[Users] error message MPI
Hamilton, Maria
babiuc at marshall.edu
Tue Oct 9 14:50:34 CDT 2018
That actually worked!
The only complaint I had was at PAPI, but after I disabled it, the compilation went all the way to the end.
Thank you!
Maria
_______________________
Dr. Maria C. Babiuc Hamilton
Department of Physics
Marshall University
S257 Science Building
Huntington, WV, 25755
Phone: (304)696-2754
________________________________________
From: Roland Haas <rhaas at illinois.edu>
Sent: Tuesday, October 9, 2018 2:28 PM
To: Hamilton, Maria
Cc: Steven R. Brandt; users at einsteintoolkit.org
Subject: Re: [Users] error message MPI
Hello Maria,
would you mind trying the following:
cd repos/carpet
git cherry-pick 5073af2c
then try and compile?
This commit is part of the proposed updated to Carpet that Steve is currently reviewing and that we will commit in short order.
Yours,
Roland
> Hello Steve,
>
> I tried again to compile cactus on osx, in fact I erase the whole cactus, did a fresh download of the current development version, brew reinstalled gcc-8 --without-multilib and brew reinstall openmpi --build-from-source --cc=gcc-8, then did a ./simfactory/bin/sim setup-silent --optionlist=osx-homebrew.cfg --runscript generic-mpi.run and ./simfactory/bin/sim build.
> The good news is that I don't have any more complains about LORENE and PAPI.
> The bad news is that I have the same errors in dh.cc
>
> COMPILING arrangements/Carpet/CarpetLib/src/dh.cc
> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::light_dboxes&)':
> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23 error: 'MPI_UB' was not declared in this scope
> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> ^~~~~~
> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23 note: suggested alternative: 'MPI_IO'
> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> ^~~~~~
> MPI_IO
> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::fast_dboxes&)':
> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23 error: 'MPI_UB' was not declared in this scope
> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> ^~~~~~
> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23 note: suggested alternative: 'MPI_IO'
> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> ^~~~~~
> MPI_IO
> make[3]: *** [dh.cc.o] Error 1
>
> Maria
>
> _______________________
> Dr. Maria C. Babiuc Hamilton
> Department of Physics
> Marshall University
> S257 Science Building
> Huntington, WV, 25755
> Phone: (304)696-2754
>
>
> ________________________________________
> From: users-bounces at einsteintoolkit.org <users-bounces at einsteintoolkit.org> on behalf of Steven R. Brandt <sbrandt at cct.lsu.edu>
> Sent: Thursday, October 4, 2018 1:21 PM
> To: users at einsteintoolkit.org
> Subject: Re: [Users] error message MPI
>
> I recently pushed a change for osx. If you redo your setup (i.e. remove
> etc/defs.local.ini and mdb/machines/your-machine.ini) and try again, it
> may help.
>
> Is mpicxx in your command path? I.e. if you type 'which mpicxx' do you
> see anything?
>
> Thanks.
>
> --Steve
>
>
> On 10/04/2018 08:43 AM, Hamilton, Maria wrote:
> > Roland,
> >
> > A quick update. My hacking managed to get the code compiled, but it hangs on when running. I'm sure I did something wrong.
> > I'll wait for your pointers after you have time to install and run Cactus on Mojave.
> >
> > Maria
> >
> > _______________________
> > Dr. Maria C. Babiuc Hamilton
> > Department of Physics
> > Marshall University
> > S257 Science Building
> > Huntington, WV, 25755
> > Phone: (304)696-2754
> >
> >
> > ________________________________________
> > From: users-bounces at einsteintoolkit.org <users-bounces at einsteintoolkit.org> on behalf of Hamilton, Maria <babiuc at marshall.edu>
> > Sent: Wednesday, October 3, 2018 10:52 PM
> > To: rhaas at illinois.edu
> > Cc: users at einsteintoolkit.org
> > Subject: Re: [Users] error message MPI
> >
> > Roland,
> >
> > OK, keep me updated. Honestly, I am afraid to update to Mojave!
> >
> > I do wander why Cactus consistently breaks down after any new updates I do on my mac laptop. Is it because of home-brew?
> > Or shall I just stick with older versions of the software libraries?
> > It finally compiled, after I commented out LORENE, PAPI, and the Meudon thorns, and did some hacking in the CarpetLib thorn.
> > Clearly, my new brew update made MPU_UB deprecated.
> > I ended up defining MPI-UB everywhere it was needed as:
> > #define MPI_UB ((MPI_Datatype)16)
> > This should have been in an mpi.h file, but apparently is not.
> > It also complained about MPI_Type_struct, which I commented out.
> >
> > I have an older Ubuntu workstation, and the new Cactus compiled there without any problems.
> >
> > I reinstalled also the new Cactus on BigGreen, the cluster at Marshall University, and it went well.
> >
> > One last thing: I could not find any ubuntu.cfg.
> > Also, I don't see a cents.cfg either.
> > Any suggestion about what to use instead?
> > I would like to have some flexibility on what version of compilers to use.
> >
> > cheers,
> > Maria
> >
> > _______________________
> > Dr. Maria C. Babiuc Hamilton
> > Department of Physics
> > Marshall University
> > S257 Science Building
> > Huntington, WV, 25755
> > Phone: (304)696-2754
> >
> >
> > ________________________________________
> > From: Roland Haas <rhaas at illinois.edu>
> > Sent: Wednesday, October 3, 2018 10:20 AM
> > To: Hamilton, Maria
> > Cc: users at einsteintoolkit.org
> > Subject: Re: [Users] error message MPI
> >
> > Hello Maria,
> >
> > this will take a while. Installing Mojave is complicated for me and I
> > likely will not get to it until at least after Oct 15th, sorry.
> >
> > Yours,
> > Roland
> >
> >> Hello Roland,
> >>
> >> OK, thanks! It would be great if you let me know how the compilation went on your new mac.
> >> The errors I had were popping out at Carpet/CarpetLib/src/dh.cc were for the compilation from scratch.
> >>
> >> I did try to use sim as well, as you suggested, and I had a cascade of errors.
> >> The first complaint was about LORENE:
> >> _______________
> >> LORENE: Installing...
> >> ~/Cactus/configs/sim/scratch
> >> LORENE: Cleaning up...
> >> LORENE: Done.
> >> Creating /Users/babiuc/Cactus/configs/sim/lib/libthorn_LORENE.a
> >> make: *** [sim] Error 2
> >> __________
> >>
> >>
> >> I commented LORENE out and I had to comment out 3 more thorns:
> >> CST error 1:
> >> -> Thorn 'Meudon_Bin_BH' requires the capability 'LORENE'.
> >> Please add a thorn that provides 'LORENE' to your ThornList or remove 'Meudon_Bin_BH' from it !
> >>
> >>
> >> CST error 2:
> >> -> Thorn 'Meudon_Bin_NS' requires the capability 'LORENE'.
> >> Please add a thorn that provides 'LORENE' to your ThornList or remove 'Meudon_Bin_NS' from it !
> >>
> >>
> >> CST error 3:
> >> -> Thorn 'Meudon_Mag_NS' requires the capability 'LORENE'.
> >> Please add a thorn that provides 'LORENE' to your ThornList or remove 'Meudon_Mag_NS' from it !
> >>
> >>
> >> Then I had an error at thorn PAPI:
> >> _______
> >> Checking status of thorn PAPI
> >> PAPI: Preparing directory structure...
> >> PAPI: Unpacking archive...
> >> ~/Cactus/configs/sim/scratch/build/PAPI ~/Cactus/configs/sim/scratch
> >> PAPI: Applying patches...
> >> ~/Cactus/configs/sim/scratch/build/PAPI/papi-5.3.0 ~/Cactus/configs/sim/scratch/build/PAPI ~/Cactus/configs/sim/scratch
> >> Cannot complete in-place edit of ./src/libpfm-3.y/examples_v2.x/ia64/mont_opcode.c: failed to rename work file './src/libpfm-3.y/examples_v2.x/ia64/XXxgZzZf' to './src/libpfm-3.y/examples_v2.x/ia64/mont_opcode.c': Bad file descriptor, <> line 32848.
> >> make[2]: *** [make.checked] Error 2
> >> make[1]: *** [/Users/babiuc/Cactus/configs/sim/lib/libthorn_PAPI.a] Error 2
> >> make[1]: *** Waiting for unfinished jobs....
> >> Creating /Users/babiuc/Cactus/configs/sim/lib/libthorn_LocalReduce.a
> >> make: *** [sim] Error 2
> >> ___________________
> >>
> >> In the end I arrived at the same error:
> >>
> >> ____
> >> COMPILING arrangements/Carpet/CarpetLib/src/dh.cc
> >> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::light_dboxes&)':
> >> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23: error: 'MPI_UB' was not declared in this scope
> >> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> >> ^~~~~~
> >> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23: note: suggested alternative: 'MPI_IO'
> >> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> >> ^~~~~~
> >> MPI_IO
> >> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::fast_dboxes&)':
> >> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23: error: 'MPI_UB' was not declared in this scope
> >> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> >> ^~~~~~
> >> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23: note: suggested alternative: 'MPI_IO'
> >> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> >> ^~~~~~
> >> MPI_IO
> >> make[3]: *** [dh.cc.o] Error 1
> >> _____________
> >>
> >>
> >> Also, a thorn seems to be empty:
> >> Missing thorn EinsteinInitialData/Hydro_RNSID
> >>
> >>
> >>
> >> Maria
> >>
> >> _______________________
> >> Dr. Maria C. Babiuc Hamilton
> >> Department of Physics
> >> Marshall University
> >> S257 Science Building
> >> Huntington, WV, 25755
> >> Phone: (304)696-2754
> >>
> >>
> >> ________________________________________
> >> From: Roland Haas <rhaas at illinois.edu>
> >> Sent: Tuesday, October 2, 2018 9:01 AM
> >> To: Hamilton, Maria
> >> Cc: users at einsteintoolkit.org
> >> Subject: Re: [Users] error message MPI
> >>
> >> Hello Maria,
> >>
> >> please try compiling from scratch. Ie do
> >>
> >> make sim-realclean (or even rm -rf configs/sim)
> >>
> >> and try compiling again. It is possible that a previous abortive
> >> attempt to compile has created a file "mpi.h" in your Cactus tree and
> >> that this file is messing up things now.
> >>
> >> If you already did start from scratch then I do not quite know what may
> >> be going on (I do not normally use a Mac).
> >>
> >> I am updating my own mac today and will see if I get similar results.
> >>
> >> Yours,
> >> Roland
> >>
> >>> Hello Roland,
> >>>
> >>> It turned out that I still have problems with MPI.
> >>> I did not update to mojave, just did a brew update/brew upgrade.
> >>> A smaller executable compiled fine, but compiling with most thorns activated, I have the following error:
> >>>
> >>> _____________________
> >>> COMPILING arrangements/Carpet/CarpetLib/src/dh.cc
> >>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::light_dboxes&)':
> >>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23: error: 'MPI_UB' was not declared in this scope
> >>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> >>> ^~~~~~
> >>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23: note: suggested alternative: 'MPI_IO'
> >>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> >>> ^~~~~~
> >>> MPI_IO
> >>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::fast_dboxes&)':
> >>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23: error: 'MPI_UB' was not declared in this scope
> >>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> >>> ^~~~~~
> >>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23: note: suggested alternative: 'MPI_IO'
> >>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
> >>> ^~~~~~
> >>> MPI_IO
> >>> ___________________
> >>>
> >>> My mpic++ does not take -compile_info, but a show gives me this:
> >>>
> >>> $ mpic++ --showme
> >>> clang++ -I/usr/local/Cellar/open-mpi/HEAD-73075b8/include -L/usr/local/opt/libevent/lib -L/usr/local/Cellar/open-mpi/HEAD-73075b8/lib -lmpi
> >>>
> >>> What do you suggest?
> >>>
> >>> thanks,
> >>> Maria
> >>>
> >>> _______________________
> >>> Dr. Maria C. Babiuc Hamilton
> >>> Department of Physics
> >>> Marshall University
> >>> S257 Science Building
> >>> Huntington, WV, 25755
> >>> Phone: (304)696-2754
> >>>
> >>>
> >>> ________________________________________
> >>> From: Roland Haas <rhaas at illinois.edu>
> >>> Sent: Monday, October 1, 2018 4:59 PM
> >>> To: Hamilton, Maria
> >>> Cc: users at einsteintoolkit.org
> >>> Subject: Re: [Users] error message MPI
> >>>
> >>> Hello Maria,
> >>>
> >>> if by update you mean an update of the OS (to Mojave) or the package
> >>> manager (Homebrew, Macports) then most likely the update made you MPI
> >>> stack unusable.
> >>>
> >>> I would try the following:
> >>>
> >>> 1. if you updated the OS to Mojave then quite likely you will have to
> >>> reinstall the package manager and all packages
> >>> (https://apple.stackexchange.com/questions/85480/how-should-i-fix-my-homebrew-installation-after-upgrading-os-x)
> >>> though if you are lucky a "brew upgrade" may do the trick
> >>>
> >>> 2. check the output of the commands the Cactus tried ie:
> >>> usr/local/bin/mpic++ -compile_info and /usr/local/bin/mpic++ --showme
> >>> to see what kind of error is produced. Likely you have to re-install
> >>> the MPI package from your package manager (same as point 1. really).
> >>>
> >>> Yours,
> >>> Roland
> >>>
> >>>> Hello,
> >>>>
> >>>>
> >>>> I'm trying to compile the development Cactus version on my Mac laptop
> >>>> after an update:
> >>>>
> >>>> $repos/CRL/GetComponents --update.
> >>>>
> >>>> Unfortunately, I ran into the following error:
> >>>>
> >>>> ********************************************************************************
> >>>>
> >>>> Running configuration script for thorn MPI:
> >>>>
> >>>> Found MPI compiler wrapper at /usr/local/bin/mpic++!
> >>>>
> >>>> sh: line 1: 30205 Abort trap: 6 /usr/local/bin/mpic++
> >>>> -compile_info 2> /dev/null
> >>>>
> >>>> sh: line 1: 30207 Abort trap: 6 /usr/local/bin/mpic++
> >>>> --showme 2> /dev/null
> >>>>
> >>>> ERROR: MPI could not be configured: neither automatic nor manual
> >>>> configuration succeeded
> >>>>
> >>>>
> >>>> CST error 1:
> >>>>
> >>>> -> Configuration script for thorn MPI returned exit code 5
> >>>>
> >>>> Error message: 'MPI could not be configured: neither automatic
> >>>> nor manual configuration succeeded'
> >>>>
> >>>>
> >>>> Finished running configuration script for thorn MPI.
> >>>>
> >>>>
> >>>> ********************************************************************************
> >>>>
> >>>> This persists after real clean, and even after I erase the
> >>>> configuration and reconfigure it.
> >>>>
> >>>> Please help,
> >>>> Maria
> >>>> ?
> >>>>
> >>>>
> >>>> _______________________
> >>>> Dr. Maria C. Babiuc Hamilton
> >>>> Department of Physics
> >>>> Marshall University
> >>>> S257 Science Building
> >>>> Huntington, WV, 25755
> >>>> Phone: (304)696-2754
> >>>>
> >>>
> >>>
> >>> --
> >>> My email is as private as my paper mail. I therefore support encrypting
> >>> and signing email messages. Get my PGP key from http://pgp.mit.edu .
> >>
> >> --
> >> My email is as private as my paper mail. I therefore support encrypting
> >> and signing email messages. Get my PGP key from http://pgp.mit.edu .
> >
> > --
> > My email is as private as my paper mail. I therefore support encrypting
> > and signing email messages. Get my PGP key from http://pgp.mit.edu .
> > _______________________________________________
> > Users mailing list
> > Users at einsteintoolkit.org
> > http://lists.einsteintoolkit.org/mailman/listinfo/users
> > _______________________________________________
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> > http://lists.einsteintoolkit.org/mailman/listinfo/users
>
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