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--- (cd nab && make install ) make[2]: Entering directory `/autofs/na1_home/seabra1/local/amber12/AmberTools/src/nab' cc -DCC='"cc"' -DCPP='"ucpp -l"' -DFLIBS='"-lsff_mpi -lpbsa -larpack -llapack -lblas -L/ccs/home/seabra1/local/amber/lib -lnetcdf -pgf90libs "' \ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI \ -o /ccs/home/seabra1/local/amber/bin/mpinab nab.c cc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c -o nab2c.o nab2c.c flex nablex.l /ccs/home/seabra1/local/amber/bin/yacc -d nabgrm.y make[2]: *** [y.tab.c] Illegal instruction make[2]: Leaving directory `/autofs/na1_home/seabra1/local/amber12/AmberTools/src/nab' make[1]: *** [parallel] Error 2 make[1]: Leaving directory `/autofs/na1_home/seabra1/local/amber12/AmberTools/src' make: *** [install] Error 2 --- About Brazil, well... I'm not sure you know, but ~95% of federal universities here (like mine) are currently on strike... Gustavo Seabra Professor Adjunto Departamento de Química Fundamental Universidade Federal de Pernambuco Fone: +55-81-2126-7450 On Mon, Jul 9, 2012 at 4:52 PM, Jason Swails <jason.swails.gmail.com> wrote: > On Mon, Jul 9, 2012 at 3:43 PM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote: > >> Hi there, >> >> Has anyone here tried to compile Amber12 on the Jaguar system (Cray >> XK6)? According to their User manual (here: >> >> http://www.olcf.ornl.gov/support/user-guides-policies/jaguar-xk6-user-guide/#6221 >> ), >> one should try and use the compile wrappers (cc, CC, ftn). So, I tried >> to use the -crayxt5 option for the configure*. However, I get an error >> like: >> >> ---- >> >> ~/local/amber> ./configure -nomtkpp -crayxt5 pgi 2>&1 | tee >> configure_crayxt5.log >> Checking for updates... >> AmberTools12 is up to date >> Amber12 is up to date >> >> Searching for python2... Found python2.6: /usr/bin/python2.6 >> >> Obtaining the PGI suite version: >> pgcc -V >> The version is 12.1-0 >> >> Testing the cc compiler: >> cc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c >> Error: Unable to compile a C program using cc -D_FILE_OFFSET_BITS=64 >> -D_LARGEFILE_SOURCE >> Please check your compiler settings or configure flags. >> Configure failed due to the errors above! >> ~/local/amber> >> >> --- >> >> Would anyone know what I'm doing wrong here? >> >> I noticed that if I use ./configure -mpi pgi, the configure works >> fine, but I'm thinking that it may not generate the best code for this >> machine. I'd really appreciate any insights here. >> >> * NOTE: I know Jaguar is a XK6, not XT5, but the configure flag is >> only supposed to check for incompatibility with mtkpp and then use cc, >> ftn and CC, so it *should* work (is this wrong?) >> > > Yes, this is wrong, because the compiler wrappers on Jaguar are hopelessly > broken :) -- I tried my hand at it myself. In my experience, the options > are either: 1) continue to bug the Jaguar support folks until the -crayxt5 > flag "just works" (because it's doing the correct thing!). 2) Work around > the issue by using the compilers directly and building your own MPI (may I > suggest the configure_mpich2 included with AmberTools). > > Hope Brazil is treating you well ;). > > All the best, > Jason > > -- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Candidate > 352-392-4032 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Jul 09 2012 - 13:30:03 PDT