Are you trying to install serial amber or parallel (mpi)?
Regards!
Gera
El lun., 17 de feb. de 2020 17:56, Nicolas Feldman <nfeldman01.qub.ac.uk>
escribió:
> It seem that I do not have the mpi library, because: configure: error:
> could not find mpi library for --enable-mpi
>
> I did the following that you recommend and receive this output:
>
>
> 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... none needed
>
> checking for gcc option to accept ISO Standard C... (cached) none needed
>
> 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... /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... 1572864
>
> 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 object... ok
>
> checking how to run the C preprocessor... gcc -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 supports -fno-rtti -fno-exceptions... no
>
> checking for gcc option to produce PIC... -fPIC -DPIC
>
> checking if gcc PIC flag -fPIC -DPIC works... yes
>
> checking if gcc static flag -static works... yes
>
> checking if gcc supports -c -o file.o... yes
>
> checking if gcc supports -c -o file.o... (cached) yes
>
> checking whether the gcc 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
>
> checking whether stripping libraries is possible... yes
>
> checking if libtool supports shared libraries... yes
>
> checking whether to build shared libraries... no
>
> 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
>
> -----Original Message-----
> From: Gerardo Zerbetto De Palma <g.zerbetto.gmail.com>
> Sent: Monday, February 17, 2020 8:49 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] installing
>
> This message is from an external sender. Please take care when responding,
> clicking links or opening attachments.
>
> Edit
> Do the following:
>
> cat /home/nico/amber18/AmberTools/src/fftw3_config.log
>
>
> El lun., 17 de feb. de 2020 17:48, Gerardo Zerbetto De Palma <
> g.zerbetto.gmail.com> escribió:
>
> > Hi again!
> > Just to make it clear: Are those the contents of fftw3_config.log file?
> > In case not, just do the following:
> >
> > cat /home/nico/amber18/AmberTools/src
> >
> > and paste contents here.
> > Regards
> > Gera!
> >
> > El lun., 17 de feb. de 2020 17:41, Nicolas Feldman
> > <nfeldman01.qub.ac.uk>
> > escribió:
> >
> >> Everything seems okey until this last few lines where a error is
> >> display
> >>
> >> Checking for zlib: OK
> >>
> >>
> >> Checking for libbz2: OK
> >>
> >>
> >> Configuring fftw-3.3 (may be time-consuming)...
> >>
> >>
> >> Error: FFTW configure returned 1
> >>
> >> FFTW configure failed! Check the fftw3_config.log file
> >>
> >> in the /home/nico/amber18/AmberTools/src directory.
> >>
> >> Configure failed due to the errors above!
> >>
> >> Nicolas Feldman
> >> PhD Student
> >> The Wellcome-Wolfson Institute for Experimental Medicine Queen's
> >> University of Belfast; 97 Lisburn Rd. Belfast, UK BT9 7BL
> >>
> >> -----Original Message-----
> >> From: Gerardo Zerbetto De Palma <g.zerbetto.gmail.com>
> >> Sent: Monday, February 17, 2020 8:39 PM
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Subject: Re: [AMBER] installing
> >>
> >> This message is from an external sender. Please take care when
> >> responding, clicking links or opening attachments.
> >>
> >> Share that error log with us!
> >> Regards
> >> Gera!
> >>
> >> El lun., 17 de feb. de 2020 17:36, Nicolas Feldman
> >> <nfeldman01.qub.ac.uk>
> >> escribió:
> >>
> >> > I'm getting this error when installing:
> >> > Error: FFTW configure returned 1
> >> > FFTW configure failed! Check the fftw3_config.log file in the
> >> > /home/[user]/amber18/AmberTools/src directory.
> >> > Configure failed due to the errors above!
> >> >
> >> > Nicolas Feldman
> >> > PhD Student
> >> > The Wellcome-Wolfson Institute for Experimental Medicine Queen's
> >> > University of Belfast; 97 Lisburn Rd. Belfast, UK BT9 7BL
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> _______________________________________________
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>
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Received on Mon Feb 17 2020 - 13:30:02 PST
