[Users] error message MPI
Hamilton, Maria
babiuc at marshall.edu
Thu Oct 4 08:43:30 CDT 2018
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 .
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