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
