[gmx-users] gromacs-3.3 build on linux. make fails

[susan james]

here's a bit more(below) of the make build that failed.
I've captured the last lines.

I think it may indeed have something to do with gcc4.
mpicc is in the path.

I'm wondering if I should set this variable:
CC=gcc4
instead of
CC=mpicc

any ideas on this?


==========================================
.
.
.
if mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include 
-I../../include -DGMXLIBDIR=\"/usr/local/gromacs-double/3.3/share/top\" 
-I/usr/local/fftw301/include  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT toputil.o 
-MD -MP -MF ".deps/toputil.Tpo" -c -o toputil.o toputil.c; \
then mv -f ".deps/toputil.Tpo" ".deps/toputil.Po"; else rm -f 
".deps/toputil.Tpo"; exit 1; fi
if mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include 
-I../../include -DGMXLIBDIR=\"/usr/local/gromacs-double/3.3/share/top\" 
-I/usr/local/fftw301/include  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT topdirs.o 
-MD -MP -MF ".deps/topdirs.Tpo" -c -o topdirs.o topdirs.c; \
then mv -f ".deps/topdirs.Tpo" ".deps/topdirs.Po"; else rm -f 
".deps/topdirs.Tpo"; exit 1; fi
if mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include 
-I../../include -DGMXLIBDIR=\"/usr/local/gromacs-double/3.3/share/top\" 
-I/usr/local/fftw301/include  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o -MD 
-MP -MF ".deps/grompp.Tpo" -c -o grompp.o grompp.c; \
then mv -f ".deps/grompp.Tpo" ".deps/grompp.Po"; else rm -f 
".deps/grompp.Tpo"; exit 1; fi
/bin/sh ../../libtool --mode=link --tag=CC mpicc  -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops  -L/usr/local/fftw301/lib  -o grompp  topio.o 
toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o 
vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o 
../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la  -L/usr/X11R6/lib64 
-lnsl -lfftw3 -lm   -lSM -lICE -lX11
mkdir .libs
mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -o .libs/grompp topio.o toppush.o topcat.o topshake.o 
convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o 
add_par.o topexcl.o toputil.o topdirs.o grompp.o 
-L/usr/local/fftw301/lib ../mdlib/.libs/libmd_mpi_d.so 
-L/usr/X11R6/lib64 -L/usr/local/fftw301-double/lib 
../gmxlib/.libs/libgmx_mpi_d.so -lnsl 
/usr/local/fftw301-double/lib/libfftw3.a -lm -lSM -lICE -lX11 
-Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib
../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to 
`_nb_kerne010_x86_64_sse2'
collect2: ld returned 1 exit status
mpicc: No such file or directory
make[3]: *** [grompp] Error 1
make[3]: Leaving directory 
`/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory 
`/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory 
`/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src'
make: *** [all-recursive] Error 1
=============================================





David van der Spoel wrote:
> susan james wrote:
>> Hello,
>>
>> I'm new to this list and hope I can get some help.
>>
>> I'm seeking help with installing double precision gromacs-3.3
>> on Centos-4 linux.
>>
>> I'm using Lam-7.1.2 built with gcc4.
>>
>> I built fftw with this configure string which succeeded:
>> ./configure --prefix=/usr/local/fftw301-double --enable-threads
>>
>> here's my gromacs configure string which succeeds:
>> ./configure --enable-shared --without-motif-libraries --disable-float 
>> --prefix=/usr/local/gromacs-double/3.3 --enable-mpi --with-fft=fftw3
>>
>> The gromacs configure succeeds:
>> ================================
>> config.status: creating man/man1/Makefile
>> config.status: creating src/config.h
>> config.status: executing depfiles commands
>>
>> * You are compiling a double precision version of Gromacs -
>>   program names will be suffixed with _d to avoid overwriting single
>>   precision files. You can override it with --program-suffix
>>
>> * Seems you are compiling with MPI support. You can install the MPI-
>>   enabled programs with suffixed names to have both MPI and non-MPI
>>   versions. This is useful e.g. on supercomputers where you usually
>>   cannot run MPI-linked programs on the login node.
>>   Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double).
>>   You only need MPI for mdrun, so if you already have non-MPI stuff
>>   installed you can issue make mdrun; make install-mdrun.
>> ================================
>>
>> the gromacs make fails.   the complete log is too large to send.
>> and, more precisely, here's where make bailed out.
>> ===================================
>> mx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM 
>> -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib
>> ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to 
>> `_nb_kerne010_x86_64_sse2'
>> collect2: ld returned 1 exit status
>> mpicc: No such file or directory
>> make[3]: *** [grompp] Error 1
>> make[3]: Leaving directory 
>> `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src/kernel'
>> make[2]: *** [all-recursive] Error 1
>> make[2]: Leaving directory 
>> `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src'
>> make[1]: *** [all] Error 2
>> make[1]: Leaving directory 
>> `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src'
>> make: *** [all-recursive] Error 1
>> =================================
>>
> for some reason it did not compile the assembly bits. it could be due to 
> gcc4, or maybe because you did a single precision compilation first. in 
> the latter case try make distclean before running configure.
> 

-- 
Susan James <sjames at lbl.gov> +1.510.486.6507
Computer Infrastructure Support, UNIX Services
Scientific Cluster Support (SCS)
Lawrence Berkeley National Laboratory
One Cyclotron Road, MS-50C
Berkeley, CA 94720