Users September 2012

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11 participants
25 discussions

Einstein Toolkit Meeting
by Frank Loeffler 02 Sep '12

02 Sep '12

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. While the fall workshop is in planning [1] we should already start to think about the question whether we are interested and willing to organize another new-user workshop next year, and if so whether we should more or less repeat what was done this year or which parts we can improve upon. No details would need to be nailed down, but if we are going ahead we should know and advertise this better sooner than later. Activity last week includes 7 active and still open bugs and four closed issues. 11 Tickets are waiting for review at the moment [2]. Please see if you can help. Frank Loeffler [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Fall_2012 [2] https://trac.einsteintoolkit.org/query?status=review&group=component&col=id…

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Re: [Users] help/advice in getting optionlist working
by Comer Duncan 02 Sep '12

02 Sep '12

Hi, Today I have done a download of Cactus (Lovelace) to my account on the Ohio Supercomputer Center front end. Here is what I did: curl -O https://raw.github.com/gridaphobe/CRL/master/GetComponents chmod a+x GetComponents ./GetComponents --parallel https://svn.einsteintoolkit.org/manifest/trunk/einsteintoolkit.th Next, I have tried building using sim with an experimental optionlist file tuned to OSC (based on one from ranger). I attach the optionlist. While in the Cactus directory I ran: simfactory/bin/sim build --optionlist=./oscmvapich2 --thornlist=thornlists/ einsteintoolkit.th >& sun.attempt2 & With this optionlist the build got farther along. It seemed to decide to build openmpi even though the env variables in the included optionlist file oscmvapich2 is replete with mentions of MPI. It claims that it finished the openmpi build. I have verified that HDF5, LORENE, and MPI have times of build entered in /nfs/05/bgs001/Cactus/configs/sim/scratch/done. I have also more'd the mpi.h file in /nfs/05/bgs001/Cactus/configs/sim/scratch/external/MPI/include so I know it exists. However, make crashes when the build spews: Creating /nfs/05/bgs001/Cactus/configs/sim/lib/libthorn_Socket.a COMPILING /nfs/05/bgs001/Cactus/configs/sim/bindings/build/Formaline/cctk_ThornBindings.c /nfs/05/bgs001/Cactus/arrangements/CactusUtils/Formaline/src/announce.cc(44): catastrophic error: cannot open source file "mpi.h" # include <mpi.h> ^ COMPILING /nfs/05/bgs001/Cactus/arrangements/CactusUtils/Formaline/src/announce.cc COMPILING /nfs/05/bgs001/Cactus/arrangements/CactusUtils/Formaline/src/file.cc /nfs/05/bgs001/Cactus/arrangements/CactusUtils/Formaline/src/announce.cc(44): catastrophic error: cannot open source file "mpi.h" # include <mpi.h> ^ compilation aborted for /nfs/05/bgs001/Cactus/configs/sim/build/Formaline/announce.cc (code 4) make[3]: *** [announce.cc.o] Error 4 make[3]: *** Waiting for unfinished jobs.... Checking status of thorn HydroBase make[2]: *** [make.checked] Error 2 make[1]: *** [/nfs/05/bgs001/Cactus/configs/sim/lib/libthorn_Formaline.a] Error 2 make[1]: *** Waiting for unfinished jobs.... COMPILING /nfs/05/bgs001/Cactus/configs/sim/bindings/build/HydroBase/cctk_ThornBindings.c COMPILING /nfs/05/bgs001/Cactus/arrangements/EinsteinBase/HydroBase/src/StartUp.c COMPILING /nfs/05/bgs001/Cactus/arrangements/EinsteinBase/HydroBase/src/Initialisation.c Creating /nfs/05/bgs001/Cactus/configs/sim/lib/libthorn_HydroBase.a make: *** [sim] Error 2 So, 1. why did sim decide to build openmpi when the system mpi exists and would seem to be known... 2. even so, if openmpi was built successfully why did make not see the mpi.h file which exists? Does all this mean that I have not gotten very close to having the optionlist file contents close enough to the OSC system-supplied code? Please help. Thanks. Comer > On Sun, Sep 2, 2012 at 2:50 PM, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: > >> >> On 2 Sep 2012, at 19:42, Comer Duncan wrote: >> >> Ok, I now see that NoMPI is claimed to be disabled if MPI is found. >> Since my experience seemed to be that no mpi was found, I would like to >> know what to do in order to find where mpi presence is tested for in the >> sim build process and what I need to do to make sure that mpi is found on >> the OSC system. As I mentioned earlier, MPI is clearly available (have used >> it in several other projects but not yet einsteintoolkit). The option list >> file I have used makes explicit mention of various env variables which >> indicate where to care and feed the system's mpi. Please help. >> >> >> Hi Comer, >> >> It's best if this discussion happens on the mailing list, as others can >> help and it will help future readers as well. I need to know which >> thornlist and which branch of the ET you are trying to use, as the handling >> of MPI has changed between the last release and the current trunk. Where >> did you download the thornlist from? Are you trying to use the standard >> thornlist, or have you put one together yourself? Do you get any warnings >> during the Cactus configuration process? >> >> >> Thanks. >> >> Comer >> >> On Sun, Sep 2, 2012 at 9:16 AM, Comer Duncan <comer.duncan(a)gmail.com>wrote: >> >>> Hi Ian, >>> >>> >>>> That is just the version of Cactus - what about theI rest of the ET? >>>> i.e. which thornlist did you use to download everything? >>>> >>> >>> Yesterday after posting my question I took another look at >>> einsteintoolkit.th which was what I used when I downloaded the tool kit >>> on May 26. Lo and behold it has the following section: >>> >>> . >>> . >>> . >>> CactusTest/TestTimers >>> CactusTest/TestTypes >>> >>> #CactusUtils/Accelerator >>> CactusUtils/Formaline >>> CactusUtils/NaNChecker >>> CactusUtils/Nice >>> CactusUtils/NoMPI <<<<<<<<<<<< !!Note? >>> #CactusUtils/OpenCLRunTime >>> CactusUtils/TerminationTrigger >>> CactusUtils/TimerReport >>> >>> CactusWave/IDScalarWave >>> CactusWave/IDScalarWaveC >>> . >>> . >>> . >>> >>> Thus, perhaps for reasons not at all clear the noted inclusion of NoMPI >>> gets in the way of 'have MPI' evaluating to true? If this is the case, >>> then commenting it would then implicitly let the build know that MPI _is_ >>> wanted?? >>> >>> One would think that MPI would be wanted by default on any computing >>> environment that one would want to do real computation on, with the >>> exception of one's laptop or desktop I guess. >>> >>> Thanks. >>> >>> Comer >>> >>>> -- >>>> Ian Hinder >>>> http://numrel.aei.mpg.de/people/hinder >>>> >>>> >>> >> >> -- >> Ian Hinder >> http://numrel.aei.mpg.de/people/hinder >> >> >

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Fwd: help/advice in getting optionlist working
by Comer Duncan 02 Sep '12

02 Sep '12

I am forwarding some queries of mine on MPI to this list in hopes of getting some help. Thanks much. Comer ---------- Forwarded message ---------- From: Comer Duncan <comer.duncan(a)gmail.com> Date: Sun, Sep 2, 2012 at 1:42 PM Subject: Re: [Users] help/advice in getting optionlist working To: Ian Hinder <ian.hinder(a)aei.mpg.de> Ok, I now see that NoMPI is claimed to be disabled if MPI is found. Since my experience seemed to be that no mpi was found, I would like to know what to do in order to find where mpi presence is tested for in the sim build process and what I need to do to make sure that mpi is found on the OSC system. As I mentioned earlier, MPI is clearly available (have used it in several other projects but not yet einsteintoolkit). The option list file I have used makes explicit mention of various env variables which indicate where to care and feed the system's mpi. Please help. Thanks. Comer On Sun, Sep 2, 2012 at 9:16 AM, Comer Duncan <comer.duncan(a)gmail.com> wrote: > Hi Ian, > > >> That is just the version of Cactus - what about theI rest of the ET? >> i.e. which thornlist did you use to download everything? >> > > Yesterday after posting my question I took another look at > einsteintoolkit.th which was what I used when I downloaded the tool kit > on May 26. Lo and behold it has the following section: > > . > . > . > CactusTest/TestTimers > CactusTest/TestTypes > > #CactusUtils/Accelerator > CactusUtils/Formaline > CactusUtils/NaNChecker > CactusUtils/Nice > CactusUtils/NoMPI <<<<<<<<<<<< !!Note? > #CactusUtils/OpenCLRunTime > CactusUtils/TerminationTrigger > CactusUtils/TimerReport > > CactusWave/IDScalarWave > CactusWave/IDScalarWaveC > . > . > . > > Thus, perhaps for reasons not at all clear the noted inclusion of NoMPI > gets in the way of 'have MPI' evaluating to true? If this is the case, > then commenting it would then implicitly let the build know that MPI _is_ > wanted?? > > One would think that MPI would be wanted by default on any computing > environment that one would want to do real computation on, with the > exception of one's laptop or desktop I guess. > > Thanks. > > Comer > >> -- >> Ian Hinder >> http://numrel.aei.mpg.de/people/hinder >> >> >

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help/advice in getting optionlist working
by Comer Duncan 01 Sep '12

01 Sep '12

Hi, Having gotten einsteintoolkit built on my local macbook, I have decided to try to get things built on the Ohio Supercomputer Center's front end. I have taken one of the config files for ranger and have used it as a base from which I made some changes with particular attention to the locations of needed things on the OSC system. I have tried the following while in the Cactus directory: ./simfactory/bin/sim setup which did complete with a basic setup (had to do this twice as I logged onto the OSC frontend two separate times and got two different machines, which is not surprising I guess). While in the Cactus directory: ./simfactory/bin/sim build --optionlist=oscoptionlist --thornlist=thornlists/einsteintoolkit.th >& attempt5.9.1.2012.out & where oscoptionlist is the edited version of the ranger optionlist I used. I am attaching this optionlist. At the end of the output file I see the following: HDF5: Installing checker... /usr/bin/install -c h5check '/nfs/05/bgs001/Cactus/configs/sim/scratch/external/HDF5/bin' ~/Cactus/configs/sim/scratch HDF5: Cleaning up... HDF5: Done. HDF5 selected, but HDF5_DIR not set. Checking some places... HDF5 not found Using bundled HDF5... Building HDF5 Checking consistency... Creating Thorn-Flesh bindings... Creating implementation bindings... Creating parameter bindings... Creating variable bindings... Creating schedule bindings... Creating function bindings... CST finished. /nfs/05/bgs001/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. make: *** [sim] Error 2 So, the system I run on uses module and the loaded modules are: -bash-4.1$ module list Currently Loaded Modules: 1) torque/2.5.12 3) modules/1.0 5) mkl/10.3.0 7) fftw3/3.3 2) moab/6.1.5 4) intel/12.1.4.319 6) mvapich2/1.7 I believe/think that the optionlist file reflects the loaded mvapich libs, but maybe I have missed something... Can you please help me get over this hurdle? Thanks for your help. Comer

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CarpetRegrid2 change
by Erik Schnetter 01 Sep '12

01 Sep '12

I just committed a change "CarpetRegrid2: Try harder to combine different refined regions". This may affect the grid structure you see during time evolution. When a refinement level consists of several regions, then CarpetRegrid2 tries to combine these into a single, cuboid region, adding additional refined points in the process. Having fewer regions with a more regular shape helps efficiency. CarpetRegrid2 then checks how many new refined points needed to be added in the process. If this number is small, the single region is kept; if this number is too large, the single region is discarded, and the original set of regions is used instead. The parameter "CarpetRegrid2::min_fraction" determines this, and setting min_fraction=1.0 disables this grid structure optimisation. This change slightly modifies this algorithm in CarpetRegrid2, and may thus lead to a different grid structure. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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Users September 2012