Miguel Quiliano Meza wrote:
Dear community.
I have been trying to install gromacs 4.5.4 in my rocks cluster version
5.4 but unfortunately the system showed "configure: error: Cannot find
fftw3 library" after launch the ./configure (you can see below)
Really I do not understand because I did before this:
# export LDFLAGS="-L/opt/rocks/lib"
# export CPPFLAGS="-I/opt/rocks/include"
# ./configure --enable-mpi --disable-float
--prefix=/share/apps/opt/gromacs
configure: error: Cannot find fftw3 library
You have a precision mismatch. By using --disable-float you are trying to
install Gromacs in double precision (which for most applications is not
necessary and results in some performance loss). Thus, you need FFTW in double
precision as well. You probably compiled FFTW in single precision, thus the
libraries are named libfftw3f, not libfftw3.
-Justin
I would be very grateful if someone could help me or give me advices. By
the way... I am trying to reproduce the steps posted in
http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/
for
"compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference
Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0"
and the option "--disable-float" is not clear for me.
Thank you in advance.
Miguel Quiliano.
P.S I attach the error
# ./configure --enable-mpi --disable-float --prefix=/share/apps/opt/gromacs
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... gcc3
checking dependency style of cc... gcc3
checking for mpxlc... no
checking for mpicc... mpicc
checking whether the MPI cc command works... yes
checking for MPI_IN_PLACE in collective operations... yes
checking for catamount... no
checking how to run the C preprocessor... mpicc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether ln -s works... yes
checking whether mpicc accepts -O3... yes
checking whether mpicc accepts -msse2... yes
checking whether mpicc accepts -funroll-all-loops... yes
checking whether mpicc accepts -std=gnu99... yes
checking whether mpicc accepts -fexcess-precision=fast... no
checking whether mpicc accepts -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops
-std=gnu99... yes
checking whether byte ordering is bigendian... no
checking that size_t can hold pointers... yes
checking for SIGUSR1... yes
checking for pipes... yes
checking floating-point format... IEEE754 (little-endian byte and word
order)
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for ld used by mpicc... /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 how to recognise dependent libraries... pass_all
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... yes
checking whether mpicc accepts -g... yes
checking dependency style of mpicc... gcc3
checking how to run the C++ preprocessor... mpicc -E
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from mpicc object... failed
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fPIC
checking if mpicc PIC flag -fPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking for mpicc option to produce PIC... -fPIC
checking if mpicc PIC flag -fPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for sqrt in -lm... yes
checking for fftw3.h... yes
checking for main in -lfftw3... no
configure: error: Cannot find fftw3 library
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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