[gmx-users] compile mdrun parallel version

Haberl Florian Florian.Haberl at chemie.uni-erlangen.de
Fri Apr 1 18:34:38 CEST 2005


Hi,

> 	Dear users,
>
> I had problems with compilation of parallel version of mdrun. Therefore
> I have followed suggestions of Andre, Oliver and David in mailing list:
>
> ---------------------------------------------------
> export  LAM_D=/usr/local/
> export FFTW_D=/usr/local/
>
> tar -jxvf lam-7.0.6.tar.bz2
> cd lam-7.0.6
> ./configure --prefix=${LAM_D} --with-tcp-short=524288 --with-rpi=usysv
> --with-rsh=ssh --with-shm-short=524288
> make
> make install
>
> cd ..
> tar -zxvf fftw-2.1.5.tar.gz
> cd fftw-2.1.5
>
> export PATH=${LAM_D}/bin:${PATH}
>
> CPPFLAGS="-I${LAM_D}/include"
> LDFLAGS="-L${LAM_D}/lib"
> ./configure --prefix=${FFTW_D} --enable-type-prefix --enable-mpi
> --enable-float
> make
> make install
>
> make distclean
>
> ./configure --prefix=${FFTW_D} --enable-type-prefix --enable-mpi
> make
> make install
>
> cd ..
> tar -zxvf gromacs-3.2.1.tar.gz
> cd gromacs-3.2.1
>
> CPPFLAGS="-I${LAM_D}/include -I${FFTW_D}/include"
> LDFLAGS="-L${LAM_D}/lib -L${FFTW_D}/lib"
>
> ./configure
> make
> make install
> make links
> --------------------------------------------------------
>
> Until this point it worked well. However, when I tried to instal mpi
> version by:
>
> -----------------------------
> make distclean
>
> ./configure --without-x --enable-mpi --program-suffix=_mpi
> make mdrun
> ---------------------------------------------
>
> I have obtained this error output:
> /usr/lib/liblam.a(show_help.o)(.text+0x897): In function `read_help':
> : undefined reference to `__ctype_b'
> /usr/lib/liblam.a(show_help.o)(.text+0xb6c): In function `print_subst':
> : undefined reference to `__ctype_b'
> /usr/lib/liblam.a(getnodes.o)(.text+0xb8): In function `getnodes':
> : undefined reference to `errno'
> /usr/lib/liblam.a(getnodes.o)(.text+0x184): In function `getntype':
> : undefined reference to `errno'
> /usr/lib/liblam.a(getrent.o)(.text+0xc6): In function `getrent':
> : undefined reference to `errno'
> /usr/lib/liblam.a(getrent.o)(.text+0x1e2): In function `getrtype':
> : undefined reference to `errno'
> /usr/lib/liblam.a(tprint.o)(.text+0x423): In function `getnum':
> : undefined reference to `__ctype_b'
> /usr/lib/liblam.a(rfclose.o)(.text+0x121): In function `lam_rfclose':
> : undefined reference to `errno'
> /usr/lib/liblam.a(kattach.o)(.text+0xa3): In function `kattach':
> : undefined reference to `errno'
> /usr/lib/liblam.a(rfaux.o)(.text+0xe8): In function `_fnparse':
> : undefined reference to `__ctype_b'
> /usr/lib/liblam.a(rflseek.o)(.text+0x101): In function `lam_rflseek':
> : undefined reference to `errno'
> /usr/lib/liblam.a(rfread.o)(.text+0xf1): In function `lam_rfread':
> : undefined reference to `errno'
> collect2: ld returned 1 exit status
> mpicc: No such file or directory
> make[1]: *** [mdrun] Error 1
> make[1]: Leaving directory
> `/home/smartin/gromacs_instalacky/gromacs-3.2.1/src/kernel'
>
> Note: Binary of mpicc I have installed in /usr/local/bin/mpicc which is in
> my PATH
>
> Can anybody give me advice how to overcome this problem?
>
I would test first if lam and mpich is installed correct, there should be
some simple test programms for this around, seems something is not
installed proper.

Have you compiled your mpich version or are this rpms,
have you used same compiler for mpich/ gromacs?

Greetings,

Florian



------------------------------------------------------------------------
 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de

------------------------------------------------------------------------



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