Hi Alexander, > The messages are warnings, and they're saying that a symbol from lammpi is > being used instead of one from the base system, so I wouldn't assume breakage > has occurred. > > Does Gadget have any test cases where there's a solution to check against? > Or even a "make check" or "make test" option that you can use? >
That's what I'm trying to figure out at the moment. Gadget2 comes with a bunch of initial condition files and associated makefiles, and the one I've tested runs. So that's promising. But there's no file to compare the output with. Oh well, I'll keep trying to figure that out. But at least it's *running*, and that's a big hurdle surmounted. Thanks very much for all your help, Todd > Todd Krause wrote: >> >> Hi Alexander, >> >> Sorry to fill your inbox. But it seems like I spoke too soon. When I >> build Gadget2 again, this time using /sw/bin/lam-mpicc as the compiler, I >> get the following warnings: >> >> /usr/bin/ld: warning suggest use of -bind_at_load, as lazy binding may >> result in errors or different symbols being used >> symbol _szone_check_counter used from dynamic library >> /sw/lib/lammpi/libmpi.dylib(scalable_malloc.o) not from earlier dynamic >> library /usr/lib/libSystem.B.dylib(scalable_malloc.So) >> symbol _szone_check_modulo used from dynamic library >> /sw/lib/lammpi/libmpi.dylib(scalable_malloc.o) not from earlier dynamic >> library /usr/lib/libSystem.B.dylib(scalable_malloc.So) >> symbol _scalable_zone_info used from dynamic library >> /sw/lib/lammpi/libmpi.dylib(scalable_malloc.o) not from earlier dynamic >> library /usr/lib/libSystem.B.dylib(scalable_malloc.So) >> symbol _szone_check_start used from dynamic library >> /sw/lib/lammpi/libmpi.dylib(scalable_malloc.o) not from earlier dynamic >> library /usr/lib/libSystem.B.dylib(scalable_malloc.So) >> symbol _malloc_jumpstart used from dynamic library >> /sw/lib/lammpi/libmpi.dylib(scalable_malloc.o) not from earlier dynamic >> library /usr/lib/libSystem.B.dylib(scalable_malloc.So) >> symbol _malloc_freezedry used from dynamic library >> /sw/lib/lammpi/libmpi.dylib(scalable_malloc.o) not from earlier dynamic >> library /usr/lib/libSystem.B.dylib(scalable_malloc.So) >> symbol _create_scalable_zone used from dynamic library >> /sw/lib/lammpi/libmpi.dylib(scalable_malloc.o) not from earlier dynamic >> library /usr/lib/libSystem.B.dylib(scalable_malloc.So) >> symbol _scalable_zone_statistics used from dynamic library >> /sw/lib/lammpi/libmpi.dylib(scalable_malloc.o) not from earlier dynamic >> library /usr/lib/libSystem.B.dylib(scalable_malloc.So) >> >> But then it seems I *am* able to run the program. I just have to make sure >> I'm using the correct mpirun, namely lam-mpicc: >> >> 08:43 PM btpro:Gadget2> lamboot >> LAM 7.1.2/MPI 2 C++/ROMIO - Indiana University >> >> 08:45 PM btpro:Gadget2> /sw/bin/lam-mpirun -np 1 ./Gadget2 >> ./parameterfiles/galaxy.param >> Note: This is a massively parallel code, but you are running with 1 >> processor only. >> Compared to an equivalent serial code, there is some unnecessary overhead. >> >> This is Gadget, version `2.0'. >> >> Running on 1 processors. >> >> Allocated 25 MByte communication buffer per processor. >> >> Communication buffer has room for 504122 particles in gravity computation >> Communication buffer has room for 204800 particles in density computation >> Communication buffer has room for 163840 particles in hydro computation >> etc. >> >> I'm wondering if you have any idea what I can about the build warnings. I'm >> worried that they mean there's a possibility that even though I'm getting >> data out of Gadget2, I'm getting garbage in essence. >> >> Anyhow, I know that's not really a Fink question, so if you don't know or >> don't have time, that's fine. My other questions about being able to >> remove the programs Fink installed still stand (though perhaps I won't >> remove them just yet, if I can make sure I'm not getting garbage out of >> Gadget2). >> >> Sorry to keep pestering you. Thanks very much for all your help. >> >> Best, >> Todd >> > >> On Fri, 20 Jul 2007, Alexander K. Hansen wrote: >> >>> Todd Krause wrote: >>>> Hi, >>>> >>>> Could someone please give me advice on how to resolve the following error >>>> I get with FFTW 2.1.5? When I try to run Gadget2, a parallel cosmology >>>> code that uses MPI and FFTW, I get >>>> >>>> 10:52 AM btpro:Gadget2> mpd & >>>> [1] 457 >>>> 10:52 AM btpro:Gadget2> mpirun -np 1 ./Gadget2 >>>> ./parameterfiles/galaxy.param >>>> dyld: Symbol not found: _lam_mpi_float >>>> Referenced from: /sw/lib/libsfftw_mpi.2.dylib >>>> Expected in: flat namespace >>>> >>>> 10:53 AM btpro:Gadget2> mpdallexit >>>> >>>> The first and last lines are starting and quitting the MPI environment. >>>> My problem was that in order to "make" Gadget2, I needed FFTW 2.1.5 with >>>> MPI enabled, and an MPI package. I installed MPICH2 myself in >>>> /usr/local, and the unstable fftw-mpi via Fink. The latter also >>>> installed gcc4.2 and lammpi. Now I get Gadget2 to "make", but it won't >>>> execute. Does anyone have any suggestions on how to fix this? >>>> >>>> I'm working on a MacBook Pro, and I have Xcode 2.4.1 installed -- in >>>> >>> fact I *reinstalled* Xcode to see if this would fix the linking >>>> problem, but to no avail. >>>> >>>> Thanks for any suggestions, >>>> Todd >>>> >>>> >>> Did you reinstall Xcode _and_ rebuild Gadget2 (or any of the other >>> packages)? >>> >>> One thing to check is whether your libfftw got misbuilt. What do you get >>> from >>> >>> otool -L /sw/lib/libsfftw_mpi.2.dylib >>> >>> ? >>> >>> -- >>> Alexander K. Hansen >>> Fink User Liaison/Documenter >>> akh AT finkproject DOT org >>> > ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. 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