<DIV>how do I unsubscribe to this?<BR><BR><B><I>"Nuno R. L. Ferreira" <nunolf@ci.uc.pt></I></B> wrote:
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">> On Mon, 3 Nov 2003, Nuno R. L. Ferreira wrote:<BR>><BR>> > Trying for the first time to compile gmx314 in a cluster!<BR>><BR>> What is the OS of your cluster? Last time I checked Digital Unix/Tru64 was<BR>> faster than linux on the same machine. But that was more than a year<BR>> ago...<BR>><BR><BR>COMPAQ XP 1000 (processor 21264A at 667 MHz, EV67)<BR>RedHat 7.2 (2.4.9-12 kernel)<BR>gcc version 2.96 20000731 (Red Hat Linux 7.1 2.96-87)<BR>Compaq Fortran Compiler X1.1.1-1684-46B5P<BR>MPICH --> MPIVERSION="1.2.3 of : 2002/01/23 21:03:59"<BR><BR><BR>> > >From what I read, some of you have similiar clusters.<BR>> > Two quick questions.<BR>> > 1) Do you compile fftw213 and gmx with the same F and C compilers?<BR>> > 2) Do you compile with gnu compilers or do you use ccc and fort? No<BR>> > problems?<BR>><BR>> In the
past ccc en fort were faster, but maybe gcc has improved. The only<BR>> way to find out is to benchmark I guess.<BR><BR>Yes , you're right. But, I had some problems with compilation, that's why<BR>I'm starting from scratch, before anoying you with my problems.<BR>But, here they are.<BR>When I compile fftw213 with CC=ccc, it gives me an error :<BR>(configure with<BR>CC=ccc, --prefix, --exec-prefix, --enable-type-prefix, --enable-mpi, --enabl<BR>e-float)<BR>Error from make.log<BR><BR>...<BR>mpicc -O3 -o test_sched test_sched.o .libs/libsfftw_mpi.a -lm<BR>../fftw/.libs/libsfftw.a -lm -lm<BR>../fftw/.libs/libsfftw.a(putils.o): In function `fftw_make_node_rgeneric':<BR>putils.o(.text+0x3bc): undefined reference to `_OtsDivide32'<BR>[...]<BR>../fftw/.libs/libsfftw.a(putils.o): In function `fftw_complete_twiddle':<BR>putils.o(.text+0x868): undefined reference to `_OtsDivide32'<BR>putils.o(.text+0x86c): undefined reference to
`_OtsDivide32'<BR>../fftw/.libs/libsfftw.a(putils.o)(.text+0x86c): more undefined references<BR>to `_OtsDivide32' follow<BR>../fftw/.libs/libsfftw.a(putils.o): In function `fftw_factor':<BR>putils.o(.text+0xe70): undefined reference to `_OtsRemainder32'<BR>[...]<BR>../fftw/.libs/libsfftw.a(putils.o)(.text+0xeb0): more undefined references<BR>to `_OtsRemainder32' follow<BR>[...]<BR>../fftw/.libs/libsfftw.a(twiddle.o)(.text+0x144): undefined reference to<BR>`_OtsRemainder64'<BR>[...]<BR>../fftw/.libs/libsfftw.a(twiddle.o)(.text+0x22c): more undefined references<BR>to `__cpml_sincos' follow<BR>[...]<BR>../fftw/.libs/libsfftw.a(twiddle.o)(.text+0x328): undefined reference to<BR>`__cpml_sincos'<BR>[...]<BR>twiddle.o(.text+0x90c): undefined reference to `__cpml_sincos'<BR>../fftw/.libs/libsfftw.a(twiddle.o)(.text+0x90c): more undefined references<BR>to `__cpml_sincos' follow<BR>collect2: ld returned 1 exit status<BR>make[1]: *** [test_sched] Error 1<BR>make[1]: Leaving directory
`/home/biomd/gmx_test/fftw-2.1.3/mpi'<BR>make: *** [all-recursive] Error 1<BR><BR><BR>After that I compiled with gcc, and all went just fine (no problems with<BR>make check also). Also compiled statically gmx314 with gcc, and apparently<BR>also compiled with no problems. After that, I have run some benchmarks (with<BR>PME and cut-off). Curiously, some of them did not write to the output files.<BR>The dppc bench ran OK on more than 1 CPU.<BR>Tried also some runs with my system (protein + solvent) and as before,<BR>grompp works fine without any errors, mdrun starts with no problems, but<BR>then just doesn't write anything to outfiles.<BR><BR>Part of my mdrun log, at the moment it stops writing. The same appens for<BR>e.g. with villin bench.<BR><BR>[snip]<BR>Initializing LINear Constraint Solver<BR>number of constraints is 12927<BR>average number of constraints coupled to one constraint is 2.0<BR><BR>Any insight from you gmx's will be
appretiated.<BR><BR>At・<BR>Nuno<BR><BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.</BLOCKQUOTE></DIV><p><hr SIZE=1>
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