Hello Maria, the commit that you cherry picked is now in master and this should be fine in the future.
Yours, Roland > 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 <[email protected]> > Sent: Tuesday, October 9, 2018 2:28 PM > To: Hamilton, Maria > Cc: Steven R. Brandt; [email protected] > 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: [email protected] <[email protected]> > > on behalf of Steven R. Brandt <[email protected]> > > Sent: Thursday, October 4, 2018 1:21 PM > > To: [email protected] > > 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: [email protected] > > > <[email protected]> on behalf of Hamilton, Maria > > > <[email protected]> > > > Sent: Wednesday, October 3, 2018 10:52 PM > > > To: [email protected] > > > Cc: [email protected] > > > 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 <[email protected]> > > > Sent: Wednesday, October 3, 2018 10:20 AM > > > To: Hamilton, Maria > > > Cc: [email protected] > > > 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 <[email protected]> > > >> Sent: Tuesday, October 2, 2018 9:01 AM > > >> To: Hamilton, Maria > > >> Cc: [email protected] > > >> 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 <[email protected]> > > >>> Sent: Monday, October 1, 2018 4:59 PM > > >>> To: Hamilton, Maria > > >>> Cc: [email protected] > > >>> 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 > > > [email protected] > > > http://lists.einsteintoolkit.org/mailman/listinfo/users > > > _______________________________________________ > > > Users mailing list > > > [email protected] > > > http://lists.einsteintoolkit.org/mailman/listinfo/users > > > > _______________________________________________ > > Users mailing list > > [email protected] > > http://lists.einsteintoolkit.org/mailman/listinfo/users > > _______________________________________________ > > Users mailing list > > [email protected] > > http://lists.einsteintoolkit.org/mailman/listinfo/users > > > -- > 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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