mar 13 06:11:36 CDT 2012
Hello,
I solved the MPI problem by setting MPI='CUSTOM'
Anyway, I still can not use successfully gmake. I tried the WaveDemo again
and was almost ready, when:
---------------------------------------------------------------------------------------
Checking status of thorn CactusBindings
Creating cactus_WaveDemo in /global/u1/f/fiestas/CACTUS_hopper/Cactus/exe
from CactusBase/Boundary CactusBase/CartGrid3D CactusBase/CoordBase
CactusConnect/HTTPD CactusConnect/HTTPDExtra CactusWave/IDScalarWaveC
CactusBase/IOASCII CactusBase/IOBasic CactusIO/IOJpeg CactusBase/IOUtil
CactusPUGHIO/IsoSurfacer CactusBase/LocalReduce CactusPUGH/PUGH
CactusPUGH/PUGHReduce CactusPUGH/PUGHSlab CactusConnect/Socket
CactusBase/SymBase CactusBase/Time CactusWave/WaveBinarySource
CactusWave/WaveToyC ExternalLibraries/libjpeg
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function
`_mp_bcs':
(.text+0x0): multiple definition of `_mp_bcs'
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x0): first
defined here
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_p':
(.text+0x7): multiple definition of `omp_set_lock'
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x20):
first defined here
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_p':
(.text+0x7): multiple definition of `_mp_p'
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x20):
first defined here
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function
`_mp_ecs':
(.text+0x60): multiple definition of `_mp_ecs'
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x10):
first defined here
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_v':
(.text+0x67): multiple definition of `omp_unset_lock'
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x30):
first defined here
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_v':
(.text+0x67): multiple definition of `_mp_v'
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x30):
first defined here
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function
`_mp_ptest':
(.text+0x70): multiple definition of `_mp_ptest'
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x40):
first defined here
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function
`_mp_incr':
(.text+0x80): multiple definition of `_mp_incr'
/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x50):
first defined here
gmake[1]: ***
[/global/u1/f/fiestas/CACTUS_hopper/Cactus/exe/cactus_WaveDemo] Error 2
gmake: *** [WaveDemo] Error 2
---------------------------------------------------------------------------------------
CactusBindings appears to me strange, because I can not find it in the
arrangements.
Somebody has an idea about this error?
Or another simple example just to check gmake?
Thanks,
Jose
On Mon, Mar 12, 2012 at 11:57 PM, Jose Fiestas Iquira <jafiestas at lbl.gov>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?
>
> 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
>>
>>
>
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