[Users] error message MPI

Hamilton, Maria babiuc at marshall.edu
Tue Oct 2 15:15:16 CDT 2018 

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 .


--
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