Hi again!
I copy a thread that is relates to you issue. Give it a try:
On Mon, May 29, 2017, Lucas wrote:
*>*
*> Last year a user posted the message in the end of the mail about the*
*> common error " could not find mpi library for --enable-mpi"*
*>*
*> I'm running into the same problem, and from the response given then it*
*> means either the user doesn't have an mpi library installed or it is*
*> not in LD_LIBRARY_PATH*
This is a difficult problem, and (notwithstanding the earlier reply)
probably
has nothing to do with LD_LIBRARY_PATH.
*>*
*> So I installed mpich,*
The problem is that we don't know what to you did to "install mpich", and
debugging the fftw parallel installtion procedure is a task beyond my
comfort zone.
If you are on Linux, make sure that you install both the mpich *and* the
mpich-dev (or mpich-devel) libraries.
But my best suggestion is this, which is what we almost always suggest for
mpi problems:
cd $AMBERHOME/AmberTools/src
./configure_mpich gnu
(You may have to download the code, as explained in the output to the
above command.) This sets up all the MPI directories *within* the AMBERHOME
directory tree, and ensures that you will have the proper functions like
mpicc and mpif90 available (assuming that $AMBERHOME/bin comes before any
other mpi stuff in your $PATH.
..give this a try....dac
El lun., 17 de feb. de 2020 18:11, Nicolas Feldman <nfeldman01.qub.ac.uk>
escribió:
> What I mean is : I do not know the purpose of mpi. Im just following the
> introction to install amber.
> https://www.ovetande.se/software/amber/install/ambertools19-windows10-wsl/
>
> 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 9:07 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.
>
> 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
> > >>
> > >
> > _______________________________________________
> > 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 - 14:00:02 PST
