[gmx-users] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR

[Justin A. Lemkul]

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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