Hello,<div>I solved the MPI problem by setting MPI='CUSTOM'</div><div><br></div><div>Anyway, I still can not use successfully gmake. I tried the WaveDemo again and was almost ready, when:</div><div><br></div><div>---------------------------------------------------------------------------------------</div>
<div><div>Checking status of thorn CactusBindings</div><div>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</div>
<div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_bcs':</div><div>(.text+0x0): multiple definition of `_mp_bcs'</div><div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x0): first defined here</div>
<div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_p':</div><div>(.text+0x7): multiple definition of `omp_set_lock'</div><div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x20): first defined here</div>
<div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_p':</div><div>(.text+0x7): multiple definition of `_mp_p'</div><div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x20): first defined here</div>
<div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_ecs':</div><div>(.text+0x60): multiple definition of `_mp_ecs'</div><div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x10): first defined here</div>
<div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_v':</div><div>(.text+0x67): multiple definition of `omp_unset_lock'</div><div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x30): first defined here</div>
<div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_v':</div><div>(.text+0x67): multiple definition of `_mp_v'</div><div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x30): first defined here</div>
<div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_ptest':</div><div>(.text+0x70): multiple definition of `_mp_ptest'</div><div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x40): first defined here</div>
<div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgmp.a(crit.o): In function `_mp_incr':</div><div>(.text+0x80): multiple definition of `_mp_incr'</div><div>/opt/pgi/11.9.0/linux86-64/11.9/lib/libpgc.a(crit_dum.o):(.text+0x50): first defined here</div>
<div>gmake[1]: *** [/global/u1/f/fiestas/CACTUS_hopper/Cactus/exe/cactus_WaveDemo] Error 2</div><div>gmake: *** [WaveDemo] Error 2</div><div>---------------------------------------------------------------------------------------<br>
</div><div><br></div><div>CactusBindings appears to me strange, because I can not find it in the arrangements. </div><div><br></div><div>Somebody has an idea about this error?</div><div><br></div><div>Or another simple example just to check gmake?</div>
<div><br></div><div>Thanks,</div><div>Jose</div><div><br></div><br><div class="gmail_quote">On Mon, Mar 12, 2012 at 11:57 PM, Jose Fiestas Iquira <span dir="ltr"><<a href="mailto:jafiestas@lbl.gov">jafiestas@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello Ian, all,<div><br></div><div>I am trying now to use gmake to create an executable using McLachlan for a simulation of binary coalescence.</div>
<div><br></div><div><div>When I do:</div><div> gmake grbinary</div><div><br>
</div><div>I obtain:</div><div><div>.....</div><div>CST finished.</div><div>/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.</div>
<div>gmake: *** [grbinary] Error 2</div></div></div><div>..........</div><div><br></div><div>I checked the configuration and I found following line while doing: gmake grbinary-config thornlist='thornlists/<a href="http://grbinary.th" target="_blank">grbinary.th</a>'</div>
<div><br></div><div>............</div><div>Configuring without MPI</div><div>............</div><div><br></div><div>So, I tried:</div><div><br></div><div>export mpi=native</div><div>gmake grbinary-config</div><div><br></div>
<div>and</div><div><br></div><div>- setting mpi=native in a config. file and using it</div><div>gmake grbinary-config options='grbinary-config.txt' </div><div><br></div><div>Initially looks OK:</div><div><br></div>
<div><div>fiestas@hopper09:~/CACTUS/Cactus> gmake grbinarypgi-config options='grbinary-config-pgi' </div><div>Cactus - version: 4.0.0</div><div>Reconfiguring grbinarypgi.</div><div>Adding configuration options from 'grbinary-config-pgi'...</div>
<div> Setting mpi to 'native'</div><div> Setting CC to 'mpicc'</div><div> Setting CXX to 'mpicxx'</div><div>End of options from 'grbinary-config-pgi'.</div>....</div><div><br></div><div>
but later I get again the message:</div><div><br></div><div>...........</div><div>Configuring without MPI</div><div>........</div><div><br></div><div>Am I doing something wrong?</div><div><br></div><div>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?</div>
<div><br></div><div>Thanks,</div><div>Jose</div><div><br></div><div><br><div class="gmail_quote">On Mon, Mar 12, 2012 at 4:24 AM, Ian Hinder <span dir="ltr"><<a href="mailto:ian.hinder@aei.mpg.de" target="_blank">ian.hinder@aei.mpg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><br>
On 10 Mar 2012, at 01:41, Jose Fiestas Iquira wrote:<br>
<br>
> Dear colleagues,<br>
><br>
> I was trying the last days to install an own application based on ETK in<br>
> NERSC machines (Hopper/Carver), having some problems during the compilation.<br>
> Before trying to find the real problem, I started from scratch and realize<br>
> I can not even checkout ETK properly.<br>
> Does somebody tried it in machines different as LONI machines since the<br>
> last release? Would appreciate any experience about it.<br>
> Below my steps:<br>
><br>
><br>
> 1. GetComponents <Einstein Toolkit> (release version)<br>
> curl -O <a href="https://raw.github.com/gridaphobe/CRL/master/GetComponents" target="_blank">https://raw.github.com/gridaphobe/CRL/master/GetComponents</a><br>
> ..............................<br>
</div>> *183 components checked out.*<br>
> * 0 components updated.*<br>
> *<br>
> *<br>
> * Unable to process simfactory2*<br>
> * Unable to process LSUThorns/QuasiLocalMeasures*<br>
> * Unable to process LSUThorns/SummationByParts*<br>
> * Unable to process LSUThorns/Vectors*<br>
<br>
These are all hosted on <a href="http://svn.cct.lsu.edu" target="_blank">svn.cct.lsu.edu</a>, 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?<br>
<br>
We might want to think about moving these repositories to a more reliable server, for example <a href="http://svn.einsteintoolkit.org" target="_blank">svn.einsteintoolkit.org</a>.<br>
<br>
Alternatively, it might be that there is a routing problem between NERSC and CCT. Can you try<br>
<br>
ping <a href="http://svn.cct.lsu.edu" target="_blank">svn.cct.lsu.edu</a><br>
<br>
from one of the affected machines?<br>
<br>
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).<br>
<br>
The Cactus thornlists are out of date - see<br>
<br>
<a href="https://trac.einsteintoolkit.org/ticket/663" target="_blank">https://trac.einsteintoolkit.org/ticket/663</a><br>
<br>
and<br>
<br>
<a href="https://trac.einsteintoolkit.org/ticket/641" target="_blank">https://trac.einsteintoolkit.org/ticket/641</a><br>
<br>
> *<br>
> *<br>
> *Summary of Warnings:*<br>
> *<br>
> *<br>
> *Could not checkout module simfactory2*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *Could not checkout module LSUThorns/QuasiLocalMeasures*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *Could not checkout module LSUThorns/SummationByParts*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *Could not checkout module LSUThorns/Vectors*<br>
> *<br>
> *<br>
><br>
> * Time Elapsed: 26 minutes, 19 seconds*<br>
<div>> ..............................................<br>
><br>
> 2. GetComponent <WaveDemo><br>
> ./GetComponents<br>
> <a href="http://cactuscode.org/documentation/tutorials/wavetoydemo/WaveDemo.th" target="_blank">http://cactuscode.org/documentation/tutorials/wavetoydemo/WaveDemo.th</a><br>
><br>
</div>> * Went OK*<br>
> *<br>
<div>> *<br>
> 3. cd Cactus<br>
> gmake WaveDemo-config<br>
> gmake WaveDemo<br>
><br>
><br>
</div>> *------------------------------------------------------*<br>
> *Warnings were generated during execution of the CST*<br>
> *------------------------------------------------------*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *CST error 1:*<br>
> * -> Duplicate thornname LocalReduce in CactusBase and CactusNumerical*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *CST error 2:*<br>
> * -> Thorn 'CarpetLib' requires the capability 'Vectors'.*<br>
> * Please add a thorn that provides 'Vectors' to your ThornList or<br>
> remove 'CarpetLib' from it !*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *CST error 3:*<br>
> * -> Thorn 'ML_BSSN' requires the capability 'Vectors'.*<br>
> * Please add a thorn that provides 'Vectors' to your ThornList or<br>
> remove 'ML_BSSN' from it !*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *CST error 4:*<br>
> * -> Thorn 'ML_BSSN_O2' requires the capability 'Vectors'.*<br>
> * Please add a thorn that provides 'Vectors' to your ThornList or<br>
> remove 'ML_BSSN_O2' from it !*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *CST error 5:*<br>
> * -> ID_BIN_BH (thorn Meudon_Bin_BH) inherits from SummationByParts*<br>
> * No thorn in your current ThornList implements SummationByParts*<br>
> * Either remove Meudon_Bin_BH, or add a thorn to your*<br>
> * ThornList implementing SummationByParts*<br>
> * Available thorns in arrangements directory implementing<br>
> SummationByParts:*<br>
> * LSUThorns/SummationByParts*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *CST error 6:*<br>
> * -> MEUDON_BIN_NS (thorn Meudon_Bin_NS) inherits from SummationByParts*<br>
> * No thorn in your current ThornList implements SummationByParts*<br>
> * Either remove Meudon_Bin_NS, or add a thorn to your*<br>
> * ThornList implementing SummationByParts*<br>
> * Available thorns in arrangements directory implementing<br>
> SummationByParts:*<br>
> * LSUThorns/SummationByParts*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *CST error 7:*<br>
> * -> Configuration script for thorn BLAS returned exit code 1*<br>
> * Error message: 'Error while building BLAS. Aborting.'*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *CST error 8:*<br>
> * -> Configuration script for thorn LAPACK returned exit code 1*<br>
> * Error message: 'Error while building LAPACK. Aborting.'*<br>
> *<br>
> *<br>
> *------------------------------------------------------*<br>
> *<br>
> *<br>
> *gmake[1]: ***<br>
> [/project/projectdirs/snfactry/hshukla/CACTUS/Cactus/configs/WaveDemo/config-data/make.thornlist]<br>
> Error 1*<br>
> *gmake: *** [WaveDemo] Error 2*<br>
> *<br>
> *<br>
> *<br>
> *<br>
<div>> *<br>
> 4. Copied LSUThorns by hand and repeated step 3 and got the same errors.<br>
</div>> *<br>
><br>
> *183 components checked out.*<br>
> * 0 components updated.*<br>
> *<br>
> *<br>
> * Unable to process simfactory2*<br>
> * Unable to process LSUThorns/QuasiLocalMeasures*<br>
> * Unable to process LSUThorns/SummationByParts*<br>
> * Unable to process LSUThorns/Vectors*<br>
> *<br>
> *<br>
> *Summary of Warnings:*<br>
> *<br>
> *<br>
> *Could not checkout module simfactory2*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *Could not checkout module LSUThorns/QuasiLocalMeasures*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *Could not checkout module LSUThorns/SummationByParts*<br>
> *<br>
> *<br>
> *<br>
> *<br>
> *Could not checkout module LSUThorns/Vectors*<br>
> *<br>
> *<br>
><br>
> * Time Elapsed: 26 minutes, 19 seconds*<br>
<div><div>><br>
> Best,<br>
> Jose<br>
> _______________________________________________<br>
> Users mailing list<br>
> <a href="mailto:Users@einsteintoolkit.org" target="_blank">Users@einsteintoolkit.org</a><br>
> <a href="http://lists.einsteintoolkit.org/mailman/listinfo/users" target="_blank">http://lists.einsteintoolkit.org/mailman/listinfo/users</a><span class="HOEnZb"><font color="#888888"><br>
<br>
--<br>
</font></span></div></div><span class="HOEnZb"><font color="#888888"><span><font color="#888888">Ian Hinder<br>
<a href="http://numrel.aei.mpg.de/people/hinder" target="_blank">http://numrel.aei.mpg.de/people/hinder</a><br>
<br>
</font></span></font></span></blockquote></div><br></div>
</blockquote></div><br></div>