[gmx-users] mdrun_make_hole installation

Moutusi Manna mou2c_21 at yahoo.co.in
Thu Jul 30 10:39:38 CEST 2009

Dear all,

want to install mdrun_make_hole in my home directory(/home/cm/install).
For that the steps i have followed are..........

1) installation of fftw

cd /home/cm/install

cp fftw-3.2.1.tar.tar ../

tar -zxvf fftw-3.2.1.tar.tar

cd fftw-3.2.1.

 ./configure --enable-float --enable-threads --prefix=/home/cm/install/fftw-3.2.1


make install

after that the files generated in /home/cm/install/fftw-3.2.1/include are.....

fftw3.f  fftw3.h

and in /home/cm/install/fftw-3.2.1/lib are 

libfftw3f.a  libfftw3f.la  libfftw3f_threads.a  libfftw3f_threads.la  pkgconfig

2) installation of gromacs-3.1.4

cd /home/cm/install

cp gromacs-3.1.4.tar.gz ../

tar -zxvf gromacs-3.1.4.tar.gz

cd gromacs-3.1.4.

cp /home/cm/Desktop/mdrun_make_hole.tar.gz . 

zcat mdrun_make_hole.tar.gz |tar -xvzf -

cd ../../ i.e. in /home/cm

vi bashrc

two lines added........

export CPPFLAGS=-I/home/cm/install/fftw-3.2.1/include

export LDFLAGS=-L/home/cm/install/fftw-3.2.1/lib

cd /home/cm/install/gromacs-3.1.4.

./configure --enable-float --prefix=/home/cm/install --program-suffix=_h


checking build system type... i686-pc-linux-gnu

checking host system type... i686-pc-linux-gnu

checking for a BSD compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for awk... awk

checking whether make sets ${MAKE}... yes

checking for cc... cc

checking for C compiler default output... a.out

checking whether the C compiler works... yes

checking whether we are cross compiling... no

checking for executable suffix...

checking for object suffix... o

checking whether we are using the GNU C compiler... yes

checking whether cc accepts -g... yes

checking for style of include used by make... GNU

checking dependency style of cc... gcc3

checking how to run the C preprocessor... cc -E

checking whether cc accepts -O6... yes

checking whether cc accepts -malign-double... yes

checking whether cc accepts -funroll-all-loops... yes

checking whether cc accepts  -O6 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -malign-double
-funroll-all-loops... yes

checking whether your compiler can handle assembly files (*.s)... yes

checking whether as fully supports intel syntax SSE & 3DNow... yes

checking for ident... /usr/bin/ident

checking whether the compiler supports ident... yes

checking for ld used by GCC... /usr/bin/ld

checking if the linker (/usr/bin/ld) is GNU ld... yes

checking for /usr/bin/ld option to reload object files... -r

checking for BSD-compatible nm... /usr/bin/nm -B

checking whether ln -s works... yes

checking how to recognise dependant libraries... file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )

checking for dlfcn.h... yes

checking the maximum length of command line arguments... 32768

checking command to parse /usr/bin/nm -B output from cc object... ok

checking for objdir... .libs

checking for ranlib... ranlib

checking for strip... strip

checking for file... /usr/bin/file

checking if cc static flag  works... yes

checking if cc supports -fno-rtti -fno-exceptions... no

checking for cc option to produce PIC... -fPIC

checking if cc PIC flag -fPIC works... yes

checking if cc PIC define -DPIC works... yes

checking if cc supports -c -o file.o... yes

checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes

checking how to hardcode library paths into programs... immediate

checking whether stripping libraries is possible... yes

checking dynamic linker characteristics... GNU/Linux ld.so

checking if libtool supports shared libraries... yes

checking whether to build shared libraries... no

checking whether to build static libraries... yes

configure: creating libtool

checking whether ln -s works... yes

checking for special C compiler options needed for large files... no

checking for _FILE_OFFSET_BITS value needed for large files... 64

checking for _LARGE_FILES value needed for large files... no

checking for _LARGEFILE_SOURCE value needed for large files... 1

checking for fseeko... yes

checking for sqrt in -lm... yes

checking for sfftw.h... no

checking for fftw.h... no

configure: error: Cannot find any single precision sfftw.h or fftw.h

Do you have single precision FFTW installed? If you are using packages,

note that you also need fftw-devel to compile GROMACS. You can find the

software at www.fftw.org, and detailed instructions at www.gromacs.org.

If you compiled FFTW yourself:

Note that the default FFTW setup is double precision. Change the FFTW

configuration to single with --enable-float. If you want MPI support,

use --enable-mpi. It is a good idea to install both single & double.

If your sysadm doesn't want to install it you can do it to a location

in your home directory and provide the correct paths in the CPPFLAGS

and LDFLAGS environment variables before running configure.

That is also necessary to do if your compiler doesn't search

/usr/local/include and /usr/local/lib by default.

You can find information at www.gromacs.org, or in the INSTALL file.



make: *** No targets specified and no makefile found.  Stop.

Please suggest any wayout.

Thanks in advance.

Moutusi Manna

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