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
