Please do not duplicate post. We do see your emails recently and need sometimes to process since we are working on other stuff to.
Btw, your error said there is no mpi library. So you need to make sure you have it
- install it if you don't have
- if you do, make sure it is in LD_LIBRARY_PATH
Make sure to goole the message since it's common error.
Hope this help
Hai Nguyen
> On Dec 22, 2016, at 3:07 PM, Michael Shokhen <michael.shokhen.biu.ac.il> wrote:
>
> Dear Amber experts,
>
>
> I have received Amber 16 error report
>
> on the mpi installation:
>
>
> cd $AMBERHOME
> ./configure -mpi gnu
>
> Please advise me how to fix the error.
>
> Thank you,
> Michael
>
>
> Configuring fftw-3.3 (may be time-consuming)...
>
> Error: FFTW configure returned 1
> FFTW configure failed! Check the fftw3_config.log file
> in the /var/spool/scratch/shokhen/amber16/AmberTools/src directory.
> Configure failed due to the errors above!
>
>
>
>
> See below the fftw3_config.log file:
>
>
>
> 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 whether to enable maintainer-specific portions of Makefiles... no
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for gcc... gcc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking for style of include used by make... GNU
> checking dependency style of gcc... gcc3
> checking whether gcc and cc understand -c and -o together... yes
> checking for C compiler vendor... gnu
> checking for gcc option to accept ISO C99... -std=gnu99
> checking for gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99
> 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 grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for fgrep... /bin/grep -F
> checking for ld used by gcc -std=gnu99... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
> checking the name lister (/usr/bin/nm -B) interface... BSD nm
> checking the maximum length of command line arguments... 1966080
> checking whether the shell understands some XSI constructs... yes
> checking whether the shell understands "+="... yes
> checking for /usr/bin/ld option to reload object files... -r
> checking for objdump... objdump
> checking how to recognize dependent libraries... pass_all
> checking for ar... ar
> checking for strip... strip
> checking for ranlib... ranlib
> checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok
> checking how to run the C preprocessor... gcc -std=gnu99 -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking for dlfcn.h... yes
> checking for objdir... .libs
> checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
> checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
> checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
> checking if gcc -std=gnu99 static flag -static works... no
> checking if gcc -std=gnu99 supports -c -o file.o... yes
> checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
> checking whether the gcc -std=gnu99 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 if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking for ocamlbuild... no
> checking for mpicc... no
> checking for hcc... no
> checking for mpcc... no
> checking for mpcc_r... no
> checking for mpxlc... no
> checking for cmpicc... no
> checking for MPI_Init... no
> checking for MPI_Init in -lmpi... no
> checking for MPI_Init in -lmpich... no
> configure: error: could not find mpi library for --enable-mpi
>
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Dec 22 2016 - 12:30:03 PST
